5205 lines
516 KiB
HTML
5205 lines
516 KiB
HTML
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
||
<html xmlns="http://www.w3.org/1999/xhtml">
|
||
<head>
|
||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
|
||
<meta name="generator" content="Doxygen 1.9.0"/>
|
||
<meta name="viewport" content="width=device-width, initial-scale=1"/>
|
||
<title>NCBI C++ ToolKit: CSearch< LEGACY, NHITS > Class Template Reference</title>
|
||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||
<script type="text/javascript" src="jquery.js"></script>
|
||
<script type="text/javascript" src="dynsections.js"></script>
|
||
<link href="doxygen.css" rel="stylesheet" type="text/css" />
|
||
<script type="text/javascript">
|
||
jQuery.getScript("/core/alerts/alerts.js", function () {
|
||
galert(['div.nav_and_browser', 'div.header', '#universal_header',
|
||
'body > *:nth-child(1)'])
|
||
});
|
||
</script>
|
||
</head>
|
||
<body>
|
||
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
|
||
<div id="titlearea">
|
||
<table cellspacing="0" cellpadding="0">
|
||
<tbody>
|
||
<tr style="height: 56px;">
|
||
<td id="projectalign" style="padding-left: 0.5em;">
|
||
<div id="projectname">NCBI C++ ToolKit
|
||
</div>
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
<!-- end header part -->
|
||
<!-- Generated by Doxygen 1.9.0 -->
|
||
<script type="text/javascript" src="menudata.js"></script>
|
||
<script type="text/javascript" src="menu.js"></script>
|
||
<script type="text/javascript">
|
||
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&dn=gpl-2.0.txt GPL-v2 */
|
||
$(function() {
|
||
initMenu('',true,true,'/toolkit/','Search');
|
||
});
|
||
/* @license-end */</script>
|
||
<div id="main-nav"></div>
|
||
</div><!-- top -->
|
||
<div class="header">
|
||
<div class="summary">
|
||
<a href="#pub-methods">Public Member Functions</a> |
|
||
<a href="#pub-static-methods">Static Public Member Functions</a> |
|
||
<a href="#pub-static-attribs">Static Public Attributes</a> |
|
||
<a href="#pro-methods">Protected Member Functions</a> |
|
||
<a href="#pro-static-methods">Static Protected Member Functions</a> |
|
||
<a href="#pri-types">Private Types</a> |
|
||
<a href="#pri-methods">Private Member Functions</a> |
|
||
<a href="#pri-attribs">Private Attributes</a> |
|
||
<a href="#pri-static-attribs">Static Private Attributes</a> |
|
||
<a href="classCSearch-members.html">List of all members</a> </div>
|
||
<div class="headertitle">
|
||
<div class="title">CSearch< LEGACY, NHITS > Class Template Reference<div class="ingroups"><a class="el" href="group__DatatoolGeneratedClasses.html">DatatoolGeneratedClasses</a> » <a class="el" href="group__dataspec__NCBI__BlastOutput2.html">Code generated by DATATOOL from 'blastxml2.asn' (module 'NCBI-BlastOutput2')</a></div></div> </div>
|
||
</div><!--header-->
|
||
<div class="contents">
|
||
<p>
|
||
<a class="el" href = "https://www.ncbi.nlm.nih.gov/toolkitbookgh/?term=CSearch">Search Toolkit Book for <i>CSearch</i></a>
|
||
</p>
|
||
|
||
<p><a class="el" href="classCSearch.html" title="CSearch –.">CSearch</a> –.
|
||
<a href="classCSearch.html#details">More...</a></p>
|
||
|
||
<p><code>#include <<a class="el" href="Search_8hpp_source.html">objects/blastxml2/Search.hpp</a>></code></p>
|
||
<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
|
||
<img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for CSearch< LEGACY, NHITS >:</div>
|
||
<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
|
||
</div>
|
||
<div id="dynsection-0-content" class="dyncontent" style="display:none;">
|
||
<div class="center"><img src="img__inherit__graph/classCSearch__inherit__graph.png" border="0" usemap="#aCSearch_3_01LEGACY_00_01NHITS_01_4_inherit__map" alt="Inheritance graph"/></div>
|
||
<map name="aCSearch_3_01LEGACY_00_01NHITS_01_4_inherit__map" id="aCSearch_3_01LEGACY_00_01NHITS_01_4_inherit__map">
|
||
<area shape="rect" title="CSearch –." alt="" coords="1179,55,1379,81"/>
|
||
<area shape="rect" href="classCSearch__Base.html" title="CSearch_Base –." alt="" coords="527,10,707,51"/>
|
||
<area shape="rect" href="classCSearch__Base.html" title=" " alt="" coords="933,40,1129,96"/>
|
||
<area shape="rect" href="classCSerialObject.html" title="Base class for all serializable objects." alt="" coords="304,76,407,103"/>
|
||
<area shape="rect" href="classCObject.html" title="CObject –." alt="" coords="184,111,255,137"/>
|
||
<area shape="rect" href="classCThread.html" title="CThread –." alt="" coords="431,127,503,153"/>
|
||
<area shape="rect" href="classCDebugDumpable.html" title=" " alt="" coords="5,111,135,137"/>
|
||
</map>
|
||
<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center></div>
|
||
<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
|
||
<img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for CSearch< LEGACY, NHITS >:</div>
|
||
<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
|
||
</div>
|
||
<div id="dynsection-1-content" class="dyncontent" style="display:none;">
|
||
<div class="center"><img src="img__coll__graph/classCSearch__coll__graph.png" border="0" usemap="#aCSearch_3_01LEGACY_00_01NHITS_01_4_coll__map" alt="Collaboration graph"/></div>
|
||
<map name="aCSearch_3_01LEGACY_00_01NHITS_01_4_coll__map" id="aCSearch_3_01LEGACY_00_01NHITS_01_4_coll__map">
|
||
<area shape="rect" title="CSearch –." alt="" coords="2868,1184,3068,1211"/>
|
||
<area shape="rect" href="classCSearch__Base.html" title="CSearch_Base –." alt="" coords="2097,379,2277,421"/>
|
||
<area shape="rect" href="classCSearch__Base.html" title=" " alt="" coords="2504,559,2700,615"/>
|
||
<area shape="rect" href="classCSerialObject.html" title="Base class for all serializable objects." alt="" coords="1729,752,1831,779"/>
|
||
<area shape="rect" href="classCObject.html" title="CObject –." alt="" coords="924,741,995,768"/>
|
||
<area shape="rect" href="classCDbIndex.html" title="Base class providing high level interface to index objects." alt="" coords="1339,535,1420,561"/>
|
||
<area shape="rect" href="classCThread.html" title="CThread –." alt="" coords="2151,1311,2223,1337"/>
|
||
<area shape="rect" href="classCDebugDumpable.html" title=" " alt="" coords="572,741,701,768"/>
|
||
<area shape="rect" href="structBLAST__SequenceBlk.html" title="Structure to hold a sequence." alt="" coords="1706,529,1854,556"/>
|
||
<area shape="rect" href="structSSeqRange.html" title="A structure containing two integers, used e.g." alt="" coords="591,663,683,689"/>
|
||
<area shape="rect" href="structBlastSeqLoc.html" title="Used to hold a set of positions, mostly used for filtering." alt="" coords="911,691,1007,717"/>
|
||
<area shape="rect" href="structBlastMaskLoc.html" title="Structure for keeping the query masking information." alt="" coords="1327,636,1432,663"/>
|
||
<area shape="rect" href="classCSeedRoots.html" title="Seed roots container for all subjects." alt="" coords="1731,117,1829,144"/>
|
||
<area shape="rect" href="structSSubjRootsInfo.html" title="SSeedRoot container for one subject." alt="" coords="1110,93,1225,120"/>
|
||
<area shape="rect" title=" " alt="" coords="579,113,695,140"/>
|
||
<area shape="rect" title=" " alt="" coords="889,500,1029,527"/>
|
||
<area shape="rect" title=" " alt="" coords="1680,228,1880,255"/>
|
||
<area shape="rect" title=" " alt="" coords="898,23,1021,49"/>
|
||
<area shape="rect" title=" " alt="" coords="177,1669,215,1696"/>
|
||
<area shape="rect" title=" " alt="" coords="898,1683,1021,1709"/>
|
||
<area shape="rect" href="structSSeedRoot.html" title="Representation of a seed root." alt="" coords="1335,48,1424,75"/>
|
||
<area shape="rect" href="structCDbIndex_1_1SSearchOptions.html" title="Simple record type used to specify index search parameters." alt="" coords="1688,600,1872,627"/>
|
||
<area shape="rect" href="classCDbIndex__Impl.html" title="Implementation of the BLAST database index." alt="" coords="1685,436,1875,463"/>
|
||
<area shape="rect" href="classCSubjectMap.html" title="Type representing subject map data." alt="" coords="909,551,1010,577"/>
|
||
<area shape="rect" href="classCVectorWrap.html" title=" " alt="" coords="559,593,715,620"/>
|
||
<area shape="rect" href="classCVectorWrap.html" title=" " alt="" coords="555,408,719,435"/>
|
||
<area shape="rect" href="classCOffsetData.html" title="Iterator specific functionality of offset list manager class." alt="" coords="1294,484,1465,511"/>
|
||
<area shape="rect" href="classCOffsetData__Base.html" title="Class representing index hash table and offset list database." alt="" coords="893,336,1026,363"/>
|
||
<area shape="rect" title=" " alt="" coords="597,459,677,485"/>
|
||
<area shape="rect" href="structSIndexHeader.html" title="Structure into which an index header is loaded." alt="" coords="907,449,1012,476"/>
|
||
<area shape="rect" href="classCMemoryFile.html" title="CMemoryFile –." alt="" coords="1329,293,1429,320"/>
|
||
<area shape="rect" href="classCMemoryFileMap.html" title="CMemoryFileMap –." alt="" coords="897,285,1022,312"/>
|
||
<area shape="rect" href="classCMemoryFile__Base.html" title="CMemoryFile_Base –." alt="" coords="568,164,705,191"/>
|
||
<area shape="rect" href="structSMemoryFileHandle.html" title=" " alt="" coords="567,239,707,265"/>
|
||
<area shape="rect" href="structSMemoryFileAttrs.html" title=" " alt="" coords="573,289,700,316"/>
|
||
<area shape="rect" href="classmap.html" title=" " alt="" coords="547,341,726,382"/>
|
||
<area shape="rect" href="classmap.html" title=" " alt="" coords="111,1283,281,1309"/>
|
||
<area shape="rect" href="classmap.html" title=" " alt="" coords="2098,1604,2277,1631"/>
|
||
<area shape="rect" title=" " alt="" coords="1351,433,1408,460"/>
|
||
<area shape="rect" href="classCRef.html" title=" " alt="" coords="1709,803,1851,829"/>
|
||
<area shape="rect" href="classpair__base__member.html" title=" " alt="" coords="870,1190,1049,1231"/>
|
||
<area shape="rect" href="classCRef.html" title="CRef –." alt="" coords="1312,1169,1447,1196"/>
|
||
<area shape="rect" href="classCRef.html" title=" " alt="" coords="1717,1412,1843,1439"/>
|
||
<area shape="rect" href="classCRef.html" title=" " alt="" coords="1689,1361,1871,1388"/>
|
||
<area shape="rect" href="classCRef.html" title=" " alt="" coords="1682,1463,1878,1489"/>
|
||
<area shape="rect" href="classCRef.html" title=" " alt="" coords="1697,1527,1863,1553"/>
|
||
<area shape="rect" href="classCRef.html" title=" " alt="" coords="1716,897,1844,924"/>
|
||
<area shape="rect" href="classCRef.html" title=" " alt="" coords="1689,1209,1871,1236"/>
|
||
<area shape="rect" href="classCRef.html" title=" " alt="" coords="1701,1133,1859,1160"/>
|
||
<area shape="rect" href="classCRef.html" title=" " alt="" coords="1702,1055,1858,1081"/>
|
||
<area shape="rect" href="classCRef.html" title=" " alt="" coords="1715,976,1845,1003"/>
|
||
<area shape="rect" title=" " alt="" coords="592,1197,681,1224"/>
|
||
<area shape="rect" href="classpair__base__member.html" title="Template used for empty base class optimization." alt="" coords="107,1799,285,1841"/>
|
||
<area shape="rect" href="classpair__base__member.html" title=" " alt="" coords="545,2054,728,2095"/>
|
||
<area shape="rect" title=" " alt="" coords="5,1807,57,1833"/>
|
||
<area shape="rect" href="classCTimeout.html" title="CTimeout – Timeout interval." alt="" coords="1741,1311,1819,1337"/>
|
||
<area shape="rect" href="classAutoPtr.html" title=" " alt="" coords="1276,2127,1483,2169"/>
|
||
<area shape="rect" href="classAutoPtr.html" title="AutoPtr –." alt="" coords="896,2033,1023,2060"/>
|
||
<area shape="rect" href="classAutoPtr.html" title=" " alt="" coords="1289,2043,1470,2085"/>
|
||
<area shape="rect" title=" " alt="" coords="149,2061,243,2088"/>
|
||
<area shape="rect" title=" " alt="" coords="1292,1655,1467,1697"/>
|
||
<area shape="rect" href="classCMassArray.html" title=" " alt="" coords="2555,1108,2649,1135"/>
|
||
<area shape="rect" href="classCLadderContainer.html" title=" " alt="" coords="2539,1584,2665,1611"/>
|
||
<area shape="rect" href="classmap__checker.html" title=" " alt="" coords="1699,1697,1861,1753"/>
|
||
<area shape="rect" href="classCAtomicCounter__WithAutoInit.html" title="CAtomicCounter_WithAutoInit –." alt="" coords="860,1821,1059,1848"/>
|
||
<area shape="rect" href="classmap__checker.html" title=" " alt="" coords="1289,1799,1469,1825"/>
|
||
<area shape="rect" href="classset.html" title=" " alt="" coords="1741,1883,1819,1909"/>
|
||
<area shape="rect" href="classset.html" title=" " alt="" coords="1305,1927,1453,1953"/>
|
||
<area shape="rect" title=" " alt="" coords="617,1841,656,1868"/>
|
||
<area shape="rect" title=" " alt="" coords="910,1959,1009,1985"/>
|
||
<area shape="rect" href="classCMSMod.html" title=" " alt="" coords="1543,5,1620,32"/>
|
||
</map>
|
||
<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center></div>
|
||
<table class="memberdecls">
|
||
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
|
||
Public Member Functions</h2></td></tr>
|
||
<tr class="memitem:ga3442b1b48278fab43e98f7874ae2d6f3"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga3442b1b48278fab43e98f7874ae2d6f3">CSearch</a> (void)</td></tr>
|
||
<tr class="separator:ga3442b1b48278fab43e98f7874ae2d6f3"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaf16544aa13d810263a0b0c5b65f06d10"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaf16544aa13d810263a0b0c5b65f06d10">~CSearch</a> (void)</td></tr>
|
||
<tr class="separator:gaf16544aa13d810263a0b0c5b65f06d10"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ab082f448e7bb480d122bb7f44050bbd6"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#ab082f448e7bb480d122bb7f44050bbd6">CSearch</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSearch__Base.html#aec07f7524cf0ec5dc6610b776b3ff4d2">TIndex_Impl</a> &index_impl, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBLAST__SequenceBlk.html">BLAST_SequenceBlk</a> *<a class="el" href="ftds14_2freetds_2tds_2unittests_2utf8__1_8c.html#aa590f90371629b8ec9b73bebe4d08501">query</a>, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqLoc.html">BlastSeqLoc</a> *locs, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSearch__Base.html#afd6cb73bb0bbdcdbde5d1f139c6cbc9c">TSearchOptions</a> &options)</td></tr>
|
||
<tr class="memdesc:ab082f448e7bb480d122bb7f44050bbd6"><td class="mdescLeft"> </td><td class="mdescRight">Object constructor. <a href="classCSearch.html#ab082f448e7bb480d122bb7f44050bbd6">More...</a><br /></td></tr>
|
||
<tr class="separator:ab082f448e7bb480d122bb7f44050bbd6"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:af30e25b14d759f030a00231ed6b22ce6"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#af30e25b14d759f030a00231ed6b22ce6">SetSubjInfo</a> ()</td></tr>
|
||
<tr class="memdesc:af30e25b14d759f030a00231ed6b22ce6"><td class="mdescLeft"> </td><td class="mdescRight">Set the parameters of the current subject sequence. <a href="classCSearch.html#af30e25b14d759f030a00231ed6b22ce6">More...</a><br /></td></tr>
|
||
<tr class="separator:af30e25b14d759f030a00231ed6b22ce6"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:aec515d80a97b58deecf3a14f3d2c9ce6"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#aec515d80a97b58deecf3a14f3d2c9ce6">DecodeOffset</a> (<a class="el" href="dbindex__sp_8hpp.html#ab24dd73d837409e50d27583ed6f4e273">TWord</a> <a class="el" href="url__tooltip__handler_8cpp.html#af1a7c6ddf735b32939485fddbaec4e75">offset</a>)</td></tr>
|
||
<tr class="memdesc:aec515d80a97b58deecf3a14f3d2c9ce6"><td class="mdescLeft"> </td><td class="mdescRight">Decode offset value into subject position. <a href="classCSearch.html#aec515d80a97b58deecf3a14f3d2c9ce6">More...</a><br /></td></tr>
|
||
<tr class="separator:aec515d80a97b58deecf3a14f3d2c9ce6"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a2cffda2df314ffc0295a96d819379c64"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a2cffda2df314ffc0295a96d819379c64">CSearch</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> tNum)</td></tr>
|
||
<tr class="separator:a2cffda2df314ffc0295a96d819379c64"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:afb321086985371baa64d67d331bfb810"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#afb321086985371baa64d67d331bfb810">~CSearch</a> (void)</td></tr>
|
||
<tr class="separator:afb321086985371baa64d67d331bfb810"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a4b038a63bf625bb3d7a94e3a7a9179b5"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a4b038a63bf625bb3d7a94e3a7a9179b5">InitBlast</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> char *blastdb, <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> use_mmap=<a class="el" href="ftds14_2freetds_2freetds_2bool_8h.html#a65e9886d74aaee76545e83dd09011727">false</a>)</td></tr>
|
||
<tr class="memdesc:a4b038a63bf625bb3d7a94e3a7a9179b5"><td class="mdescLeft"> </td><td class="mdescRight">init blast databases. <a href="classCSearch.html#a4b038a63bf625bb3d7a94e3a7a9179b5">More...</a><br /></td></tr>
|
||
<tr class="separator:a4b038a63bf625bb3d7a94e3a7a9179b5"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a5e985bb7e8acd2e85be9e4fe2ee023e6"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a5e985bb7e8acd2e85be9e4fe2ee023e6">Search</a> (<a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSRequest.html">CMSRequest</a> > MyRequestIn, <a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSResponse.html">CMSResponse</a> > MyResponseIn, <a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSModSpecSet.html">CMSModSpecSet</a> > Modset, <a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSSearchSettings.html">CMSSearchSettings</a> > SettingsIn, <a class="el" href="omssa_8hpp.html#a9ffe9cb00c8437193b4225feecd4ab36">TOMSSACallback</a> Callback=0, void *CallbackData=0)</td></tr>
|
||
<tr class="memdesc:a5e985bb7e8acd2e85be9e4fe2ee023e6"><td class="mdescLeft"> </td><td class="mdescRight">Performs the ms/ms search. <a href="classCSearch.html#a5e985bb7e8acd2e85be9e4fe2ee023e6">More...</a><br /></td></tr>
|
||
<tr class="separator:a5e985bb7e8acd2e85be9e4fe2ee023e6"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:aaa0a4ed9116b40d1867c12dce88d0dc4"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#aaa0a4ed9116b40d1867c12dce88d0dc4">SetupSearch</a> (<a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSRequest.html">CMSRequest</a> > MyRequestIn, <a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSResponse.html">CMSResponse</a> > MyResponseIn, <a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSModSpecSet.html">CMSModSpecSet</a> > Modset, <a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSSearchSettings.html">CMSSearchSettings</a> > SettingsIn, <a class="el" href="omssa_8hpp.html#a9ffe9cb00c8437193b4225feecd4ab36">TOMSSACallback</a> Callback=0, void *CallbackData=0)</td></tr>
|
||
<tr class="memdesc:aaa0a4ed9116b40d1867c12dce88d0dc4"><td class="mdescLeft"> </td><td class="mdescRight">Setup the ms/ms search. <a href="classCSearch.html#aaa0a4ed9116b40d1867c12dce88d0dc4">More...</a><br /></td></tr>
|
||
<tr class="separator:aaa0a4ed9116b40d1867c12dce88d0dc4"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a7c92570f5a6ab9ff8a1e2bdadc373969"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCMSMatchedPeakSet.html">CMSMatchedPeakSet</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a7c92570f5a6ab9ff8a1e2bdadc373969">PepCharge</a> (<a class="el" href="classCMSHit.html">CMSHit</a> &Hit, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> SeriesCharge, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> Ion, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> MinIntensity, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> Which, <a class="el" href="classCMSPeak.html">CMSPeak</a> *Peaks, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> Maxproductions)</td></tr>
|
||
<tr class="memdesc:a7c92570f5a6ab9ff8a1e2bdadc373969"><td class="mdescLeft"> </td><td class="mdescRight">fill out MatchedPeakSet <a href="classCSearch.html#a7c92570f5a6ab9ff8a1e2bdadc373969">More...</a><br /></td></tr>
|
||
<tr class="separator:a7c92570f5a6ab9ff8a1e2bdadc373969"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a0029addacfa8c89a9eb3e94df3dd6e63"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a0029addacfa8c89a9eb3e94df3dd6e63">SetRankScore</a> (void)</td></tr>
|
||
<tr class="memdesc:a0029addacfa8c89a9eb3e94df3dd6e63"><td class="mdescLeft"> </td><td class="mdescRight">Sets the scoring to use rank statistics. <a href="classCSearch.html#a0029addacfa8c89a9eb3e94df3dd6e63">More...</a><br /></td></tr>
|
||
<tr class="separator:a0029addacfa8c89a9eb3e94df3dd6e63"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ad6568eb8d7547a6af3a8b5ca303ed000"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#ad6568eb8d7547a6af3a8b5ca303ed000">SetPoissonOnly</a> (void)</td></tr>
|
||
<tr class="memdesc:ad6568eb8d7547a6af3a8b5ca303ed000"><td class="mdescLeft"> </td><td class="mdescRight">Sets the scoring to use rank statistics only with Poisson. <a href="classCSearch.html#ad6568eb8d7547a6af3a8b5ca303ed000">More...</a><br /></td></tr>
|
||
<tr class="separator:ad6568eb8d7547a6af3a8b5ca303ed000"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a833f4a13658de188ea0a461fd2419b90"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a833f4a13658de188ea0a461fd2419b90">GetPoissonOnly</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:a833f4a13658de188ea0a461fd2419b90"><td class="mdescLeft"> </td><td class="mdescRight">Gets the scoring to use rank statistics only with Poisson. <a href="classCSearch.html#a833f4a13658de188ea0a461fd2419b90">More...</a><br /></td></tr>
|
||
<tr class="separator:a833f4a13658de188ea0a461fd2419b90"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a07e07ceccdb937756560dfcd245fb328"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a07e07ceccdb937756560dfcd245fb328">SetIterative</a> (void)</td></tr>
|
||
<tr class="memdesc:a07e07ceccdb937756560dfcd245fb328"><td class="mdescLeft"> </td><td class="mdescRight">Sets iterate search. <a href="classCSearch.html#a07e07ceccdb937756560dfcd245fb328">More...</a><br /></td></tr>
|
||
<tr class="separator:a07e07ceccdb937756560dfcd245fb328"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a116591c2917d62d1ffea2b178e5a7485"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a116591c2917d62d1ffea2b178e5a7485">GetIterative</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:a116591c2917d62d1ffea2b178e5a7485"><td class="mdescLeft"> </td><td class="mdescRight">Gets iterate search. <a href="classCSearch.html#a116591c2917d62d1ffea2b178e5a7485">More...</a><br /></td></tr>
|
||
<tr class="separator:a116591c2917d62d1ffea2b178e5a7485"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ab0dec8be370a16f7736e36c07841b3f5"><td class="memItemLeft" align="right" valign="top">virtual void * </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#ab0dec8be370a16f7736e36c07841b3f5">Main</a> (void)</td></tr>
|
||
<tr class="memdesc:ab0dec8be370a16f7736e36c07841b3f5"><td class="mdescLeft"> </td><td class="mdescRight">Derived (user-created) class must provide a real thread function. <a href="classCSearch.html#ab0dec8be370a16f7736e36c07841b3f5">More...</a><br /></td></tr>
|
||
<tr class="separator:ab0dec8be370a16f7736e36c07841b3f5"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a41bbf21492f67c93eff4235396d56443"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a41bbf21492f67c93eff4235396d56443">OnExit</a> (void)</td></tr>
|
||
<tr class="memdesc:a41bbf21492f67c93eff4235396d56443"><td class="mdescLeft"> </td><td class="mdescRight">Override this to execute finalization code. <a href="classCSearch.html#a41bbf21492f67c93eff4235396d56443">More...</a><br /></td></tr>
|
||
<tr class="separator:a41bbf21492f67c93eff4235396d56443"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a5d6e9641c571ad98ffdca0ae950e5d0d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a5d6e9641c571ad98ffdca0ae950e5d0d">CopySettings</a> (<a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCSearch.html">CSearch</a> > fromObj)</td></tr>
|
||
<tr class="separator:a5d6e9641c571ad98ffdca0ae950e5d0d"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a637f77ccd43f042285819109df4b4aa0"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a637f77ccd43f042285819109df4b4aa0">TestPersist</a> (void)</td></tr>
|
||
<tr class="separator:a637f77ccd43f042285819109df4b4aa0"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a096b35d0875e07b62218b8ff95760d06"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a096b35d0875e07b62218b8ff95760d06">SetResult</a> (<a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSPeakSet.html">CMSPeakSet</a> > PeakSet)</td></tr>
|
||
<tr class="separator:a096b35d0875e07b62218b8ff95760d06"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pub_methods_classCSearch__Base"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classCSearch__Base')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classCSearch__Base.html">CSearch_Base< LEGACY, NHITS, derived_t ></a></td></tr>
|
||
<tr class="memitem:ga648bed56db5de3e15bd028db62a4bce8 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga648bed56db5de3e15bd028db62a4bce8">CSearch_Base</a> (void)</td></tr>
|
||
<tr class="separator:ga648bed56db5de3e15bd028db62a4bce8 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gae584163c5b1433b04f90d5b1dc3c7caf inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gae584163c5b1433b04f90d5b1dc3c7caf">~CSearch_Base</a> (void)</td></tr>
|
||
<tr class="separator:gae584163c5b1433b04f90d5b1dc3c7caf inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga782d0d3e5875d5ec121b4c3e1adaefe8 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga782d0d3e5875d5ec121b4c3e1adaefe8">DECLARE_INTERNAL_TYPE_INFO</a> ()</td></tr>
|
||
<tr class="separator:ga782d0d3e5875d5ec121b4c3e1adaefe8 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga2e245722b693746547f3eb716cbab9df inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga2e245722b693746547f3eb716cbab9df">IsSetQuery_id</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga2e245722b693746547f3eb716cbab9df inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">SeqId of query <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Query_id data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga2e245722b693746547f3eb716cbab9df">More...</a><br /></td></tr>
|
||
<tr class="separator:ga2e245722b693746547f3eb716cbab9df inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga038104ff3a99cffd64d0033f84e64a8b inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga038104ff3a99cffd64d0033f84e64a8b">CanGetQuery_id</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga038104ff3a99cffd64d0033f84e64a8b inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetQuery_id method. <a href="group__dataspec__NCBI__BlastOutput2.html#ga038104ff3a99cffd64d0033f84e64a8b">More...</a><br /></td></tr>
|
||
<tr class="separator:ga038104ff3a99cffd64d0033f84e64a8b inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gac35c6c45a0c0e60de1de4f83749257fb inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gac35c6c45a0c0e60de1de4f83749257fb">ResetQuery_id</a> (void)</td></tr>
|
||
<tr class="memdesc:gac35c6c45a0c0e60de1de4f83749257fb inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Query_id data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gac35c6c45a0c0e60de1de4f83749257fb">More...</a><br /></td></tr>
|
||
<tr class="separator:gac35c6c45a0c0e60de1de4f83749257fb inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga22c92f1051a35de1974edc9a6b52328c inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga8a4c8e2c3c50387bcbe01b8533c2cbe4">TQuery_id</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga22c92f1051a35de1974edc9a6b52328c">GetQuery_id</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga22c92f1051a35de1974edc9a6b52328c inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Query_id member data. <a href="group__dataspec__NCBI__BlastOutput2.html#ga22c92f1051a35de1974edc9a6b52328c">More...</a><br /></td></tr>
|
||
<tr class="separator:ga22c92f1051a35de1974edc9a6b52328c inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga4b4f8347965db5c7bcccc423052afaf4 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga4b4f8347965db5c7bcccc423052afaf4">SetQuery_id</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga8a4c8e2c3c50387bcbe01b8533c2cbe4">TQuery_id</a> &<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="memdesc:ga4b4f8347965db5c7bcccc423052afaf4 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Query_id data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga4b4f8347965db5c7bcccc423052afaf4">More...</a><br /></td></tr>
|
||
<tr class="separator:ga4b4f8347965db5c7bcccc423052afaf4 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga928af34074546ffee7ef36bbdf6eb129 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga928af34074546ffee7ef36bbdf6eb129">SetQuery_id</a> (<a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga8a4c8e2c3c50387bcbe01b8533c2cbe4">TQuery_id</a> &&<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="separator:ga928af34074546ffee7ef36bbdf6eb129 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gae3a80f25e393c1a6ecbe354a8b2efd4b inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga8a4c8e2c3c50387bcbe01b8533c2cbe4">TQuery_id</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gae3a80f25e393c1a6ecbe354a8b2efd4b">SetQuery_id</a> (void)</td></tr>
|
||
<tr class="memdesc:gae3a80f25e393c1a6ecbe354a8b2efd4b inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Query_id data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gae3a80f25e393c1a6ecbe354a8b2efd4b">More...</a><br /></td></tr>
|
||
<tr class="separator:gae3a80f25e393c1a6ecbe354a8b2efd4b inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gadb18d5a2b984d01eda93c3dfaaac7b72 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gadb18d5a2b984d01eda93c3dfaaac7b72">IsSetQuery_title</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gadb18d5a2b984d01eda93c3dfaaac7b72 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Definition line of query <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Query_title data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gadb18d5a2b984d01eda93c3dfaaac7b72">More...</a><br /></td></tr>
|
||
<tr class="separator:gadb18d5a2b984d01eda93c3dfaaac7b72 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga761facc1844cca66fead91a801210825 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga761facc1844cca66fead91a801210825">CanGetQuery_title</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga761facc1844cca66fead91a801210825 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetQuery_title method. <a href="group__dataspec__NCBI__BlastOutput2.html#ga761facc1844cca66fead91a801210825">More...</a><br /></td></tr>
|
||
<tr class="separator:ga761facc1844cca66fead91a801210825 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga08f84f03bd0f087bad503d27707ee858 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga08f84f03bd0f087bad503d27707ee858">ResetQuery_title</a> (void)</td></tr>
|
||
<tr class="memdesc:ga08f84f03bd0f087bad503d27707ee858 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Query_title data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga08f84f03bd0f087bad503d27707ee858">More...</a><br /></td></tr>
|
||
<tr class="separator:ga08f84f03bd0f087bad503d27707ee858 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaa34d943b8dacfbcc9205eeeed3e945c8 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga6889d230d2397ffe927d232f29566fab">TQuery_title</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaa34d943b8dacfbcc9205eeeed3e945c8">GetQuery_title</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gaa34d943b8dacfbcc9205eeeed3e945c8 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Query_title member data. <a href="group__dataspec__NCBI__BlastOutput2.html#gaa34d943b8dacfbcc9205eeeed3e945c8">More...</a><br /></td></tr>
|
||
<tr class="separator:gaa34d943b8dacfbcc9205eeeed3e945c8 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga28764b9824b943edf46395b25d7be0da inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga28764b9824b943edf46395b25d7be0da">SetQuery_title</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga6889d230d2397ffe927d232f29566fab">TQuery_title</a> &<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="memdesc:ga28764b9824b943edf46395b25d7be0da inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Query_title data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga28764b9824b943edf46395b25d7be0da">More...</a><br /></td></tr>
|
||
<tr class="separator:ga28764b9824b943edf46395b25d7be0da inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga45b9166008309273e342b7f097778263 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga45b9166008309273e342b7f097778263">SetQuery_title</a> (<a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga6889d230d2397ffe927d232f29566fab">TQuery_title</a> &&<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="separator:ga45b9166008309273e342b7f097778263 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga6db1516ef6d10e11915ae43d1488a49b inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga6889d230d2397ffe927d232f29566fab">TQuery_title</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga6db1516ef6d10e11915ae43d1488a49b">SetQuery_title</a> (void)</td></tr>
|
||
<tr class="memdesc:ga6db1516ef6d10e11915ae43d1488a49b inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Query_title data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga6db1516ef6d10e11915ae43d1488a49b">More...</a><br /></td></tr>
|
||
<tr class="separator:ga6db1516ef6d10e11915ae43d1488a49b inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga0c7c21007894767b934b3f8696ef350d inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga0c7c21007894767b934b3f8696ef350d">IsSetQuery_len</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga0c7c21007894767b934b3f8696ef350d inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">length of query sequence <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Query_len data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga0c7c21007894767b934b3f8696ef350d">More...</a><br /></td></tr>
|
||
<tr class="separator:ga0c7c21007894767b934b3f8696ef350d inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga61cc9e30e61e8a76a531acd76484826d inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga61cc9e30e61e8a76a531acd76484826d">CanGetQuery_len</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga61cc9e30e61e8a76a531acd76484826d inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetQuery_len method. <a href="group__dataspec__NCBI__BlastOutput2.html#ga61cc9e30e61e8a76a531acd76484826d">More...</a><br /></td></tr>
|
||
<tr class="separator:ga61cc9e30e61e8a76a531acd76484826d inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gad30b1de939fe6e168185328d8fcdf2ca inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gad30b1de939fe6e168185328d8fcdf2ca">ResetQuery_len</a> (void)</td></tr>
|
||
<tr class="memdesc:gad30b1de939fe6e168185328d8fcdf2ca inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Query_len data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gad30b1de939fe6e168185328d8fcdf2ca">More...</a><br /></td></tr>
|
||
<tr class="separator:gad30b1de939fe6e168185328d8fcdf2ca inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaf7dd1830422c0e04669cba5ce6294949 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga8ea8393dbd772563cef38ec2d8abf993">TQuery_len</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaf7dd1830422c0e04669cba5ce6294949">GetQuery_len</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gaf7dd1830422c0e04669cba5ce6294949 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Query_len member data. <a href="group__dataspec__NCBI__BlastOutput2.html#gaf7dd1830422c0e04669cba5ce6294949">More...</a><br /></td></tr>
|
||
<tr class="separator:gaf7dd1830422c0e04669cba5ce6294949 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga5d6620b7f4d0af79254cd9eb91a9f181 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga5d6620b7f4d0af79254cd9eb91a9f181">SetQuery_len</a> (<a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga8ea8393dbd772563cef38ec2d8abf993">TQuery_len</a> <a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="memdesc:ga5d6620b7f4d0af79254cd9eb91a9f181 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Query_len data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga5d6620b7f4d0af79254cd9eb91a9f181">More...</a><br /></td></tr>
|
||
<tr class="separator:ga5d6620b7f4d0af79254cd9eb91a9f181 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaa876c8653d1c44de42329b2658155e40 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga8ea8393dbd772563cef38ec2d8abf993">TQuery_len</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaa876c8653d1c44de42329b2658155e40">SetQuery_len</a> (void)</td></tr>
|
||
<tr class="memdesc:gaa876c8653d1c44de42329b2658155e40 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Query_len data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gaa876c8653d1c44de42329b2658155e40">More...</a><br /></td></tr>
|
||
<tr class="separator:gaa876c8653d1c44de42329b2658155e40 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gabde07846f453acecbe97e13ea2177810 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gabde07846f453acecbe97e13ea2177810">IsSetQuery_masking</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gabde07846f453acecbe97e13ea2177810 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Masked offsets. <a href="group__dataspec__NCBI__BlastOutput2.html#gabde07846f453acecbe97e13ea2177810">More...</a><br /></td></tr>
|
||
<tr class="separator:gabde07846f453acecbe97e13ea2177810 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gac37afc538706a5cdca98447a845c063b inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gac37afc538706a5cdca98447a845c063b">CanGetQuery_masking</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gac37afc538706a5cdca98447a845c063b inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetQuery_masking method. <a href="group__dataspec__NCBI__BlastOutput2.html#gac37afc538706a5cdca98447a845c063b">More...</a><br /></td></tr>
|
||
<tr class="separator:gac37afc538706a5cdca98447a845c063b inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gada4837760a9704bf674a7cee78221f7a inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gada4837760a9704bf674a7cee78221f7a">ResetQuery_masking</a> (void)</td></tr>
|
||
<tr class="memdesc:gada4837760a9704bf674a7cee78221f7a inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Query_masking data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gada4837760a9704bf674a7cee78221f7a">More...</a><br /></td></tr>
|
||
<tr class="separator:gada4837760a9704bf674a7cee78221f7a inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga9d15e1dc213bb53388e2e352a7f4980f inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga946dbe57e0dc1cbb265e82ed159fedb8">TQuery_masking</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga9d15e1dc213bb53388e2e352a7f4980f">GetQuery_masking</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga9d15e1dc213bb53388e2e352a7f4980f inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Query_masking member data. <a href="group__dataspec__NCBI__BlastOutput2.html#ga9d15e1dc213bb53388e2e352a7f4980f">More...</a><br /></td></tr>
|
||
<tr class="separator:ga9d15e1dc213bb53388e2e352a7f4980f inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gac41309812a3fb04528134ab9c635fb8d inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga946dbe57e0dc1cbb265e82ed159fedb8">TQuery_masking</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gac41309812a3fb04528134ab9c635fb8d">SetQuery_masking</a> (void)</td></tr>
|
||
<tr class="memdesc:gac41309812a3fb04528134ab9c635fb8d inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Query_masking data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gac41309812a3fb04528134ab9c635fb8d">More...</a><br /></td></tr>
|
||
<tr class="separator:gac41309812a3fb04528134ab9c635fb8d inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga119f12de47d5adae8beeeba33e85e010 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga119f12de47d5adae8beeeba33e85e010">IsSetHits</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga119f12de47d5adae8beeeba33e85e010 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Hits one for every db sequence <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Hits data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga119f12de47d5adae8beeeba33e85e010">More...</a><br /></td></tr>
|
||
<tr class="separator:ga119f12de47d5adae8beeeba33e85e010 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gac86dbe53e0c748e6633ddf76a3ad7cad inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gac86dbe53e0c748e6633ddf76a3ad7cad">CanGetHits</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gac86dbe53e0c748e6633ddf76a3ad7cad inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetHits method. <a href="group__dataspec__NCBI__BlastOutput2.html#gac86dbe53e0c748e6633ddf76a3ad7cad">More...</a><br /></td></tr>
|
||
<tr class="separator:gac86dbe53e0c748e6633ddf76a3ad7cad inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gac7dd059ea17bdac6fe02244ef20cba2c inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gac7dd059ea17bdac6fe02244ef20cba2c">ResetHits</a> (void)</td></tr>
|
||
<tr class="memdesc:gac7dd059ea17bdac6fe02244ef20cba2c inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Hits data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gac7dd059ea17bdac6fe02244ef20cba2c">More...</a><br /></td></tr>
|
||
<tr class="separator:gac7dd059ea17bdac6fe02244ef20cba2c inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga5896f2a30f2cd935fcc907cf13d0e538 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaec3ad1ac4ef81a8e040acf64663d0605">THits</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga5896f2a30f2cd935fcc907cf13d0e538">GetHits</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga5896f2a30f2cd935fcc907cf13d0e538 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Hits member data. <a href="group__dataspec__NCBI__BlastOutput2.html#ga5896f2a30f2cd935fcc907cf13d0e538">More...</a><br /></td></tr>
|
||
<tr class="separator:ga5896f2a30f2cd935fcc907cf13d0e538 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga09983ee2082d8656dbb4e1f0c0c3ffc9 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaec3ad1ac4ef81a8e040acf64663d0605">THits</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga09983ee2082d8656dbb4e1f0c0c3ffc9">SetHits</a> (void)</td></tr>
|
||
<tr class="memdesc:ga09983ee2082d8656dbb4e1f0c0c3ffc9 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Hits data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga09983ee2082d8656dbb4e1f0c0c3ffc9">More...</a><br /></td></tr>
|
||
<tr class="separator:ga09983ee2082d8656dbb4e1f0c0c3ffc9 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaea907712d8f9f17cb0dd0e12621c6064 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaea907712d8f9f17cb0dd0e12621c6064">IsSetStat</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gaea907712d8f9f17cb0dd0e12621c6064 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">search statistics <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Stat data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gaea907712d8f9f17cb0dd0e12621c6064">More...</a><br /></td></tr>
|
||
<tr class="separator:gaea907712d8f9f17cb0dd0e12621c6064 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga9b2fb0137f97ffffd4c2f456628c43a9 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga9b2fb0137f97ffffd4c2f456628c43a9">CanGetStat</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga9b2fb0137f97ffffd4c2f456628c43a9 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetStat method. <a href="group__dataspec__NCBI__BlastOutput2.html#ga9b2fb0137f97ffffd4c2f456628c43a9">More...</a><br /></td></tr>
|
||
<tr class="separator:ga9b2fb0137f97ffffd4c2f456628c43a9 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaa4e603cbecface69bd2ada71d27adf1e inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaa4e603cbecface69bd2ada71d27adf1e">ResetStat</a> (void)</td></tr>
|
||
<tr class="memdesc:gaa4e603cbecface69bd2ada71d27adf1e inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Stat data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gaa4e603cbecface69bd2ada71d27adf1e">More...</a><br /></td></tr>
|
||
<tr class="separator:gaa4e603cbecface69bd2ada71d27adf1e inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga1a2e045f2ad21810298e992bf84213c6 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga75c7897ec8cbd783c05f6767e298a04a">TStat</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga1a2e045f2ad21810298e992bf84213c6">GetStat</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga1a2e045f2ad21810298e992bf84213c6 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Stat member data. <a href="group__dataspec__NCBI__BlastOutput2.html#ga1a2e045f2ad21810298e992bf84213c6">More...</a><br /></td></tr>
|
||
<tr class="separator:ga1a2e045f2ad21810298e992bf84213c6 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaa3458f262ffe4e51dda99912e5d5d72c inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaa3458f262ffe4e51dda99912e5d5d72c">SetStat</a> (<a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga75c7897ec8cbd783c05f6767e298a04a">TStat</a> &<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="memdesc:gaa3458f262ffe4e51dda99912e5d5d72c inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Stat data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gaa3458f262ffe4e51dda99912e5d5d72c">More...</a><br /></td></tr>
|
||
<tr class="separator:gaa3458f262ffe4e51dda99912e5d5d72c inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga6ec9e20a8cd232a11e02cd938105c4da inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga75c7897ec8cbd783c05f6767e298a04a">TStat</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga6ec9e20a8cd232a11e02cd938105c4da">SetStat</a> (void)</td></tr>
|
||
<tr class="memdesc:ga6ec9e20a8cd232a11e02cd938105c4da inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Stat data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga6ec9e20a8cd232a11e02cd938105c4da">More...</a><br /></td></tr>
|
||
<tr class="separator:ga6ec9e20a8cd232a11e02cd938105c4da inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga7da9367caf8310b3ed01a091bdcd148f inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga7da9367caf8310b3ed01a091bdcd148f">IsSetMessage</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga7da9367caf8310b3ed01a091bdcd148f inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Some (error?) information <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Message data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga7da9367caf8310b3ed01a091bdcd148f">More...</a><br /></td></tr>
|
||
<tr class="separator:ga7da9367caf8310b3ed01a091bdcd148f inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga299305abd650aecbf80344cca75bda78 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga299305abd650aecbf80344cca75bda78">CanGetMessage</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga299305abd650aecbf80344cca75bda78 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetMessage method. <a href="group__dataspec__NCBI__BlastOutput2.html#ga299305abd650aecbf80344cca75bda78">More...</a><br /></td></tr>
|
||
<tr class="separator:ga299305abd650aecbf80344cca75bda78 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaaa05f862d7048755db015e8422ae5e2c inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaaa05f862d7048755db015e8422ae5e2c">ResetMessage</a> (void)</td></tr>
|
||
<tr class="memdesc:gaaa05f862d7048755db015e8422ae5e2c inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Message data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gaaa05f862d7048755db015e8422ae5e2c">More...</a><br /></td></tr>
|
||
<tr class="separator:gaaa05f862d7048755db015e8422ae5e2c inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga7e154c303799de81c7cf5105319a7a64 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga634156ee97752762050d14533d82cd1b">TMessage</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga7e154c303799de81c7cf5105319a7a64">GetMessage</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga7e154c303799de81c7cf5105319a7a64 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Message member data. <a href="group__dataspec__NCBI__BlastOutput2.html#ga7e154c303799de81c7cf5105319a7a64">More...</a><br /></td></tr>
|
||
<tr class="separator:ga7e154c303799de81c7cf5105319a7a64 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga32c84829f9300167e67e01ec314e5451 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga32c84829f9300167e67e01ec314e5451">SetMessage</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga634156ee97752762050d14533d82cd1b">TMessage</a> &<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="memdesc:ga32c84829f9300167e67e01ec314e5451 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Message data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga32c84829f9300167e67e01ec314e5451">More...</a><br /></td></tr>
|
||
<tr class="separator:ga32c84829f9300167e67e01ec314e5451 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga51e4fbb5df07eca309e850271d0b5e42 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga51e4fbb5df07eca309e850271d0b5e42">SetMessage</a> (<a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga634156ee97752762050d14533d82cd1b">TMessage</a> &&<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="separator:ga51e4fbb5df07eca309e850271d0b5e42 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga9bee566fe52fcf1da44b6c17bc83c689 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga634156ee97752762050d14533d82cd1b">TMessage</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga9bee566fe52fcf1da44b6c17bc83c689">SetMessage</a> (void)</td></tr>
|
||
<tr class="memdesc:ga9bee566fe52fcf1da44b6c17bc83c689 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Message data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga9bee566fe52fcf1da44b6c17bc83c689">More...</a><br /></td></tr>
|
||
<tr class="separator:ga9bee566fe52fcf1da44b6c17bc83c689 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga53fefe504715c071fc867a573e7de2b2 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga53fefe504715c071fc867a573e7de2b2">Reset</a> (void)</td></tr>
|
||
<tr class="memdesc:ga53fefe504715c071fc867a573e7de2b2 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset the whole object. <a href="group__dataspec__NCBI__BlastOutput2.html#ga53fefe504715c071fc867a573e7de2b2">More...</a><br /></td></tr>
|
||
<tr class="separator:ga53fefe504715c071fc867a573e7de2b2 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:acc8ff0abad3a431a1ed643a5baa6a1af inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#acc8ff0abad3a431a1ed643a5baa6a1af">CSearch_Base</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSearch__Base.html#aec07f7524cf0ec5dc6610b776b3ff4d2">TIndex_Impl</a> &index_impl, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBLAST__SequenceBlk.html">BLAST_SequenceBlk</a> *<a class="el" href="ftds14_2freetds_2tds_2unittests_2utf8__1_8c.html#aa590f90371629b8ec9b73bebe4d08501">query</a>, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqLoc.html">BlastSeqLoc</a> *locs, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSearch__Base.html#afd6cb73bb0bbdcdbde5d1f139c6cbc9c">TSearchOptions</a> &options)</td></tr>
|
||
<tr class="memdesc:acc8ff0abad3a431a1ed643a5baa6a1af inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Object constructor. <a href="classCSearch__Base.html#acc8ff0abad3a431a1ed643a5baa6a1af">More...</a><br /></td></tr>
|
||
<tr class="separator:acc8ff0abad3a431a1ed643a5baa6a1af inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a7826756ad955f44bb5d56956e1fad3a8 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCConstRef.html">CConstRef</a>< <a class="el" href="classCDbIndex_1_1CSearchResults.html">CDbIndex::CSearchResults</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a7826756ad955f44bb5d56956e1fad3a8">operator()</a> ()</td></tr>
|
||
<tr class="memdesc:a7826756ad955f44bb5d56956e1fad3a8 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Performs the search. <a href="classCSearch__Base.html#a7826756ad955f44bb5d56956e1fad3a8">More...</a><br /></td></tr>
|
||
<tr class="separator:a7826756ad955f44bb5d56956e1fad3a8 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pub_methods_classCSerialObject"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classCSerialObject')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classCSerialObject.html">CSerialObject</a></td></tr>
|
||
<tr class="memitem:ga8575b1015c4a4f3336b6e1c0a4324b71 inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#ga8575b1015c4a4f3336b6e1c0a4324b71">CSerialObject</a> (void)</td></tr>
|
||
<tr class="separator:ga8575b1015c4a4f3336b6e1c0a4324b71 inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaf278b96157abad20b5d944fb83d32fb1 inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#gaf278b96157abad20b5d944fb83d32fb1">~CSerialObject</a> (void)</td></tr>
|
||
<tr class="separator:gaf278b96157abad20b5d944fb83d32fb1 inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gacb5d8a2e6878e58aeaeaf342081f0b7f inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCTypeInfo.html">CTypeInfo</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#gacb5d8a2e6878e58aeaeaf342081f0b7f">GetThisTypeInfo</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> =0</td></tr>
|
||
<tr class="separator:gacb5d8a2e6878e58aeaeaf342081f0b7f inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga6c7f903717f7a272091acf5124cfd903 inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#ga6c7f903717f7a272091acf5124cfd903">Assign</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSerialObject.html">CSerialObject</a> &source, <a class="el" href="group__GenClassSupport.html#ga059327d78b8d9e780d720f141674f241">ESerialRecursionMode</a> how=<a class="el" href="group__GenClassSupport.html#gga059327d78b8d9e780d720f141674f241abe759672df31c77b76afeea2cd4c0db7">eRecursive</a>)</td></tr>
|
||
<tr class="memdesc:ga6c7f903717f7a272091acf5124cfd903 inherit pub_methods_classCSerialObject"><td class="mdescLeft"> </td><td class="mdescRight">Set object to copy of another one. <a href="group__GenClassSupport.html#ga6c7f903717f7a272091acf5124cfd903">More...</a><br /></td></tr>
|
||
<tr class="separator:ga6c7f903717f7a272091acf5124cfd903 inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gae694abd95a4753598c398540f3467d99 inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#gae694abd95a4753598c398540f3467d99">Equals</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSerialObject.html">CSerialObject</a> &object, <a class="el" href="group__GenClassSupport.html#ga059327d78b8d9e780d720f141674f241">ESerialRecursionMode</a> how=<a class="el" href="group__GenClassSupport.html#gga059327d78b8d9e780d720f141674f241abe759672df31c77b76afeea2cd4c0db7">eRecursive</a>) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gae694abd95a4753598c398540f3467d99 inherit pub_methods_classCSerialObject"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if both objects contain the same values. <a href="group__GenClassSupport.html#gae694abd95a4753598c398540f3467d99">More...</a><br /></td></tr>
|
||
<tr class="separator:gae694abd95a4753598c398540f3467d99 inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga0daf4906b8f2e6382118c4a018491761 inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#ga0daf4906b8f2e6382118c4a018491761">DebugDump</a> (<a class="el" href="classCDebugDumpContext.html">CDebugDumpContext</a> ddc, unsigned <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> <a class="el" href="ct__nlmzip__trees_8cpp.html#a431c74c4b26732a3a7de689109eb6b65">depth</a>) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga0daf4906b8f2e6382118c4a018491761 inherit pub_methods_classCSerialObject"><td class="mdescLeft"> </td><td class="mdescRight">Define method for dumping debug information. <a href="group__GenClassSupport.html#ga0daf4906b8f2e6382118c4a018491761">More...</a><br /></td></tr>
|
||
<tr class="separator:ga0daf4906b8f2e6382118c4a018491761 inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga7382b4cd30306d9444f85abd912ff61e inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#ga7382b4cd30306d9444f85abd912ff61e">ThrowUnassigned</a> (<a class="el" href="group__GenClassSupport.html#ga4045c609bd35431331d0055309404111">TMemberIndex</a> index) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="separator:ga7382b4cd30306d9444f85abd912ff61e inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gab5506012856f3627d88368a24e1eb254 inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#gab5506012856f3627d88368a24e1eb254">ThrowUnassigned</a> (<a class="el" href="group__GenClassSupport.html#ga4045c609bd35431331d0055309404111">TMemberIndex</a> index, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> char *<a class="el" href="dbapi__sample__base_8hpp.html#a8334353b550f5c3b6d2ea57d716ab2e2">file_name</a>, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> file_line) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="separator:gab5506012856f3627d88368a24e1eb254 inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga937551d0a9c61c7ff537ac19ec37904d inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#ga937551d0a9c61c7ff537ac19ec37904d">HasNamespaceName</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga937551d0a9c61c7ff537ac19ec37904d inherit pub_methods_classCSerialObject"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if object data type has namespace name. <a href="group__GenClassSupport.html#ga937551d0a9c61c7ff537ac19ec37904d">More...</a><br /></td></tr>
|
||
<tr class="separator:ga937551d0a9c61c7ff537ac19ec37904d inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga901688404844d3c9be43320e1d51c485 inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#ga901688404844d3c9be43320e1d51c485">GetNamespaceName</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga901688404844d3c9be43320e1d51c485 inherit pub_methods_classCSerialObject"><td class="mdescLeft"> </td><td class="mdescRight">Get namespace name. <a href="group__GenClassSupport.html#ga901688404844d3c9be43320e1d51c485">More...</a><br /></td></tr>
|
||
<tr class="separator:ga901688404844d3c9be43320e1d51c485 inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gacfc7e87713da36496323f5477db80219 inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#gacfc7e87713da36496323f5477db80219">HasNamespacePrefix</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gacfc7e87713da36496323f5477db80219 inherit pub_methods_classCSerialObject"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if data type has namespace prefix. <a href="group__GenClassSupport.html#gacfc7e87713da36496323f5477db80219">More...</a><br /></td></tr>
|
||
<tr class="separator:gacfc7e87713da36496323f5477db80219 inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gae8fa62abf96f3ed3cec903dce6a6a33a inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#gae8fa62abf96f3ed3cec903dce6a6a33a">GetNamespacePrefix</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gae8fa62abf96f3ed3cec903dce6a6a33a inherit pub_methods_classCSerialObject"><td class="mdescLeft"> </td><td class="mdescRight">Get namespace prefix. <a href="group__GenClassSupport.html#gae8fa62abf96f3ed3cec903dce6a6a33a">More...</a><br /></td></tr>
|
||
<tr class="separator:gae8fa62abf96f3ed3cec903dce6a6a33a inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pub_methods_classCObject"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classCObject')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classCObject.html">CObject</a></td></tr>
|
||
<tr class="memitem:gae38a8715a230c7ed588993c0206d8cb4 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#gae38a8715a230c7ed588993c0206d8cb4">CObject</a> (void)</td></tr>
|
||
<tr class="memdesc:gae38a8715a230c7ed588993c0206d8cb4 inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="group__Object.html#gae38a8715a230c7ed588993c0206d8cb4">More...</a><br /></td></tr>
|
||
<tr class="separator:gae38a8715a230c7ed588993c0206d8cb4 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gae89833a29aad16e7cb252314d2e7f4ab inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#gae89833a29aad16e7cb252314d2e7f4ab">CObject</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCObject.html">CObject</a> &src)</td></tr>
|
||
<tr class="memdesc:gae89833a29aad16e7cb252314d2e7f4ab inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor. <a href="group__Object.html#gae89833a29aad16e7cb252314d2e7f4ab">More...</a><br /></td></tr>
|
||
<tr class="separator:gae89833a29aad16e7cb252314d2e7f4ab inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga5125d96ff932bcd471a734fd174b2022 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga5125d96ff932bcd471a734fd174b2022">~CObject</a> (void)</td></tr>
|
||
<tr class="memdesc:ga5125d96ff932bcd471a734fd174b2022 inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="group__Object.html#ga5125d96ff932bcd471a734fd174b2022">More...</a><br /></td></tr>
|
||
<tr class="separator:ga5125d96ff932bcd471a734fd174b2022 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gab2090742c0465c4229f6e0b57c2de566 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCObject.html">CObject</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#gab2090742c0465c4229f6e0b57c2de566">operator=</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCObject.html">CObject</a> &src) <a class="el" href="group__Exception.html#ga8b97bb3687e603604470b18da8e56e91">THROWS_NONE</a></td></tr>
|
||
<tr class="memdesc:gab2090742c0465c4229f6e0b57c2de566 inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator. <a href="group__Object.html#gab2090742c0465c4229f6e0b57c2de566">More...</a><br /></td></tr>
|
||
<tr class="separator:gab2090742c0465c4229f6e0b57c2de566 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaad370ec0ee157f6082b9845338cb2809 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#gaad370ec0ee157f6082b9845338cb2809">CanBeDeleted</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__Exception.html#ga8b97bb3687e603604470b18da8e56e91">THROWS_NONE</a></td></tr>
|
||
<tr class="memdesc:gaad370ec0ee157f6082b9845338cb2809 inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if object can be deleted. <a href="group__Object.html#gaad370ec0ee157f6082b9845338cb2809">More...</a><br /></td></tr>
|
||
<tr class="separator:gaad370ec0ee157f6082b9845338cb2809 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaf5cddacd7194af14e759f3d89325679b inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#gaf5cddacd7194af14e759f3d89325679b">IsAllocatedInPool</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__Exception.html#ga8b97bb3687e603604470b18da8e56e91">THROWS_NONE</a></td></tr>
|
||
<tr class="memdesc:gaf5cddacd7194af14e759f3d89325679b inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if object is allocated in memory pool (not system heap) <a href="group__Object.html#gaf5cddacd7194af14e759f3d89325679b">More...</a><br /></td></tr>
|
||
<tr class="separator:gaf5cddacd7194af14e759f3d89325679b inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga9f9bbe6d075c90238a43585999d303d9 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga9f9bbe6d075c90238a43585999d303d9">Referenced</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__Exception.html#ga8b97bb3687e603604470b18da8e56e91">THROWS_NONE</a></td></tr>
|
||
<tr class="memdesc:ga9f9bbe6d075c90238a43585999d303d9 inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if object is referenced. <a href="group__Object.html#ga9f9bbe6d075c90238a43585999d303d9">More...</a><br /></td></tr>
|
||
<tr class="separator:ga9f9bbe6d075c90238a43585999d303d9 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaac3600b16f957a209f857aff7f79bf91 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#gaac3600b16f957a209f857aff7f79bf91">ReferencedOnlyOnce</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__Exception.html#ga8b97bb3687e603604470b18da8e56e91">THROWS_NONE</a></td></tr>
|
||
<tr class="memdesc:gaac3600b16f957a209f857aff7f79bf91 inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if object is referenced only once. <a href="group__Object.html#gaac3600b16f957a209f857aff7f79bf91">More...</a><br /></td></tr>
|
||
<tr class="separator:gaac3600b16f957a209f857aff7f79bf91 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga7161c8a13b08e627baa2ea0d75d679dc inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga7161c8a13b08e627baa2ea0d75d679dc">AddReference</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga7161c8a13b08e627baa2ea0d75d679dc inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Add reference to object. <a href="group__Object.html#ga7161c8a13b08e627baa2ea0d75d679dc">More...</a><br /></td></tr>
|
||
<tr class="separator:ga7161c8a13b08e627baa2ea0d75d679dc inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga827e9544b3a20642fcb736160f203bab inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga827e9544b3a20642fcb736160f203bab">RemoveReference</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga827e9544b3a20642fcb736160f203bab inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Remove reference to object. <a href="group__Object.html#ga827e9544b3a20642fcb736160f203bab">More...</a><br /></td></tr>
|
||
<tr class="separator:ga827e9544b3a20642fcb736160f203bab inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga5f08a74874b48c0e4a3d8e54343d4c90 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga5f08a74874b48c0e4a3d8e54343d4c90">ReleaseReference</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga5f08a74874b48c0e4a3d8e54343d4c90 inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Remove reference without deleting object. <a href="group__Object.html#ga5f08a74874b48c0e4a3d8e54343d4c90">More...</a><br /></td></tr>
|
||
<tr class="separator:ga5f08a74874b48c0e4a3d8e54343d4c90 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga52d3bc7d4f90411a190da81d7fd8d931 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga52d3bc7d4f90411a190da81d7fd8d931">DoNotDeleteThisObject</a> (void)</td></tr>
|
||
<tr class="memdesc:ga52d3bc7d4f90411a190da81d7fd8d931 inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Mark this object as not allocated in heap – do not delete this object. <a href="group__Object.html#ga52d3bc7d4f90411a190da81d7fd8d931">More...</a><br /></td></tr>
|
||
<tr class="separator:ga52d3bc7d4f90411a190da81d7fd8d931 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga35fd00918a29221f823c8e8d5d67fee2 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga35fd00918a29221f823c8e8d5d67fee2">DoDeleteThisObject</a> (void)</td></tr>
|
||
<tr class="memdesc:ga35fd00918a29221f823c8e8d5d67fee2 inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Mark this object as allocated in heap – object can be deleted. <a href="group__Object.html#ga35fd00918a29221f823c8e8d5d67fee2">More...</a><br /></td></tr>
|
||
<tr class="separator:ga35fd00918a29221f823c8e8d5d67fee2 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga9a8f931b70ac3730f364ad6078580424 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga9a8f931b70ac3730f364ad6078580424">operator new</a> (size_t <a class="el" href="introspection__html_8hpp.html#ac27165163e7cf75ff278799c2eedf09a">size</a>)</td></tr>
|
||
<tr class="memdesc:ga9a8f931b70ac3730f364ad6078580424 inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Define new operator for memory allocation. <a href="group__Object.html#ga9a8f931b70ac3730f364ad6078580424">More...</a><br /></td></tr>
|
||
<tr class="separator:ga9a8f931b70ac3730f364ad6078580424 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gabb964e1c3096b1efe242a3c63bbb8120 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#gabb964e1c3096b1efe242a3c63bbb8120">operator new[]</a> (size_t <a class="el" href="introspection__html_8hpp.html#ac27165163e7cf75ff278799c2eedf09a">size</a>)</td></tr>
|
||
<tr class="memdesc:gabb964e1c3096b1efe242a3c63bbb8120 inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Define new[] operator for 'array' memory allocation. <a href="group__Object.html#gabb964e1c3096b1efe242a3c63bbb8120">More...</a><br /></td></tr>
|
||
<tr class="separator:gabb964e1c3096b1efe242a3c63bbb8120 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gafde2770a20ee356b8a60cc81cca42366 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#gafde2770a20ee356b8a60cc81cca42366">operator delete</a> (void *ptr)</td></tr>
|
||
<tr class="memdesc:gafde2770a20ee356b8a60cc81cca42366 inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Define delete operator for memory deallocation. <a href="group__Object.html#gafde2770a20ee356b8a60cc81cca42366">More...</a><br /></td></tr>
|
||
<tr class="separator:gafde2770a20ee356b8a60cc81cca42366 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga5ea75357098dc7fea6cca8fb81620856 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga5ea75357098dc7fea6cca8fb81620856">operator delete[]</a> (void *ptr)</td></tr>
|
||
<tr class="memdesc:ga5ea75357098dc7fea6cca8fb81620856 inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Define delete[] operator for memory deallocation. <a href="group__Object.html#ga5ea75357098dc7fea6cca8fb81620856">More...</a><br /></td></tr>
|
||
<tr class="separator:ga5ea75357098dc7fea6cca8fb81620856 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga37f436bf6f5a3d46b7363e104fccedf3 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga37f436bf6f5a3d46b7363e104fccedf3">operator new</a> (size_t <a class="el" href="introspection__html_8hpp.html#ac27165163e7cf75ff278799c2eedf09a">size</a>, void *place)</td></tr>
|
||
<tr class="memdesc:ga37f436bf6f5a3d46b7363e104fccedf3 inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Define new operator. <a href="group__Object.html#ga37f436bf6f5a3d46b7363e104fccedf3">More...</a><br /></td></tr>
|
||
<tr class="separator:ga37f436bf6f5a3d46b7363e104fccedf3 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga54499c2fd0381ad8505bc120d5da84ff inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga54499c2fd0381ad8505bc120d5da84ff">operator delete</a> (void *ptr, void *place)</td></tr>
|
||
<tr class="memdesc:ga54499c2fd0381ad8505bc120d5da84ff inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Define delete operator. <a href="group__Object.html#ga54499c2fd0381ad8505bc120d5da84ff">More...</a><br /></td></tr>
|
||
<tr class="separator:ga54499c2fd0381ad8505bc120d5da84ff inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga981e7384172734070f47a3a9b53d0c3c inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga981e7384172734070f47a3a9b53d0c3c">operator new</a> (size_t <a class="el" href="introspection__html_8hpp.html#ac27165163e7cf75ff278799c2eedf09a">size</a>, <a class="el" href="classCObjectMemoryPool.html">CObjectMemoryPool</a> *place)</td></tr>
|
||
<tr class="memdesc:ga981e7384172734070f47a3a9b53d0c3c inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Define new operator using memory pool. <a href="group__Object.html#ga981e7384172734070f47a3a9b53d0c3c">More...</a><br /></td></tr>
|
||
<tr class="separator:ga981e7384172734070f47a3a9b53d0c3c inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga5c29219485b863e8a846c3076d321c7e inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga5c29219485b863e8a846c3076d321c7e">operator delete</a> (void *ptr, <a class="el" href="classCObjectMemoryPool.html">CObjectMemoryPool</a> *place)</td></tr>
|
||
<tr class="memdesc:ga5c29219485b863e8a846c3076d321c7e inherit pub_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Define delete operator. <a href="group__Object.html#ga5c29219485b863e8a846c3076d321c7e">More...</a><br /></td></tr>
|
||
<tr class="separator:ga5c29219485b863e8a846c3076d321c7e inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pub_methods_classCDebugDumpable"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classCDebugDumpable')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classCDebugDumpable.html">CDebugDumpable</a></td></tr>
|
||
<tr class="memitem:ae8723856215191ef748f19ff73e8ba4e inherit pub_methods_classCDebugDumpable"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCDebugDumpable.html#ae8723856215191ef748f19ff73e8ba4e">CDebugDumpable</a> (void)</td></tr>
|
||
<tr class="separator:ae8723856215191ef748f19ff73e8ba4e inherit pub_methods_classCDebugDumpable"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:acdeaaedfabb4cc4a64108dbb854f4b51 inherit pub_methods_classCDebugDumpable"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classCDebugDumpable.html#acdeaaedfabb4cc4a64108dbb854f4b51">~CDebugDumpable</a> (void)</td></tr>
|
||
<tr class="separator:acdeaaedfabb4cc4a64108dbb854f4b51 inherit pub_methods_classCDebugDumpable"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a4ff9ec248a38f17b7d8deb3f78318a37 inherit pub_methods_classCDebugDumpable"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCDebugDumpable.html#a4ff9ec248a38f17b7d8deb3f78318a37">DebugDumpText</a> (ostream &<a class="el" href="events__unit__test_8cpp.html#ac3c18c078fe416626b6c1dcc3e780245">out</a>, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> &bundle, unsigned <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> <a class="el" href="ct__nlmzip__trees_8cpp.html#a431c74c4b26732a3a7de689109eb6b65">depth</a>) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="separator:a4ff9ec248a38f17b7d8deb3f78318a37 inherit pub_methods_classCDebugDumpable"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:aa0101dfdc0ae0cbd0cb1609c96f96229 inherit pub_methods_classCDebugDumpable"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCDebugDumpable.html#aa0101dfdc0ae0cbd0cb1609c96f96229">DebugDumpFormat</a> (<a class="el" href="classCDebugDumpFormatter.html">CDebugDumpFormatter</a> &ddf, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> &bundle, unsigned <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> <a class="el" href="ct__nlmzip__trees_8cpp.html#a431c74c4b26732a3a7de689109eb6b65">depth</a>) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="separator:aa0101dfdc0ae0cbd0cb1609c96f96229 inherit pub_methods_classCDebugDumpable"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a19047c92521e5f3ad2a14bab26a49b51 inherit pub_methods_classCDebugDumpable"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCDebugDumpable.html#a19047c92521e5f3ad2a14bab26a49b51">DumpToConsole</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="separator:a19047c92521e5f3ad2a14bab26a49b51 inherit pub_methods_classCDebugDumpable"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pub_methods_classCSearch__Base"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classCSearch__Base')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classCSearch__Base.html">CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > ></a></td></tr>
|
||
<tr class="memitem:ga648bed56db5de3e15bd028db62a4bce8 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga648bed56db5de3e15bd028db62a4bce8">CSearch_Base</a> (void)</td></tr>
|
||
<tr class="separator:ga648bed56db5de3e15bd028db62a4bce8 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:acc8ff0abad3a431a1ed643a5baa6a1af inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#acc8ff0abad3a431a1ed643a5baa6a1af">CSearch_Base</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSearch__Base.html#aec07f7524cf0ec5dc6610b776b3ff4d2">TIndex_Impl</a> &index_impl, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBLAST__SequenceBlk.html">BLAST_SequenceBlk</a> *<a class="el" href="ftds14_2freetds_2tds_2unittests_2utf8__1_8c.html#aa590f90371629b8ec9b73bebe4d08501">query</a>, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqLoc.html">BlastSeqLoc</a> *locs, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSearch__Base.html#afd6cb73bb0bbdcdbde5d1f139c6cbc9c">TSearchOptions</a> &options)</td></tr>
|
||
<tr class="memdesc:acc8ff0abad3a431a1ed643a5baa6a1af inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Object constructor. <a href="classCSearch__Base.html#acc8ff0abad3a431a1ed643a5baa6a1af">More...</a><br /></td></tr>
|
||
<tr class="separator:acc8ff0abad3a431a1ed643a5baa6a1af inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gae584163c5b1433b04f90d5b1dc3c7caf inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gae584163c5b1433b04f90d5b1dc3c7caf">~CSearch_Base</a> (void)</td></tr>
|
||
<tr class="separator:gae584163c5b1433b04f90d5b1dc3c7caf inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga782d0d3e5875d5ec121b4c3e1adaefe8 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga782d0d3e5875d5ec121b4c3e1adaefe8">DECLARE_INTERNAL_TYPE_INFO</a> ()</td></tr>
|
||
<tr class="separator:ga782d0d3e5875d5ec121b4c3e1adaefe8 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga2e245722b693746547f3eb716cbab9df inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga2e245722b693746547f3eb716cbab9df">IsSetQuery_id</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga2e245722b693746547f3eb716cbab9df inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">SeqId of query <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Query_id data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga2e245722b693746547f3eb716cbab9df">More...</a><br /></td></tr>
|
||
<tr class="separator:ga2e245722b693746547f3eb716cbab9df inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga038104ff3a99cffd64d0033f84e64a8b inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga038104ff3a99cffd64d0033f84e64a8b">CanGetQuery_id</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga038104ff3a99cffd64d0033f84e64a8b inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetQuery_id method. <a href="group__dataspec__NCBI__BlastOutput2.html#ga038104ff3a99cffd64d0033f84e64a8b">More...</a><br /></td></tr>
|
||
<tr class="separator:ga038104ff3a99cffd64d0033f84e64a8b inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gac35c6c45a0c0e60de1de4f83749257fb inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gac35c6c45a0c0e60de1de4f83749257fb">ResetQuery_id</a> (void)</td></tr>
|
||
<tr class="memdesc:gac35c6c45a0c0e60de1de4f83749257fb inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Query_id data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gac35c6c45a0c0e60de1de4f83749257fb">More...</a><br /></td></tr>
|
||
<tr class="separator:gac35c6c45a0c0e60de1de4f83749257fb inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga22c92f1051a35de1974edc9a6b52328c inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga8a4c8e2c3c50387bcbe01b8533c2cbe4">TQuery_id</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga22c92f1051a35de1974edc9a6b52328c">GetQuery_id</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga22c92f1051a35de1974edc9a6b52328c inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Query_id member data. <a href="group__dataspec__NCBI__BlastOutput2.html#ga22c92f1051a35de1974edc9a6b52328c">More...</a><br /></td></tr>
|
||
<tr class="separator:ga22c92f1051a35de1974edc9a6b52328c inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga4b4f8347965db5c7bcccc423052afaf4 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga4b4f8347965db5c7bcccc423052afaf4">SetQuery_id</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga8a4c8e2c3c50387bcbe01b8533c2cbe4">TQuery_id</a> &<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="memdesc:ga4b4f8347965db5c7bcccc423052afaf4 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Query_id data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga4b4f8347965db5c7bcccc423052afaf4">More...</a><br /></td></tr>
|
||
<tr class="separator:ga4b4f8347965db5c7bcccc423052afaf4 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga928af34074546ffee7ef36bbdf6eb129 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga928af34074546ffee7ef36bbdf6eb129">SetQuery_id</a> (<a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga8a4c8e2c3c50387bcbe01b8533c2cbe4">TQuery_id</a> &&<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="separator:ga928af34074546ffee7ef36bbdf6eb129 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gae3a80f25e393c1a6ecbe354a8b2efd4b inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga8a4c8e2c3c50387bcbe01b8533c2cbe4">TQuery_id</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gae3a80f25e393c1a6ecbe354a8b2efd4b">SetQuery_id</a> (void)</td></tr>
|
||
<tr class="memdesc:gae3a80f25e393c1a6ecbe354a8b2efd4b inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Query_id data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gae3a80f25e393c1a6ecbe354a8b2efd4b">More...</a><br /></td></tr>
|
||
<tr class="separator:gae3a80f25e393c1a6ecbe354a8b2efd4b inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gadb18d5a2b984d01eda93c3dfaaac7b72 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gadb18d5a2b984d01eda93c3dfaaac7b72">IsSetQuery_title</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gadb18d5a2b984d01eda93c3dfaaac7b72 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Definition line of query <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Query_title data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gadb18d5a2b984d01eda93c3dfaaac7b72">More...</a><br /></td></tr>
|
||
<tr class="separator:gadb18d5a2b984d01eda93c3dfaaac7b72 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga761facc1844cca66fead91a801210825 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga761facc1844cca66fead91a801210825">CanGetQuery_title</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga761facc1844cca66fead91a801210825 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetQuery_title method. <a href="group__dataspec__NCBI__BlastOutput2.html#ga761facc1844cca66fead91a801210825">More...</a><br /></td></tr>
|
||
<tr class="separator:ga761facc1844cca66fead91a801210825 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga08f84f03bd0f087bad503d27707ee858 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga08f84f03bd0f087bad503d27707ee858">ResetQuery_title</a> (void)</td></tr>
|
||
<tr class="memdesc:ga08f84f03bd0f087bad503d27707ee858 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Query_title data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga08f84f03bd0f087bad503d27707ee858">More...</a><br /></td></tr>
|
||
<tr class="separator:ga08f84f03bd0f087bad503d27707ee858 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaa34d943b8dacfbcc9205eeeed3e945c8 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga6889d230d2397ffe927d232f29566fab">TQuery_title</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaa34d943b8dacfbcc9205eeeed3e945c8">GetQuery_title</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gaa34d943b8dacfbcc9205eeeed3e945c8 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Query_title member data. <a href="group__dataspec__NCBI__BlastOutput2.html#gaa34d943b8dacfbcc9205eeeed3e945c8">More...</a><br /></td></tr>
|
||
<tr class="separator:gaa34d943b8dacfbcc9205eeeed3e945c8 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga28764b9824b943edf46395b25d7be0da inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga28764b9824b943edf46395b25d7be0da">SetQuery_title</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga6889d230d2397ffe927d232f29566fab">TQuery_title</a> &<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="memdesc:ga28764b9824b943edf46395b25d7be0da inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Query_title data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga28764b9824b943edf46395b25d7be0da">More...</a><br /></td></tr>
|
||
<tr class="separator:ga28764b9824b943edf46395b25d7be0da inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga45b9166008309273e342b7f097778263 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga45b9166008309273e342b7f097778263">SetQuery_title</a> (<a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga6889d230d2397ffe927d232f29566fab">TQuery_title</a> &&<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="separator:ga45b9166008309273e342b7f097778263 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga6db1516ef6d10e11915ae43d1488a49b inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga6889d230d2397ffe927d232f29566fab">TQuery_title</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga6db1516ef6d10e11915ae43d1488a49b">SetQuery_title</a> (void)</td></tr>
|
||
<tr class="memdesc:ga6db1516ef6d10e11915ae43d1488a49b inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Query_title data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga6db1516ef6d10e11915ae43d1488a49b">More...</a><br /></td></tr>
|
||
<tr class="separator:ga6db1516ef6d10e11915ae43d1488a49b inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga0c7c21007894767b934b3f8696ef350d inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga0c7c21007894767b934b3f8696ef350d">IsSetQuery_len</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga0c7c21007894767b934b3f8696ef350d inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">length of query sequence <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Query_len data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga0c7c21007894767b934b3f8696ef350d">More...</a><br /></td></tr>
|
||
<tr class="separator:ga0c7c21007894767b934b3f8696ef350d inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga61cc9e30e61e8a76a531acd76484826d inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga61cc9e30e61e8a76a531acd76484826d">CanGetQuery_len</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga61cc9e30e61e8a76a531acd76484826d inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetQuery_len method. <a href="group__dataspec__NCBI__BlastOutput2.html#ga61cc9e30e61e8a76a531acd76484826d">More...</a><br /></td></tr>
|
||
<tr class="separator:ga61cc9e30e61e8a76a531acd76484826d inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gad30b1de939fe6e168185328d8fcdf2ca inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gad30b1de939fe6e168185328d8fcdf2ca">ResetQuery_len</a> (void)</td></tr>
|
||
<tr class="memdesc:gad30b1de939fe6e168185328d8fcdf2ca inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Query_len data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gad30b1de939fe6e168185328d8fcdf2ca">More...</a><br /></td></tr>
|
||
<tr class="separator:gad30b1de939fe6e168185328d8fcdf2ca inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaf7dd1830422c0e04669cba5ce6294949 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga8ea8393dbd772563cef38ec2d8abf993">TQuery_len</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaf7dd1830422c0e04669cba5ce6294949">GetQuery_len</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gaf7dd1830422c0e04669cba5ce6294949 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Query_len member data. <a href="group__dataspec__NCBI__BlastOutput2.html#gaf7dd1830422c0e04669cba5ce6294949">More...</a><br /></td></tr>
|
||
<tr class="separator:gaf7dd1830422c0e04669cba5ce6294949 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga5d6620b7f4d0af79254cd9eb91a9f181 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga5d6620b7f4d0af79254cd9eb91a9f181">SetQuery_len</a> (<a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga8ea8393dbd772563cef38ec2d8abf993">TQuery_len</a> <a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="memdesc:ga5d6620b7f4d0af79254cd9eb91a9f181 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Query_len data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga5d6620b7f4d0af79254cd9eb91a9f181">More...</a><br /></td></tr>
|
||
<tr class="separator:ga5d6620b7f4d0af79254cd9eb91a9f181 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaa876c8653d1c44de42329b2658155e40 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga8ea8393dbd772563cef38ec2d8abf993">TQuery_len</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaa876c8653d1c44de42329b2658155e40">SetQuery_len</a> (void)</td></tr>
|
||
<tr class="memdesc:gaa876c8653d1c44de42329b2658155e40 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Query_len data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gaa876c8653d1c44de42329b2658155e40">More...</a><br /></td></tr>
|
||
<tr class="separator:gaa876c8653d1c44de42329b2658155e40 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gabde07846f453acecbe97e13ea2177810 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gabde07846f453acecbe97e13ea2177810">IsSetQuery_masking</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gabde07846f453acecbe97e13ea2177810 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Masked offsets. <a href="group__dataspec__NCBI__BlastOutput2.html#gabde07846f453acecbe97e13ea2177810">More...</a><br /></td></tr>
|
||
<tr class="separator:gabde07846f453acecbe97e13ea2177810 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gac37afc538706a5cdca98447a845c063b inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gac37afc538706a5cdca98447a845c063b">CanGetQuery_masking</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gac37afc538706a5cdca98447a845c063b inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetQuery_masking method. <a href="group__dataspec__NCBI__BlastOutput2.html#gac37afc538706a5cdca98447a845c063b">More...</a><br /></td></tr>
|
||
<tr class="separator:gac37afc538706a5cdca98447a845c063b inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gada4837760a9704bf674a7cee78221f7a inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gada4837760a9704bf674a7cee78221f7a">ResetQuery_masking</a> (void)</td></tr>
|
||
<tr class="memdesc:gada4837760a9704bf674a7cee78221f7a inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Query_masking data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gada4837760a9704bf674a7cee78221f7a">More...</a><br /></td></tr>
|
||
<tr class="separator:gada4837760a9704bf674a7cee78221f7a inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga9d15e1dc213bb53388e2e352a7f4980f inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga946dbe57e0dc1cbb265e82ed159fedb8">TQuery_masking</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga9d15e1dc213bb53388e2e352a7f4980f">GetQuery_masking</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga9d15e1dc213bb53388e2e352a7f4980f inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Query_masking member data. <a href="group__dataspec__NCBI__BlastOutput2.html#ga9d15e1dc213bb53388e2e352a7f4980f">More...</a><br /></td></tr>
|
||
<tr class="separator:ga9d15e1dc213bb53388e2e352a7f4980f inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gac41309812a3fb04528134ab9c635fb8d inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga946dbe57e0dc1cbb265e82ed159fedb8">TQuery_masking</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gac41309812a3fb04528134ab9c635fb8d">SetQuery_masking</a> (void)</td></tr>
|
||
<tr class="memdesc:gac41309812a3fb04528134ab9c635fb8d inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Query_masking data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gac41309812a3fb04528134ab9c635fb8d">More...</a><br /></td></tr>
|
||
<tr class="separator:gac41309812a3fb04528134ab9c635fb8d inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga119f12de47d5adae8beeeba33e85e010 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga119f12de47d5adae8beeeba33e85e010">IsSetHits</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga119f12de47d5adae8beeeba33e85e010 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Hits one for every db sequence <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Hits data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga119f12de47d5adae8beeeba33e85e010">More...</a><br /></td></tr>
|
||
<tr class="separator:ga119f12de47d5adae8beeeba33e85e010 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gac86dbe53e0c748e6633ddf76a3ad7cad inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gac86dbe53e0c748e6633ddf76a3ad7cad">CanGetHits</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gac86dbe53e0c748e6633ddf76a3ad7cad inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetHits method. <a href="group__dataspec__NCBI__BlastOutput2.html#gac86dbe53e0c748e6633ddf76a3ad7cad">More...</a><br /></td></tr>
|
||
<tr class="separator:gac86dbe53e0c748e6633ddf76a3ad7cad inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gac7dd059ea17bdac6fe02244ef20cba2c inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gac7dd059ea17bdac6fe02244ef20cba2c">ResetHits</a> (void)</td></tr>
|
||
<tr class="memdesc:gac7dd059ea17bdac6fe02244ef20cba2c inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Hits data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gac7dd059ea17bdac6fe02244ef20cba2c">More...</a><br /></td></tr>
|
||
<tr class="separator:gac7dd059ea17bdac6fe02244ef20cba2c inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga5896f2a30f2cd935fcc907cf13d0e538 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaec3ad1ac4ef81a8e040acf64663d0605">THits</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga5896f2a30f2cd935fcc907cf13d0e538">GetHits</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga5896f2a30f2cd935fcc907cf13d0e538 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Hits member data. <a href="group__dataspec__NCBI__BlastOutput2.html#ga5896f2a30f2cd935fcc907cf13d0e538">More...</a><br /></td></tr>
|
||
<tr class="separator:ga5896f2a30f2cd935fcc907cf13d0e538 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga09983ee2082d8656dbb4e1f0c0c3ffc9 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaec3ad1ac4ef81a8e040acf64663d0605">THits</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga09983ee2082d8656dbb4e1f0c0c3ffc9">SetHits</a> (void)</td></tr>
|
||
<tr class="memdesc:ga09983ee2082d8656dbb4e1f0c0c3ffc9 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Hits data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga09983ee2082d8656dbb4e1f0c0c3ffc9">More...</a><br /></td></tr>
|
||
<tr class="separator:ga09983ee2082d8656dbb4e1f0c0c3ffc9 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaea907712d8f9f17cb0dd0e12621c6064 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaea907712d8f9f17cb0dd0e12621c6064">IsSetStat</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gaea907712d8f9f17cb0dd0e12621c6064 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">search statistics <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Stat data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gaea907712d8f9f17cb0dd0e12621c6064">More...</a><br /></td></tr>
|
||
<tr class="separator:gaea907712d8f9f17cb0dd0e12621c6064 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga9b2fb0137f97ffffd4c2f456628c43a9 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga9b2fb0137f97ffffd4c2f456628c43a9">CanGetStat</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga9b2fb0137f97ffffd4c2f456628c43a9 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetStat method. <a href="group__dataspec__NCBI__BlastOutput2.html#ga9b2fb0137f97ffffd4c2f456628c43a9">More...</a><br /></td></tr>
|
||
<tr class="separator:ga9b2fb0137f97ffffd4c2f456628c43a9 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaa4e603cbecface69bd2ada71d27adf1e inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaa4e603cbecface69bd2ada71d27adf1e">ResetStat</a> (void)</td></tr>
|
||
<tr class="memdesc:gaa4e603cbecface69bd2ada71d27adf1e inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Stat data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gaa4e603cbecface69bd2ada71d27adf1e">More...</a><br /></td></tr>
|
||
<tr class="separator:gaa4e603cbecface69bd2ada71d27adf1e inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga1a2e045f2ad21810298e992bf84213c6 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga75c7897ec8cbd783c05f6767e298a04a">TStat</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga1a2e045f2ad21810298e992bf84213c6">GetStat</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga1a2e045f2ad21810298e992bf84213c6 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Stat member data. <a href="group__dataspec__NCBI__BlastOutput2.html#ga1a2e045f2ad21810298e992bf84213c6">More...</a><br /></td></tr>
|
||
<tr class="separator:ga1a2e045f2ad21810298e992bf84213c6 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaa3458f262ffe4e51dda99912e5d5d72c inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaa3458f262ffe4e51dda99912e5d5d72c">SetStat</a> (<a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga75c7897ec8cbd783c05f6767e298a04a">TStat</a> &<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="memdesc:gaa3458f262ffe4e51dda99912e5d5d72c inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Stat data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gaa3458f262ffe4e51dda99912e5d5d72c">More...</a><br /></td></tr>
|
||
<tr class="separator:gaa3458f262ffe4e51dda99912e5d5d72c inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga6ec9e20a8cd232a11e02cd938105c4da inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga75c7897ec8cbd783c05f6767e298a04a">TStat</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga6ec9e20a8cd232a11e02cd938105c4da">SetStat</a> (void)</td></tr>
|
||
<tr class="memdesc:ga6ec9e20a8cd232a11e02cd938105c4da inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Stat data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga6ec9e20a8cd232a11e02cd938105c4da">More...</a><br /></td></tr>
|
||
<tr class="separator:ga6ec9e20a8cd232a11e02cd938105c4da inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga7da9367caf8310b3ed01a091bdcd148f inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga7da9367caf8310b3ed01a091bdcd148f">IsSetMessage</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga7da9367caf8310b3ed01a091bdcd148f inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Some (error?) information <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Message data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga7da9367caf8310b3ed01a091bdcd148f">More...</a><br /></td></tr>
|
||
<tr class="separator:ga7da9367caf8310b3ed01a091bdcd148f inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga299305abd650aecbf80344cca75bda78 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga299305abd650aecbf80344cca75bda78">CanGetMessage</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga299305abd650aecbf80344cca75bda78 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetMessage method. <a href="group__dataspec__NCBI__BlastOutput2.html#ga299305abd650aecbf80344cca75bda78">More...</a><br /></td></tr>
|
||
<tr class="separator:ga299305abd650aecbf80344cca75bda78 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaaa05f862d7048755db015e8422ae5e2c inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaaa05f862d7048755db015e8422ae5e2c">ResetMessage</a> (void)</td></tr>
|
||
<tr class="memdesc:gaaa05f862d7048755db015e8422ae5e2c inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Message data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gaaa05f862d7048755db015e8422ae5e2c">More...</a><br /></td></tr>
|
||
<tr class="separator:gaaa05f862d7048755db015e8422ae5e2c inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga7e154c303799de81c7cf5105319a7a64 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga634156ee97752762050d14533d82cd1b">TMessage</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga7e154c303799de81c7cf5105319a7a64">GetMessage</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga7e154c303799de81c7cf5105319a7a64 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Message member data. <a href="group__dataspec__NCBI__BlastOutput2.html#ga7e154c303799de81c7cf5105319a7a64">More...</a><br /></td></tr>
|
||
<tr class="separator:ga7e154c303799de81c7cf5105319a7a64 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga32c84829f9300167e67e01ec314e5451 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga32c84829f9300167e67e01ec314e5451">SetMessage</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga634156ee97752762050d14533d82cd1b">TMessage</a> &<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="memdesc:ga32c84829f9300167e67e01ec314e5451 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Message data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga32c84829f9300167e67e01ec314e5451">More...</a><br /></td></tr>
|
||
<tr class="separator:ga32c84829f9300167e67e01ec314e5451 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga51e4fbb5df07eca309e850271d0b5e42 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga51e4fbb5df07eca309e850271d0b5e42">SetMessage</a> (<a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga634156ee97752762050d14533d82cd1b">TMessage</a> &&<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="separator:ga51e4fbb5df07eca309e850271d0b5e42 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga9bee566fe52fcf1da44b6c17bc83c689 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga634156ee97752762050d14533d82cd1b">TMessage</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga9bee566fe52fcf1da44b6c17bc83c689">SetMessage</a> (void)</td></tr>
|
||
<tr class="memdesc:ga9bee566fe52fcf1da44b6c17bc83c689 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Message data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga9bee566fe52fcf1da44b6c17bc83c689">More...</a><br /></td></tr>
|
||
<tr class="separator:ga9bee566fe52fcf1da44b6c17bc83c689 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga53fefe504715c071fc867a573e7de2b2 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga53fefe504715c071fc867a573e7de2b2">Reset</a> (void)</td></tr>
|
||
<tr class="memdesc:ga53fefe504715c071fc867a573e7de2b2 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset the whole object. <a href="group__dataspec__NCBI__BlastOutput2.html#ga53fefe504715c071fc867a573e7de2b2">More...</a><br /></td></tr>
|
||
<tr class="separator:ga53fefe504715c071fc867a573e7de2b2 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a7826756ad955f44bb5d56956e1fad3a8 inherit pub_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCConstRef.html">CConstRef</a>< <a class="el" href="classCDbIndex_1_1CSearchResults.html">CDbIndex::CSearchResults</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a7826756ad955f44bb5d56956e1fad3a8">operator()</a> ()</td></tr>
|
||
<tr class="memdesc:a7826756ad955f44bb5d56956e1fad3a8 inherit pub_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Performs the search. <a href="classCSearch__Base.html#a7826756ad955f44bb5d56956e1fad3a8">More...</a><br /></td></tr>
|
||
<tr class="separator:a7826756ad955f44bb5d56956e1fad3a8 inherit pub_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pub_methods_classCThread"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classCThread')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classCThread.html">CThread</a></td></tr>
|
||
<tr class="memitem:ga7d62c510f91ace22c6564a471ea03295 inherit pub_methods_classCThread"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#ga7d62c510f91ace22c6564a471ea03295">CThread</a> (void)</td></tr>
|
||
<tr class="memdesc:ga7d62c510f91ace22c6564a471ea03295 inherit pub_methods_classCThread"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="group__Threads.html#ga7d62c510f91ace22c6564a471ea03295">More...</a><br /></td></tr>
|
||
<tr class="separator:ga7d62c510f91ace22c6564a471ea03295 inherit pub_methods_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga1ca598d60e42a600f8f323c25792042d inherit pub_methods_classCThread"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#ga1ca598d60e42a600f8f323c25792042d">Run</a> (<a class="el" href="group__Threads.html#gac3152c5d190b92ef5ebe8cacef8a487e">TRunMode</a> <a class="el" href="mdb__load_8c.html#ac8bf36fe0577cba66bccda3a6f7e80a4">flags</a>=<a class="el" href="group__Threads.html#gga473cd5553ed973732c17aee90e193e28a8ea5c12dd97d39a22b5e848de9221d0e">fRunDefault</a>)</td></tr>
|
||
<tr class="memdesc:ga1ca598d60e42a600f8f323c25792042d inherit pub_methods_classCThread"><td class="mdescLeft"> </td><td class="mdescRight">Run the thread. <a href="group__Threads.html#ga1ca598d60e42a600f8f323c25792042d">More...</a><br /></td></tr>
|
||
<tr class="separator:ga1ca598d60e42a600f8f323c25792042d inherit pub_methods_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga636c135bff92bc4b4f36784ba10eee26 inherit pub_methods_classCThread"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#ga636c135bff92bc4b4f36784ba10eee26">Detach</a> (void)</td></tr>
|
||
<tr class="memdesc:ga636c135bff92bc4b4f36784ba10eee26 inherit pub_methods_classCThread"><td class="mdescLeft"> </td><td class="mdescRight">Inform the thread that user does not need to wait for its termination. <a href="group__Threads.html#ga636c135bff92bc4b4f36784ba10eee26">More...</a><br /></td></tr>
|
||
<tr class="separator:ga636c135bff92bc4b4f36784ba10eee26 inherit pub_methods_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaed05bdc2a6e76f19896b3e69dedf8a3e inherit pub_methods_classCThread"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#gaed05bdc2a6e76f19896b3e69dedf8a3e">Join</a> (void **exit_data=0)</td></tr>
|
||
<tr class="memdesc:gaed05bdc2a6e76f19896b3e69dedf8a3e inherit pub_methods_classCThread"><td class="mdescLeft"> </td><td class="mdescRight">Wait for the thread termination. <a href="group__Threads.html#gaed05bdc2a6e76f19896b3e69dedf8a3e">More...</a><br /></td></tr>
|
||
<tr class="separator:gaed05bdc2a6e76f19896b3e69dedf8a3e inherit pub_methods_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga5b86f79850582db0fd2ecf7e0e5efb54 inherit pub_methods_classCThread"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#ga5b86f79850582db0fd2ecf7e0e5efb54">Discard</a> (void)</td></tr>
|
||
<tr class="memdesc:ga5b86f79850582db0fd2ecf7e0e5efb54 inherit pub_methods_classCThread"><td class="mdescLeft"> </td><td class="mdescRight">If the thread has not been <a class="el" href="group__Threads.html#ga1ca598d60e42a600f8f323c25792042d" title="Run the thread.">Run()</a> yet, then schedule the thread object for destruction, and return TRUE. <a href="group__Threads.html#ga5b86f79850582db0fd2ecf7e0e5efb54">More...</a><br /></td></tr>
|
||
<tr class="separator:ga5b86f79850582db0fd2ecf7e0e5efb54 inherit pub_methods_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaabce0c6679aad2724eea0751cce0eb92 inherit pub_methods_classCThread"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#gaabce0c6679aad2724eea0751cce0eb92">IsTerminated</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gaabce0c6679aad2724eea0751cce0eb92 inherit pub_methods_classCThread"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if the thread has been terminated. <a href="group__Threads.html#gaabce0c6679aad2724eea0751cce0eb92">More...</a><br /></td></tr>
|
||
<tr class="separator:gaabce0c6679aad2724eea0751cce0eb92 inherit pub_methods_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
</table><table class="memberdecls">
|
||
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-methods"></a>
|
||
Static Public Member Functions</h2></td></tr>
|
||
<tr class="memitem:ac066a9f07f05ae02f3dc47e114cd4c29"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#ac066a9f07f05ae02f3dc47e114cd4c29">ResetGlobals</a> (void)</td></tr>
|
||
<tr class="memdesc:ac066a9f07f05ae02f3dc47e114cd4c29"><td class="mdescLeft"> </td><td class="mdescRight">Reset global parameters used in threaded search. <a href="classCSearch.html#ac066a9f07f05ae02f3dc47e114cd4c29">More...</a><br /></td></tr>
|
||
<tr class="separator:ac066a9f07f05ae02f3dc47e114cd4c29"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pub_static_methods_classCSerialObject"><td colspan="2" onclick="javascript:toggleInherit('pub_static_methods_classCSerialObject')"><img src="closed.png" alt="-"/> Static Public Member Functions inherited from <a class="el" href="classCSerialObject.html">CSerialObject</a></td></tr>
|
||
<tr class="memitem:gab2a92c7a5b5900317294b85e854db07e inherit pub_static_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#gab2a92c7a5b5900317294b85e854db07e">SetVerifyDataThread</a> (<a class="el" href="group__GenClassSupport.html#ga58e0144d240fc7ad45518d4c3ba735e1">ESerialVerifyData</a> <a class="el" href="ftds14_2freetds_2dblib_2unittests_2t0002_8c.html#a80ddcf418c95fb872f5eeccb9908b4c7">verify</a>)</td></tr>
|
||
<tr class="separator:gab2a92c7a5b5900317294b85e854db07e inherit pub_static_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga2e3bead397d7ec0fffde866cd890267e inherit pub_static_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#ga2e3bead397d7ec0fffde866cd890267e">SetVerifyDataGlobal</a> (<a class="el" href="group__GenClassSupport.html#ga58e0144d240fc7ad45518d4c3ba735e1">ESerialVerifyData</a> <a class="el" href="ftds14_2freetds_2dblib_2unittests_2t0002_8c.html#a80ddcf418c95fb872f5eeccb9908b4c7">verify</a>)</td></tr>
|
||
<tr class="separator:ga2e3bead397d7ec0fffde866cd890267e inherit pub_static_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gada3dbb83951d0bed9bde06c6c4ede9e2 inherit pub_static_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#gada3dbb83951d0bed9bde06c6c4ede9e2">UnassignedString</a> (void)</td></tr>
|
||
<tr class="separator:gada3dbb83951d0bed9bde06c6c4ede9e2 inherit pub_static_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga123d82fb69550b6418ad5d69e752873a inherit pub_static_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__STL.html#ga88e22aab83a29bae20f5354e89b041e3">CStringUTF8</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#ga123d82fb69550b6418ad5d69e752873a">UnassignedStringUTF8</a> (void)</td></tr>
|
||
<tr class="separator:ga123d82fb69550b6418ad5d69e752873a inherit pub_static_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga1d897c6ce0f541df2487600cedd9f40a inherit pub_static_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> char </td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#ga1d897c6ce0f541df2487600cedd9f40a">UnassignedByte</a> (void)</td></tr>
|
||
<tr class="separator:ga1d897c6ce0f541df2487600cedd9f40a inherit pub_static_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pub_static_methods_classCObject"><td colspan="2" onclick="javascript:toggleInherit('pub_static_methods_classCObject')"><img src="closed.png" alt="-"/> Static Public Member Functions inherited from <a class="el" href="classCObject.html">CObject</a></td></tr>
|
||
<tr class="memitem:ga63f363685df177bedf4a7f4ed7797a07 inherit pub_static_methods_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__WinDLL.html#gab1bd38411cb05b5e6f85c9735a486682">NCBI_XNCBI_EXPORT</a> void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga63f363685df177bedf4a7f4ed7797a07">ThrowNullPointerException</a> (void)</td></tr>
|
||
<tr class="memdesc:ga63f363685df177bedf4a7f4ed7797a07 inherit pub_static_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Define method to throw null pointer exception. <a href="group__Object.html#ga63f363685df177bedf4a7f4ed7797a07">More...</a><br /></td></tr>
|
||
<tr class="separator:ga63f363685df177bedf4a7f4ed7797a07 inherit pub_static_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gae042a181e665dd40945c1c1a7a6bc5d1 inherit pub_static_methods_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__WinDLL.html#gab1bd38411cb05b5e6f85c9735a486682">NCBI_XNCBI_EXPORT</a> void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#gae042a181e665dd40945c1c1a7a6bc5d1">ThrowNullPointerException</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> type_info &<a class="el" href="structtype.html">type</a>)</td></tr>
|
||
<tr class="separator:gae042a181e665dd40945c1c1a7a6bc5d1 inherit pub_static_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga4b6f1beef2a1f37c68f7f3b1aac471d8 inherit pub_static_methods_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__Object.html#ga3cf5f3ac0aef32c4aab1fa66513588cc">EAllocFillMode</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga4b6f1beef2a1f37c68f7f3b1aac471d8">GetAllocFillMode</a> (void)</td></tr>
|
||
<tr class="separator:ga4b6f1beef2a1f37c68f7f3b1aac471d8 inherit pub_static_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga42eceef165a83cc081837a373ab6dd67 inherit pub_static_methods_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga42eceef165a83cc081837a373ab6dd67">SetAllocFillMode</a> (<a class="el" href="group__Object.html#ga3cf5f3ac0aef32c4aab1fa66513588cc">EAllocFillMode</a> <a class="el" href="mdb__load_8c.html#a1ea5d0cb93f22f7d0fdf804bd68c3326">mode</a>)</td></tr>
|
||
<tr class="separator:ga42eceef165a83cc081837a373ab6dd67 inherit pub_static_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga05dafbb430a19e98affa48e669d694f7 inherit pub_static_methods_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga05dafbb430a19e98affa48e669d694f7">SetAllocFillMode</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> &<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="memdesc:ga05dafbb430a19e98affa48e669d694f7 inherit pub_static_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Set mode from configuration parameter value. <a href="group__Object.html#ga05dafbb430a19e98affa48e669d694f7">More...</a><br /></td></tr>
|
||
<tr class="separator:ga05dafbb430a19e98affa48e669d694f7 inherit pub_static_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pub_static_methods_classCDebugDumpable"><td colspan="2" onclick="javascript:toggleInherit('pub_static_methods_classCDebugDumpable')"><img src="closed.png" alt="-"/> Static Public Member Functions inherited from <a class="el" href="classCDebugDumpable.html">CDebugDumpable</a></td></tr>
|
||
<tr class="memitem:ab6ba54280c562230f65733cca0560c83 inherit pub_static_methods_classCDebugDumpable"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCDebugDumpable.html#ab6ba54280c562230f65733cca0560c83">EnableDebugDump</a> (<a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> on)</td></tr>
|
||
<tr class="separator:ab6ba54280c562230f65733cca0560c83 inherit pub_static_methods_classCDebugDumpable"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pub_static_methods_classCThread"><td colspan="2" onclick="javascript:toggleInherit('pub_static_methods_classCThread')"><img src="closed.png" alt="-"/> Static Public Member Functions inherited from <a class="el" href="classCThread.html">CThread</a></td></tr>
|
||
<tr class="memitem:ga214a02b7590e19a1d387ac65e11f9d64 inherit pub_static_methods_classCThread"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#ga214a02b7590e19a1d387ac65e11f9d64">Exit</a> (void *exit_data)</td></tr>
|
||
<tr class="memdesc:ga214a02b7590e19a1d387ac65e11f9d64 inherit pub_static_methods_classCThread"><td class="mdescLeft"> </td><td class="mdescRight">Cancel current thread. <a href="group__Threads.html#ga214a02b7590e19a1d387ac65e11f9d64">More...</a><br /></td></tr>
|
||
<tr class="separator:ga214a02b7590e19a1d387ac65e11f9d64 inherit pub_static_methods_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga316a37bcebecee1fa90226f780c21dab inherit pub_static_methods_classCThread"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__Threads.html#ga839c07ee43332439913a3d84fee9cbb0">TID</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#ga316a37bcebecee1fa90226f780c21dab">GetSelf</a> (void)</td></tr>
|
||
<tr class="separator:ga316a37bcebecee1fa90226f780c21dab inherit pub_static_methods_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gabbd6915c0648dde7a938774a8cd7d841 inherit pub_static_methods_classCThread"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#gabbd6915c0648dde7a938774a8cd7d841">IsMain</a> (void)</td></tr>
|
||
<tr class="separator:gabbd6915c0648dde7a938774a8cd7d841 inherit pub_static_methods_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gae232df3d1f2a62cd1299f828a6974c78 inherit pub_static_methods_classCThread"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="classCThread.html">CThread</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#gae232df3d1f2a62cd1299f828a6974c78">GetCurrentThread</a> (void)</td></tr>
|
||
<tr class="memdesc:gae232df3d1f2a62cd1299f828a6974c78 inherit pub_static_methods_classCThread"><td class="mdescLeft"> </td><td class="mdescRight">Get current <a class="el" href="classCThread.html" title="CThread –.">CThread</a> object (or NULL, if main thread) <a href="group__Threads.html#gae232df3d1f2a62cd1299f828a6974c78">More...</a><br /></td></tr>
|
||
<tr class="separator:gae232df3d1f2a62cd1299f828a6974c78 inherit pub_static_methods_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga38f47f7c75b00e1508b239acc6920f28 inherit pub_static_methods_classCThread"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#ga38f47f7c75b00e1508b239acc6920f28">GetSystemID</a> (<a class="el" href="group__Threads.html#gad6305f0699beed5e84a917b60e4c1b27">TThreadSystemID</a> *id)</td></tr>
|
||
<tr class="memdesc:ga38f47f7c75b00e1508b239acc6920f28 inherit pub_static_methods_classCThread"><td class="mdescLeft"> </td><td class="mdescRight">Get system ID of the current thread - for internal use only. <a href="group__Threads.html#ga38f47f7c75b00e1508b239acc6920f28">More...</a><br /></td></tr>
|
||
<tr class="separator:ga38f47f7c75b00e1508b239acc6920f28 inherit pub_static_methods_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gabb94ef34cb877a52250f4f26a5ba90f6 inherit pub_static_methods_classCThread"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> unsigned <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#gabb94ef34cb877a52250f4f26a5ba90f6">GetThreadsCount</a> ()</td></tr>
|
||
<tr class="memdesc:gabb94ef34cb877a52250f4f26a5ba90f6 inherit pub_static_methods_classCThread"><td class="mdescLeft"> </td><td class="mdescRight">Get total amount of threads This amount does not contain main thread. <a href="group__Threads.html#gabb94ef34cb877a52250f4f26a5ba90f6">More...</a><br /></td></tr>
|
||
<tr class="separator:gabb94ef34cb877a52250f4f26a5ba90f6 inherit pub_static_methods_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga6d6c565f2857603825f1b9778c3faefd inherit pub_static_methods_classCThread"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#ga6d6c565f2857603825f1b9778c3faefd">SetCurrentThreadName</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCTempString.html">CTempString</a> &)</td></tr>
|
||
<tr class="memdesc:ga6d6c565f2857603825f1b9778c3faefd inherit pub_static_methods_classCThread"><td class="mdescLeft"> </td><td class="mdescRight">Set name for the current thread. <a href="group__Threads.html#ga6d6c565f2857603825f1b9778c3faefd">More...</a><br /></td></tr>
|
||
<tr class="separator:ga6d6c565f2857603825f1b9778c3faefd inherit pub_static_methods_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga8a2901de96abda8cbaff142046ebeda8 inherit pub_static_methods_classCThread"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#ga8a2901de96abda8cbaff142046ebeda8">InitializeMainThreadId</a> (void)</td></tr>
|
||
<tr class="memdesc:ga8a2901de96abda8cbaff142046ebeda8 inherit pub_static_methods_classCThread"><td class="mdescLeft"> </td><td class="mdescRight">Initialize main thread's TID. <a href="group__Threads.html#ga8a2901de96abda8cbaff142046ebeda8">More...</a><br /></td></tr>
|
||
<tr class="separator:ga8a2901de96abda8cbaff142046ebeda8 inherit pub_static_methods_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga407372e86959a12ec9d24e9aea851153 inherit pub_static_methods_classCThread"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#ga407372e86959a12ec9d24e9aea851153">IsAppExiting</a> (void)</td></tr>
|
||
<tr class="memdesc:ga407372e86959a12ec9d24e9aea851153 inherit pub_static_methods_classCThread"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if the application is exiting (entered the destructor). <a href="group__Threads.html#ga407372e86959a12ec9d24e9aea851153">More...</a><br /></td></tr>
|
||
<tr class="separator:ga407372e86959a12ec9d24e9aea851153 inherit pub_static_methods_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gadc4318072acc25d95eb4d9746af388c6 inherit pub_static_methods_classCThread"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#gadc4318072acc25d95eb4d9746af388c6">SetWaitForAllThreadsTimeout</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCTimeout.html">CTimeout</a> &timeout)</td></tr>
|
||
<tr class="memdesc:gadc4318072acc25d95eb4d9746af388c6 inherit pub_static_methods_classCThread"><td class="mdescLeft"> </td><td class="mdescRight">Set timeout for stopping all threads on application exit. <a href="group__Threads.html#gadc4318072acc25d95eb4d9746af388c6">More...</a><br /></td></tr>
|
||
<tr class="separator:gadc4318072acc25d95eb4d9746af388c6 inherit pub_static_methods_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
</table><table class="memberdecls">
|
||
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-attribs"></a>
|
||
Static Public Attributes</h2></td></tr>
|
||
<tr class="memitem:adb2d68ee893f402a1f1520a25ada487b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSPeakSet.html">CMSPeakSet</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#adb2d68ee893f402a1f1520a25ada487b">SharedPeakSet</a> = <a class="el" href="group__AppFramework.html#ggae62facd370a837a6e56086869977621baf9a713ed26dee661a259730e650987e4">null</a></td></tr>
|
||
<tr class="separator:adb2d68ee893f402a1f1520a25ada487b"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pub_static_attribs_classCSerialObject"><td colspan="2" onclick="javascript:toggleInherit('pub_static_attribs_classCSerialObject')"><img src="closed.png" alt="-"/> Static Public Attributes inherited from <a class="el" href="classCSerialObject.html">CSerialObject</a></td></tr>
|
||
<tr class="memitem:gacf732f6a9f64037d0cad32a72f7522ea inherit pub_static_attribs_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#gacf732f6a9f64037d0cad32a72f7522ea">ms_UnassignedStr</a> = "<*unassigned*>"</td></tr>
|
||
<tr class="separator:gacf732f6a9f64037d0cad32a72f7522ea inherit pub_static_attribs_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga6baaf827f8d2e4f98be84d91d511a716 inherit pub_static_attribs_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> char </td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#ga6baaf827f8d2e4f98be84d91d511a716">ms_UnassignedByte</a> = char(0xcd)</td></tr>
|
||
<tr class="separator:ga6baaf827f8d2e4f98be84d91d511a716 inherit pub_static_attribs_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pub_static_attribs_classCObject"><td colspan="2" onclick="javascript:toggleInherit('pub_static_attribs_classCObject')"><img src="closed.png" alt="-"/> Static Public Attributes inherited from <a class="el" href="classCObject.html">CObject</a></td></tr>
|
||
<tr class="memitem:ga6b2ef05fc91950a79ed938def4fd705d inherit pub_static_attribs_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__Object.html#ga2e073b6c5b9c29648510bd99ebe00a5c">TCount</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga6b2ef05fc91950a79ed938def4fd705d">eCounterBitsCanBeDeleted</a> = 1 << 0</td></tr>
|
||
<tr class="memdesc:ga6b2ef05fc91950a79ed938def4fd705d inherit pub_static_attribs_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Define possible object states. <a href="group__Object.html#ga6b2ef05fc91950a79ed938def4fd705d">More...</a><br /></td></tr>
|
||
<tr class="separator:ga6b2ef05fc91950a79ed938def4fd705d inherit pub_static_attribs_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gae6d5b68d219dbdb40e88737873a3488c inherit pub_static_attribs_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__Object.html#ga2e073b6c5b9c29648510bd99ebe00a5c">TCount</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#gae6d5b68d219dbdb40e88737873a3488c">eCounterBitsInPlainHeap</a> = 1 << 1</td></tr>
|
||
<tr class="memdesc:gae6d5b68d219dbdb40e88737873a3488c inherit pub_static_attribs_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Heap signature was found. <a href="group__Object.html#gae6d5b68d219dbdb40e88737873a3488c">More...</a><br /></td></tr>
|
||
<tr class="separator:gae6d5b68d219dbdb40e88737873a3488c inherit pub_static_attribs_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga33e4da9c60adbc3cf2a0ca45ce21a2ba inherit pub_static_attribs_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__Object.html#ga2e073b6c5b9c29648510bd99ebe00a5c">TCount</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga33e4da9c60adbc3cf2a0ca45ce21a2ba">eCounterBitsPlaceMask</a></td></tr>
|
||
<tr class="memdesc:ga33e4da9c60adbc3cf2a0ca45ce21a2ba inherit pub_static_attribs_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Mask for 'in heap' state flags. <a href="group__Object.html#ga33e4da9c60adbc3cf2a0ca45ce21a2ba">More...</a><br /></td></tr>
|
||
<tr class="separator:ga33e4da9c60adbc3cf2a0ca45ce21a2ba inherit pub_static_attribs_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga0a412d4ea79669d73671f89cb3e798a2 inherit pub_static_attribs_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga0a412d4ea79669d73671f89cb3e798a2">eCounterStep</a> = 1 << 2</td></tr>
|
||
<tr class="memdesc:ga0a412d4ea79669d73671f89cb3e798a2 inherit pub_static_attribs_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Skip over the "in heap" bits. <a href="group__Object.html#ga0a412d4ea79669d73671f89cb3e798a2">More...</a><br /></td></tr>
|
||
<tr class="separator:ga0a412d4ea79669d73671f89cb3e798a2 inherit pub_static_attribs_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gab5880debef7cc7eb2a2891f440cd7569 inherit pub_static_attribs_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__Object.html#ga2e073b6c5b9c29648510bd99ebe00a5c">TCount</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#gab5880debef7cc7eb2a2891f440cd7569">eCounterValid</a> = <a class="el" href="group__Object.html#ga2e073b6c5b9c29648510bd99ebe00a5c">TCount</a>(1) << (sizeof(<a class="el" href="group__Object.html#ga2e073b6c5b9c29648510bd99ebe00a5c">TCount</a>) * 8 - 2)</td></tr>
|
||
<tr class="memdesc:gab5880debef7cc7eb2a2891f440cd7569 inherit pub_static_attribs_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Minimal value for valid objects (reference counter is zero) Must be a single bit value. <a href="group__Object.html#gab5880debef7cc7eb2a2891f440cd7569">More...</a><br /></td></tr>
|
||
<tr class="separator:gab5880debef7cc7eb2a2891f440cd7569 inherit pub_static_attribs_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaff6eaaf8b9c4040a05fe2325ab75f44e inherit pub_static_attribs_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__Object.html#ga2e073b6c5b9c29648510bd99ebe00a5c">TCount</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#gaff6eaaf8b9c4040a05fe2325ab75f44e">eCounterStateMask</a></td></tr>
|
||
<tr class="memdesc:gaff6eaaf8b9c4040a05fe2325ab75f44e inherit pub_static_attribs_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Valid object, and object in heap. <a href="group__Object.html#gaff6eaaf8b9c4040a05fe2325ab75f44e">More...</a><br /></td></tr>
|
||
<tr class="separator:gaff6eaaf8b9c4040a05fe2325ab75f44e inherit pub_static_attribs_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
</table><table class="memberdecls">
|
||
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-methods"></a>
|
||
Protected Member Functions</h2></td></tr>
|
||
<tr class="memitem:a74da212c53668b580dd0d6784e4c99cd"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a74da212c53668b580dd0d6784e4c99cd">DoubleCompare</a> (list< <a class="el" href="classCMSMatchedPeakSet.html">CMSMatchedPeakSet</a> * > &SingleForward, list< <a class="el" href="classCMSMatchedPeakSet.html">CMSMatchedPeakSet</a> * > &SingleBackward, list< <a class="el" href="classCMSMatchedPeakSet.html">CMSMatchedPeakSet</a> * > &Double, <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> DoubleForward)</td></tr>
|
||
<tr class="separator:a74da212c53668b580dd0d6784e4c99cd"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a5b43109372a8440c837e70afe74271cd"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a5b43109372a8440c837e70afe74271cd">MatchAndSort</a> (<a class="el" href="classCMSPeak.html">CMSPeak</a> *Peaks, <a class="el" href="classCMSHit.html">CMSHit</a> &Hit, <a class="el" href="mspeak_8hpp.html#a96730e665542e37f1b3da213391525cf">EMSPeakListTypes</a> Which, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> minintensity, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> TSeriesChargePairList::const_iterator &iPairList, list< <a class="el" href="classCMSMatchedPeakSet.html">CMSMatchedPeakSet</a> * > &SingleForward, list< <a class="el" href="classCMSMatchedPeakSet.html">CMSMatchedPeakSet</a> * > &SingleBackward)</td></tr>
|
||
<tr class="memdesc:a5b43109372a8440c837e70afe74271cd"><td class="mdescLeft"> </td><td class="mdescRight">Creates match ion match lists. <a href="classCSearch.html#a5b43109372a8440c837e70afe74271cd">More...</a><br /></td></tr>
|
||
<tr class="separator:a5b43109372a8440c837e70afe74271cd"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a2a897d5d32fb118ab2270b410cb1d309"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a2a897d5d32fb118ab2270b410cb1d309">Spectrum2Peak</a> (<a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSPeakSet.html">CMSPeakSet</a> > PeakSet)</td></tr>
|
||
<tr class="separator:a2a897d5d32fb118ab2270b410cb1d309"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a97552a0ba34fd079fa3ae704450448fa"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a97552a0ba34fd079fa3ae704450448fa">CountModSites</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> &NumModSites, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> NumMod, <a class="el" href="classCMod.html">CMod</a> ModList[])</td></tr>
|
||
<tr class="memdesc:a97552a0ba34fd079fa3ae704450448fa"><td class="mdescLeft"> </td><td class="mdescRight">count the number of unique sites modified <a href="classCSearch.html#a97552a0ba34fd079fa3ae704450448fa">More...</a><br /></td></tr>
|
||
<tr class="separator:a97552a0ba34fd079fa3ae704450448fa"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:aa719dd5213417bea90158e151546b4b3"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#aa719dd5213417bea90158e151546b4b3">SetIons</a> (list< <a class="el" href="msscore_8hpp.html#ac70bf0eb50fe802a40d5cd4495516b03">EMSIonSeries</a> > &Ions)</td></tr>
|
||
<tr class="memdesc:aa719dd5213417bea90158e151546b4b3"><td class="mdescLeft"> </td><td class="mdescRight">set up the ions to use <a href="classCSearch.html#aa719dd5213417bea90158e151546b4b3">More...</a><br /></td></tr>
|
||
<tr class="separator:aa719dd5213417bea90158e151546b4b3"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:aa59a3ac07d68a71a67d820344a92101a"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#aa59a3ac07d68a71a67d820344a92101a">CreateLadders</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> char *<a class="el" href="classSequence.html">Sequence</a>, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> iSearch, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> position, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> endposition, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> *Masses, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> iMissed, <a class="el" href="classCAA.html">CAA</a> &AA, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> iMod, <a class="el" href="classCMod.html">CMod</a> ModList[], <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> NumMod)</td></tr>
|
||
<tr class="memdesc:aa59a3ac07d68a71a67d820344a92101a"><td class="mdescLeft"> </td><td class="mdescRight">create the ladders from sequence <a href="classCSearch.html#aa59a3ac07d68a71a67d820344a92101a">More...</a><br /></td></tr>
|
||
<tr class="separator:aa59a3ac07d68a71a67d820344a92101a"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a5c9a98b50a19cfd4f4b36f4cf74e3467"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a5c9a98b50a19cfd4f4b36f4cf74e3467">CompareLadders</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> iMod, <a class="el" href="classCMSPeak.html">CMSPeak</a> *Peaks, <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> OrLadders, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="mspeak_8hpp.html#a390bf355505d5e3cd42686bd76a67042">TMassPeak</a> *MassPeak)</td></tr>
|
||
<tr class="memdesc:a5c9a98b50a19cfd4f4b36f4cf74e3467"><td class="mdescLeft"> </td><td class="mdescRight">compare ladders to experiment <a href="classCSearch.html#a5c9a98b50a19cfd4f4b36f4cf74e3467">More...</a><br /></td></tr>
|
||
<tr class="separator:a5c9a98b50a19cfd4f4b36f4cf74e3467"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a9a257aad48c39a9680af16f5ffc3ff82"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a9a257aad48c39a9680af16f5ffc3ff82">CompareLaddersTop</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> iMod, <a class="el" href="classCMSPeak.html">CMSPeak</a> *Peaks, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="mspeak_8hpp.html#a390bf355505d5e3cd42686bd76a67042">TMassPeak</a> *MassPeak)</td></tr>
|
||
<tr class="separator:a9a257aad48c39a9680af16f5ffc3ff82"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a372b2bcc105eb0b6efd9d01cb02fe6d8"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a372b2bcc105eb0b6efd9d01cb02fe6d8">CheckFixed</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> <a class="el" href="lex_8newick_8cpp.html#acb559820d9ca11295b4500f179ef6392">i</a>, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> NumFixed, <a class="el" href="classCMod.html">CMod</a> ModList[], <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> *ModIndex)</td></tr>
|
||
<tr class="memdesc:a372b2bcc105eb0b6efd9d01cb02fe6d8"><td class="mdescLeft"> </td><td class="mdescRight">Checks to see that given modindex points to a site shared by a fixed mod. <a href="classCSearch.html#a372b2bcc105eb0b6efd9d01cb02fe6d8">More...</a><br /></td></tr>
|
||
<tr class="separator:a372b2bcc105eb0b6efd9d01cb02fe6d8"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a6a3db8e4323473dd503c595154253420"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a6a3db8e4323473dd503c595154253420">InitModIndex</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> *ModIndex, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> &iMod, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> NumMod, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> NumModSites, <a class="el" href="classCMod.html">CMod</a> ModList[])</td></tr>
|
||
<tr class="separator:a6a3db8e4323473dd503c595154253420"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a016929b10fdf9e5b016113de9d3e32e4"><td class="memItemLeft" align="right" valign="top">unsigned </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a016929b10fdf9e5b016113de9d3e32e4">MakeBoolMask</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> *ModIndex, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> iMod)</td></tr>
|
||
<tr class="separator:a016929b10fdf9e5b016113de9d3e32e4"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a2630407c949d7b0b3136af103d74897c"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a2630407c949d7b0b3136af103d74897c">MakeBoolMap</a> (<a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> *ModMask, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> *ModIndex, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> &iMod, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> &NumMod)</td></tr>
|
||
<tr class="separator:a2630407c949d7b0b3136af103d74897c"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a23d70f957aafb37b5aee39174630f305"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a23d70f957aafb37b5aee39174630f305">CalcModIndex</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> *ModIndex, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> &iMod, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> &NumMod, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> NumFixed, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> NumModSites, <a class="el" href="classCMod.html">CMod</a> CModList[])</td></tr>
|
||
<tr class="separator:a23d70f957aafb37b5aee39174630f305"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a5012de4013ae530046aa163e174f835b"><td class="memItemLeft" align="right" valign="top">unsigned </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a5012de4013ae530046aa163e174f835b">MakeIntFromBoolMap</a> (<a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> *ModMask, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> &NumMod)</td></tr>
|
||
<tr class="separator:a5012de4013ae530046aa163e174f835b"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ac59e5496b857452d021b63a6fdcdf009"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#ac59e5496b857452d021b63a6fdcdf009">Getnumseq</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="separator:ac59e5496b857452d021b63a6fdcdf009"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a1ba3ebe55f67dfd66295d574128c087f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a1ba3ebe55f67dfd66295d574128c087f">AddModsToHit</a> (<a class="el" href="classCMSHits.html">CMSHits</a> *Hit, <a class="el" href="classCMSHit.html">CMSHit</a> *MSHit)</td></tr>
|
||
<tr class="memdesc:a1ba3ebe55f67dfd66295d574128c087f"><td class="mdescLeft"> </td><td class="mdescRight">Adds modification information to hitset. <a href="classCSearch.html#a1ba3ebe55f67dfd66295d574128c087f">More...</a><br /></td></tr>
|
||
<tr class="separator:a1ba3ebe55f67dfd66295d574128c087f"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a700db5bb0d32f23cb372df1128aa220b"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a700db5bb0d32f23cb372df1128aa220b">AddIonsToHit</a> (<a class="el" href="classCMSHits.html">CMSHits</a> *Hit, <a class="el" href="classCMSHit.html">CMSHit</a> *MSHit)</td></tr>
|
||
<tr class="memdesc:a700db5bb0d32f23cb372df1128aa220b"><td class="mdescLeft"> </td><td class="mdescRight">Adds ion information to hitset. <a href="classCSearch.html#a700db5bb0d32f23cb372df1128aa220b">More...</a><br /></td></tr>
|
||
<tr class="separator:a700db5bb0d32f23cb372df1128aa220b"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:aaf1ea6b0a864974e1f42f7f45af6f9b1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#aaf1ea6b0a864974e1f42f7f45af6f9b1">CreateSequence</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> Start, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> Stop, <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> &seqstring, <a class="el" href="classCSeqDBSequence.html">CSeqDBSequence</a> &<a class="el" href="classSequence.html">Sequence</a>)</td></tr>
|
||
<tr class="memdesc:aaf1ea6b0a864974e1f42f7f45af6f9b1"><td class="mdescLeft"> </td><td class="mdescRight">Generate a peptide sequence. <a href="classCSearch.html#aaf1ea6b0a864974e1f42f7f45af6f9b1">More...</a><br /></td></tr>
|
||
<tr class="separator:aaf1ea6b0a864974e1f42f7f45af6f9b1"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a4a3fb267ab67ccd78b2b3a7200c3821a"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a4a3fb267ab67ccd78b2b3a7200c3821a">WriteBioseqs</a> (void)</td></tr>
|
||
<tr class="memdesc:a4a3fb267ab67ccd78b2b3a7200c3821a"><td class="mdescLeft"> </td><td class="mdescRight">write oidset to result <a href="classCSearch.html#a4a3fb267ab67ccd78b2b3a7200c3821a">More...</a><br /></td></tr>
|
||
<tr class="separator:a4a3fb267ab67ccd78b2b3a7200c3821a"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:abc4645a96133b78f3d16fff99b169852"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#abc4645a96133b78f3d16fff99b169852">CalcNSort</a> (<a class="el" href="omssa_8hpp.html#ad8a34208f6d4d5bfff7322ac0a82f9a4">TScoreList</a> &ScoreList, double Threshold, <a class="el" href="classCMSPeak.html">CMSPeak</a> *Peaks)</td></tr>
|
||
<tr class="memdesc:abc4645a96133b78f3d16fff99b169852"><td class="mdescLeft"> </td><td class="mdescRight">calculate the evalues of the top hits and sort <a href="classCSearch.html#abc4645a96133b78f3d16fff99b169852">More...</a><br /></td></tr>
|
||
<tr class="separator:abc4645a96133b78f3d16fff99b169852"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a0b96efd3650fe192a63b9f36cb6f1861"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a0b96efd3650fe192a63b9f36cb6f1861">DeleteVariableOverlap</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> &NumMod, <a class="el" href="classCMod.html">CMod</a> ModList[])</td></tr>
|
||
<tr class="memdesc:a0b96efd3650fe192a63b9f36cb6f1861"><td class="mdescLeft"> </td><td class="mdescRight">delete variable mods that overlap with fixed mods <a href="classCSearch.html#a0b96efd3650fe192a63b9f36cb6f1861">More...</a><br /></td></tr>
|
||
<tr class="separator:a0b96efd3650fe192a63b9f36cb6f1861"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a0fcf525f5779fa355036968974bf0716"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a0fcf525f5779fa355036968974bf0716">UpdateWithNewPep</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> Missed, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> char *PepStart[], <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> char *PepEnd[], <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> NumMod[], <a class="el" href="classCMod.html">CMod</a> ModList[][32], <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> Masses[], <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> EndMasses[], <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> NumModSites[], <a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSModSpecSet.html">CMSModSpecSet</a> > &Modset)</td></tr>
|
||
<tr class="memdesc:a0fcf525f5779fa355036968974bf0716"><td class="mdescLeft"> </td><td class="mdescRight">update sites and masses for new peptide <a href="classCSearch.html#a0fcf525f5779fa355036968974bf0716">More...</a><br /></td></tr>
|
||
<tr class="separator:a0fcf525f5779fa355036968974bf0716"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a595bed291dc6ca4685397e914b05cdc3"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a595bed291dc6ca4685397e914b05cdc3">CreateModCombinations</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> Missed, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> char *PepStart[], <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> Masses[], <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> EndMasses[], <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> NumMod[], <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> NumMassAndMask[], <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> NumModSites[], <a class="el" href="classCMod.html">CMod</a> ModList[][32])</td></tr>
|
||
<tr class="separator:a595bed291dc6ca4685397e914b05cdc3"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:aa4b35edf347f79e7f05cea071e3c6a19"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#aa4b35edf347f79e7f05cea071e3c6a19">InitLadders</a> (std::list< <a class="el" href="msscore_8hpp.html#ac70bf0eb50fe802a40d5cd4495516b03">EMSIonSeries</a> > &Ions)</td></tr>
|
||
<tr class="memdesc:aa4b35edf347f79e7f05cea071e3c6a19"><td class="mdescLeft"> </td><td class="mdescRight">initialize mass ladders <a href="classCSearch.html#aa4b35edf347f79e7f05cea071e3c6a19">More...</a><br /></td></tr>
|
||
<tr class="separator:aa4b35edf347f79e7f05cea071e3c6a19"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:abe8b6214346549d5a66db282e79e52e1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#abe8b6214346549d5a66db282e79e52e1">MakeOidSet</a> (void)</td></tr>
|
||
<tr class="memdesc:abe8b6214346549d5a66db282e79e52e1"><td class="mdescLeft"> </td><td class="mdescRight">makes map of oid from previous search used in iterative searching <a href="classCSearch.html#abe8b6214346549d5a66db282e79e52e1">More...</a><br /></td></tr>
|
||
<tr class="separator:abe8b6214346549d5a66db282e79e52e1"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ad9ddeebd9a5f9835d465ce7e306c697f"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#ad9ddeebd9a5f9835d465ce7e306c697f">ReSearch</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> Number) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ad9ddeebd9a5f9835d465ce7e306c697f"><td class="mdescLeft"> </td><td class="mdescRight">examines a hitset to see if any good hits <a href="classCSearch.html#ad9ddeebd9a5f9835d465ce7e306c697f">More...</a><br /></td></tr>
|
||
<tr class="separator:ad9ddeebd9a5f9835d465ce7e306c697f"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a089138cdcb2856ca6603948a408e194c"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCMSResponse.html#a10ac4d245cf91be83306cac7793a6377">CMSResponse::TOidSet</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a089138cdcb2856ca6603948a408e194c">SetOidSet</a> (void)</td></tr>
|
||
<tr class="memdesc:a089138cdcb2856ca6603948a408e194c"><td class="mdescLeft"> </td><td class="mdescRight">get the oidset <a href="classCSearch.html#a089138cdcb2856ca6603948a408e194c">More...</a><br /></td></tr>
|
||
<tr class="separator:a089138cdcb2856ca6603948a408e194c"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a858463feb06dac70536f85ea51b67a11"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCMSResponse.html#a10ac4d245cf91be83306cac7793a6377">CMSResponse::TOidSet</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a858463feb06dac70536f85ea51b67a11">GetOidSet</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:a858463feb06dac70536f85ea51b67a11"><td class="mdescLeft"> </td><td class="mdescRight">get the oidset <a href="classCSearch.html#a858463feb06dac70536f85ea51b67a11">More...</a><br /></td></tr>
|
||
<tr class="separator:a858463feb06dac70536f85ea51b67a11"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a6725f89bb3ad2921ba45315d9c5fbbdb"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a6725f89bb3ad2921ba45315d9c5fbbdb">SetRestrictedSearch</a> (void)</td></tr>
|
||
<tr class="memdesc:a6725f89bb3ad2921ba45315d9c5fbbdb"><td class="mdescLeft"> </td><td class="mdescRight">is this search restricted to the oid set? <a href="classCSearch.html#a6725f89bb3ad2921ba45315d9c5fbbdb">More...</a><br /></td></tr>
|
||
<tr class="separator:a6725f89bb3ad2921ba45315d9c5fbbdb"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a867076b42b583d945df34ae8fc65f8a7"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a867076b42b583d945df34ae8fc65f8a7">GetRestrictedSearch</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:a867076b42b583d945df34ae8fc65f8a7"><td class="mdescLeft"> </td><td class="mdescRight">is this search restricted to the oid set? <a href="classCSearch.html#a867076b42b583d945df34ae8fc65f8a7">More...</a><br /></td></tr>
|
||
<tr class="separator:a867076b42b583d945df34ae8fc65f8a7"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a4abbe6dc72e495a4595ffd7ba0a7d912"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Portability.html#gad571e821cdf5dcc936b6beb906ad5a89">Int1</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a4abbe6dc72e495a4595ffd7ba0a7d912">GetLadderCalc</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> <a class="el" href="lex_8newick_8cpp.html#acb559820d9ca11295b4500f179ef6392">i</a>) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:a4abbe6dc72e495a4595ffd7ba0a7d912"><td class="mdescLeft"> </td><td class="mdescRight">Get the bit that indicates whether a ladder was calculated. <a href="classCSearch.html#a4abbe6dc72e495a4595ffd7ba0a7d912">More...</a><br /></td></tr>
|
||
<tr class="separator:a4abbe6dc72e495a4595ffd7ba0a7d912"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a1207c6c341781f4b9a3cc95a75ccd158"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Portability.html#gad571e821cdf5dcc936b6beb906ad5a89">Int1</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a1207c6c341781f4b9a3cc95a75ccd158">SetLadderCalc</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> <a class="el" href="lex_8newick_8cpp.html#acb559820d9ca11295b4500f179ef6392">i</a>)</td></tr>
|
||
<tr class="memdesc:a1207c6c341781f4b9a3cc95a75ccd158"><td class="mdescLeft"> </td><td class="mdescRight">Set the bit that indicates whether a ladder was calculated. <a href="classCSearch.html#a1207c6c341781f4b9a3cc95a75ccd158">More...</a><br /></td></tr>
|
||
<tr class="separator:a1207c6c341781f4b9a3cc95a75ccd158"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a5f3558924cdf0e9e64444cff2bad31a1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a5f3558924cdf0e9e64444cff2bad31a1">ClearLadderCalc</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> Max)</td></tr>
|
||
<tr class="memdesc:a5f3558924cdf0e9e64444cff2bad31a1"><td class="mdescLeft"> </td><td class="mdescRight">Clear the ladder calc array up to max index. <a href="classCSearch.html#a5f3558924cdf0e9e64444cff2bad31a1">More...</a><br /></td></tr>
|
||
<tr class="separator:a5f3558924cdf0e9e64444cff2bad31a1"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a5e21827850070f3805984a8ec22f7ca2"><td class="memItemLeft" align="right" valign="top"><a class="el" href="omssa_8hpp.html#a5742ee0bc8e594f879b5d020791738e4">TMassMask</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a5e21827850070f3805984a8ec22f7ca2">SetMassAndMask</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> <a class="el" href="lex_8newick_8cpp.html#acb559820d9ca11295b4500f179ef6392">i</a>, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> j)</td></tr>
|
||
<tr class="memdesc:a5e21827850070f3805984a8ec22f7ca2"><td class="mdescLeft"> </td><td class="mdescRight">Set the mask and mass of mod bit array. <a href="classCSearch.html#a5e21827850070f3805984a8ec22f7ca2">More...</a><br /></td></tr>
|
||
<tr class="separator:a5e21827850070f3805984a8ec22f7ca2"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ab379f3355f0dc89c0d50ef135b59133a"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSSearchSettings.html">CMSSearchSettings</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#ab379f3355f0dc89c0d50ef135b59133a">SetSettings</a> (void)</td></tr>
|
||
<tr class="memdesc:ab379f3355f0dc89c0d50ef135b59133a"><td class="mdescLeft"> </td><td class="mdescRight">Set search settings. <a href="classCSearch.html#ab379f3355f0dc89c0d50ef135b59133a">More...</a><br /></td></tr>
|
||
<tr class="separator:ab379f3355f0dc89c0d50ef135b59133a"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a6cde243e25dd495d88c213c29bbceeaf"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCConstRef.html">CConstRef</a>< <a class="el" href="classCMSSearchSettings.html">CMSSearchSettings</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a6cde243e25dd495d88c213c29bbceeaf">GetSettings</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:a6cde243e25dd495d88c213c29bbceeaf"><td class="mdescLeft"> </td><td class="mdescRight">Get search settings. <a href="classCSearch.html#a6cde243e25dd495d88c213c29bbceeaf">More...</a><br /></td></tr>
|
||
<tr class="separator:a6cde243e25dd495d88c213c29bbceeaf"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a69c302b985e6fbbc4743cae6528b2459"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSRequest.html">CMSRequest</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a69c302b985e6fbbc4743cae6528b2459">SetRequest</a> (void)</td></tr>
|
||
<tr class="memdesc:a69c302b985e6fbbc4743cae6528b2459"><td class="mdescLeft"> </td><td class="mdescRight">Set search request. <a href="classCSearch.html#a69c302b985e6fbbc4743cae6528b2459">More...</a><br /></td></tr>
|
||
<tr class="separator:a69c302b985e6fbbc4743cae6528b2459"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a38cc1279d2c040a2354f0ac02036bb62"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCConstRef.html">CConstRef</a>< <a class="el" href="classCMSRequest.html">CMSRequest</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a38cc1279d2c040a2354f0ac02036bb62">GetRequest</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:a38cc1279d2c040a2354f0ac02036bb62"><td class="mdescLeft"> </td><td class="mdescRight">Get search request. <a href="classCSearch.html#a38cc1279d2c040a2354f0ac02036bb62">More...</a><br /></td></tr>
|
||
<tr class="separator:a38cc1279d2c040a2354f0ac02036bb62"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a2a7af7c803ecb9d836edee6a96bc0f66"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSResponse.html">CMSResponse</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a2a7af7c803ecb9d836edee6a96bc0f66">SetResponse</a> (void)</td></tr>
|
||
<tr class="memdesc:a2a7af7c803ecb9d836edee6a96bc0f66"><td class="mdescLeft"> </td><td class="mdescRight">Set search response. <a href="classCSearch.html#a2a7af7c803ecb9d836edee6a96bc0f66">More...</a><br /></td></tr>
|
||
<tr class="separator:a2a7af7c803ecb9d836edee6a96bc0f66"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a6ea4e23a8ab44c7938979d0b6f134f6b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCConstRef.html">CConstRef</a>< <a class="el" href="classCMSResponse.html">CMSResponse</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a6ea4e23a8ab44c7938979d0b6f134f6b">GetResponse</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:a6ea4e23a8ab44c7938979d0b6f134f6b"><td class="mdescLeft"> </td><td class="mdescRight">Get search response. <a href="classCSearch.html#a6ea4e23a8ab44c7938979d0b6f134f6b">More...</a><br /></td></tr>
|
||
<tr class="separator:a6ea4e23a8ab44c7938979d0b6f134f6b"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a8caa7e28ab2f6e799a45cca224aef58b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCCleave.html">CCleave</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a8caa7e28ab2f6e799a45cca224aef58b">SetEnzyme</a> (void)</td></tr>
|
||
<tr class="memdesc:a8caa7e28ab2f6e799a45cca224aef58b"><td class="mdescLeft"> </td><td class="mdescRight">Set search enzyme. <a href="classCSearch.html#a8caa7e28ab2f6e799a45cca224aef58b">More...</a><br /></td></tr>
|
||
<tr class="separator:a8caa7e28ab2f6e799a45cca224aef58b"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a6585a6b9070686c7ecb0242b379c1e6d"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCConstRef.html">CConstRef</a>< <a class="el" href="classCCleave.html">CCleave</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a6585a6b9070686c7ecb0242b379c1e6d">GetEnzyme</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:a6585a6b9070686c7ecb0242b379c1e6d"><td class="mdescLeft"> </td><td class="mdescRight">Get search enzyme. <a href="classCSearch.html#a6585a6b9070686c7ecb0242b379c1e6d">More...</a><br /></td></tr>
|
||
<tr class="separator:a6585a6b9070686c7ecb0242b379c1e6d"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a225222f019e481ef0c9b21df51d9fea3"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCLadderContainer.html">CLadderContainer</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a225222f019e481ef0c9b21df51d9fea3">SetLadderContainer</a> (void)</td></tr>
|
||
<tr class="memdesc:a225222f019e481ef0c9b21df51d9fea3"><td class="mdescLeft"> </td><td class="mdescRight">set the ladder container <a href="classCSearch.html#a225222f019e481ef0c9b21df51d9fea3">More...</a><br /></td></tr>
|
||
<tr class="separator:a225222f019e481ef0c9b21df51d9fea3"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a0fd54889c5ae97be8b5e942d275db348"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCLadderContainer.html">CLadderContainer</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a0fd54889c5ae97be8b5e942d275db348">GetLadderContainer</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:a0fd54889c5ae97be8b5e942d275db348"><td class="mdescLeft"> </td><td class="mdescRight">get the ladder container <a href="classCSearch.html#a0fd54889c5ae97be8b5e942d275db348">More...</a><br /></td></tr>
|
||
<tr class="separator:a0fd54889c5ae97be8b5e942d275db348"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pro_methods_classCSearch__Base"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classCSearch__Base')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classCSearch__Base.html">CSearch_Base< LEGACY, NHITS, derived_t ></a></td></tr>
|
||
<tr class="memitem:a0d12f6e9c414bf9ff9441d68575cc547 inherit pro_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a0d12f6e9c414bf9ff9441d68575cc547">SearchInt</a> ()</td></tr>
|
||
<tr class="memdesc:a0d12f6e9c414bf9ff9441d68575cc547 inherit pro_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Helper method to search a particular segment of the query. <a href="classCSearch__Base.html#a0d12f6e9c414bf9ff9441d68575cc547">More...</a><br /></td></tr>
|
||
<tr class="separator:a0d12f6e9c414bf9ff9441d68575cc547 inherit pro_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a0880cd2c419311ce50d33774608c773a inherit pro_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a0880cd2c419311ce50d33774608c773a">ProcessBoundaryOffset</a> (<a class="el" href="dbindex__sp_8hpp.html#ab24dd73d837409e50d27583ed6f4e273">TWord</a> <a class="el" href="url__tooltip__handler_8cpp.html#af1a7c6ddf735b32939485fddbaec4e75">offset</a>, <a class="el" href="dbindex__sp_8hpp.html#ab24dd73d837409e50d27583ed6f4e273">TWord</a> <a class="el" href="convert__bounds_8c.html#a07dd8affd48f8ab7592d89bbf2be8516">bounds</a>)</td></tr>
|
||
<tr class="memdesc:a0880cd2c419311ce50d33774608c773a inherit pro_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Process a seed candidate that is close to the masked out or ambigous region of the subject. <a href="classCSearch__Base.html#a0880cd2c419311ce50d33774608c773a">More...</a><br /></td></tr>
|
||
<tr class="separator:a0880cd2c419311ce50d33774608c773a inherit pro_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a73f7d8582b770fe839ac732e0dbf9a81 inherit pro_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a73f7d8582b770fe839ac732e0dbf9a81">ProcessOffset</a> (<a class="el" href="dbindex__sp_8hpp.html#ab24dd73d837409e50d27583ed6f4e273">TWord</a> <a class="el" href="url__tooltip__handler_8cpp.html#af1a7c6ddf735b32939485fddbaec4e75">offset</a>)</td></tr>
|
||
<tr class="memdesc:a73f7d8582b770fe839ac732e0dbf9a81 inherit pro_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Process a regular seed candidate. <a href="classCSearch__Base.html#a73f7d8582b770fe839ac732e0dbf9a81">More...</a><br /></td></tr>
|
||
<tr class="separator:a73f7d8582b770fe839ac732e0dbf9a81 inherit pro_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:af0b74c8f0cd69b1ff2deccf26b63ae2a inherit pro_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#af0b74c8f0cd69b1ff2deccf26b63ae2a">ExtendLeft</a> (<a class="el" href="classCSearch__Base.html#a4a4961ff496fcd512762e7eab2636125">TTrackedSeed</a> &<a class="el" href="test__table_8cpp.html#a1447ad288a0a73454510f5777bdc3ed1">seed</a>, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> nmax=~(<a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a>) 0) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:af0b74c8f0cd69b1ff2deccf26b63ae2a inherit pro_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Extend a seed candidate to the left. <a href="classCSearch__Base.html#af0b74c8f0cd69b1ff2deccf26b63ae2a">More...</a><br /></td></tr>
|
||
<tr class="separator:af0b74c8f0cd69b1ff2deccf26b63ae2a inherit pro_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ac0698386f4f373485fde3a5a2c62469c inherit pro_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#ac0698386f4f373485fde3a5a2c62469c">ExtendRight</a> (<a class="el" href="classCSearch__Base.html#a4a4961ff496fcd512762e7eab2636125">TTrackedSeed</a> &<a class="el" href="test__table_8cpp.html#a1447ad288a0a73454510f5777bdc3ed1">seed</a>, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> nmax=~(<a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a>) 0) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ac0698386f4f373485fde3a5a2c62469c inherit pro_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Extend a seed candidate to the right. <a href="classCSearch__Base.html#ac0698386f4f373485fde3a5a2c62469c">More...</a><br /></td></tr>
|
||
<tr class="separator:ac0698386f4f373485fde3a5a2c62469c inherit pro_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:acc7b999c38d5eed0cda9b0b41c26c0bb inherit pro_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#acc7b999c38d5eed0cda9b0b41c26c0bb">ComputeSeeds</a> ()</td></tr>
|
||
<tr class="memdesc:acc7b999c38d5eed0cda9b0b41c26c0bb inherit pro_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Compute the seeds after all roots are collected. <a href="classCSearch__Base.html#acc7b999c38d5eed0cda9b0b41c26c0bb">More...</a><br /></td></tr>
|
||
<tr class="separator:acc7b999c38d5eed0cda9b0b41c26c0bb inherit pro_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a877ed8f06744864d1068885fa11e2601 inherit pro_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">unsigned long </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a877ed8f06744864d1068885fa11e2601">ProcessRoot</a> (<a class="el" href="classCSearch__Base.html#ab21f98298eed96cca1c114aab009b741">TTrackedSeeds</a> &seeds, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structSSeedRoot.html">SSeedRoot</a> *root)</td></tr>
|
||
<tr class="memdesc:a877ed8f06744864d1068885fa11e2601 inherit pro_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Process a single root. <a href="classCSearch__Base.html#a877ed8f06744864d1068885fa11e2601">More...</a><br /></td></tr>
|
||
<tr class="separator:a877ed8f06744864d1068885fa11e2601 inherit pro_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pro_methods_classCObject"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classCObject')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classCObject.html">CObject</a></td></tr>
|
||
<tr class="memitem:ga7b33b6d311860b76f3a8a79fcb7f9938 inherit pro_methods_classCObject"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga7b33b6d311860b76f3a8a79fcb7f9938">DeleteThis</a> (void)</td></tr>
|
||
<tr class="memdesc:ga7b33b6d311860b76f3a8a79fcb7f9938 inherit pro_methods_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Virtual method "deleting" this object. <a href="group__Object.html#ga7b33b6d311860b76f3a8a79fcb7f9938">More...</a><br /></td></tr>
|
||
<tr class="separator:ga7b33b6d311860b76f3a8a79fcb7f9938 inherit pro_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pro_methods_classCSearch__Base"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classCSearch__Base')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classCSearch__Base.html">CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > ></a></td></tr>
|
||
<tr class="memitem:a0d12f6e9c414bf9ff9441d68575cc547 inherit pro_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a0d12f6e9c414bf9ff9441d68575cc547">SearchInt</a> ()</td></tr>
|
||
<tr class="memdesc:a0d12f6e9c414bf9ff9441d68575cc547 inherit pro_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Helper method to search a particular segment of the query. <a href="classCSearch__Base.html#a0d12f6e9c414bf9ff9441d68575cc547">More...</a><br /></td></tr>
|
||
<tr class="separator:a0d12f6e9c414bf9ff9441d68575cc547 inherit pro_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a0880cd2c419311ce50d33774608c773a inherit pro_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a0880cd2c419311ce50d33774608c773a">ProcessBoundaryOffset</a> (<a class="el" href="dbindex__sp_8hpp.html#ab24dd73d837409e50d27583ed6f4e273">TWord</a> <a class="el" href="url__tooltip__handler_8cpp.html#af1a7c6ddf735b32939485fddbaec4e75">offset</a>, <a class="el" href="dbindex__sp_8hpp.html#ab24dd73d837409e50d27583ed6f4e273">TWord</a> <a class="el" href="convert__bounds_8c.html#a07dd8affd48f8ab7592d89bbf2be8516">bounds</a>)</td></tr>
|
||
<tr class="memdesc:a0880cd2c419311ce50d33774608c773a inherit pro_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Process a seed candidate that is close to the masked out or ambigous region of the subject. <a href="classCSearch__Base.html#a0880cd2c419311ce50d33774608c773a">More...</a><br /></td></tr>
|
||
<tr class="separator:a0880cd2c419311ce50d33774608c773a inherit pro_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a73f7d8582b770fe839ac732e0dbf9a81 inherit pro_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a73f7d8582b770fe839ac732e0dbf9a81">ProcessOffset</a> (<a class="el" href="dbindex__sp_8hpp.html#ab24dd73d837409e50d27583ed6f4e273">TWord</a> <a class="el" href="url__tooltip__handler_8cpp.html#af1a7c6ddf735b32939485fddbaec4e75">offset</a>)</td></tr>
|
||
<tr class="memdesc:a73f7d8582b770fe839ac732e0dbf9a81 inherit pro_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Process a regular seed candidate. <a href="classCSearch__Base.html#a73f7d8582b770fe839ac732e0dbf9a81">More...</a><br /></td></tr>
|
||
<tr class="separator:a73f7d8582b770fe839ac732e0dbf9a81 inherit pro_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:af0b74c8f0cd69b1ff2deccf26b63ae2a inherit pro_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#af0b74c8f0cd69b1ff2deccf26b63ae2a">ExtendLeft</a> (<a class="el" href="classCSearch__Base.html#a4a4961ff496fcd512762e7eab2636125">TTrackedSeed</a> &<a class="el" href="test__table_8cpp.html#a1447ad288a0a73454510f5777bdc3ed1">seed</a>, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> nmax=~(<a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a>) 0) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:af0b74c8f0cd69b1ff2deccf26b63ae2a inherit pro_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Extend a seed candidate to the left. <a href="classCSearch__Base.html#af0b74c8f0cd69b1ff2deccf26b63ae2a">More...</a><br /></td></tr>
|
||
<tr class="separator:af0b74c8f0cd69b1ff2deccf26b63ae2a inherit pro_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ac0698386f4f373485fde3a5a2c62469c inherit pro_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#ac0698386f4f373485fde3a5a2c62469c">ExtendRight</a> (<a class="el" href="classCSearch__Base.html#a4a4961ff496fcd512762e7eab2636125">TTrackedSeed</a> &<a class="el" href="test__table_8cpp.html#a1447ad288a0a73454510f5777bdc3ed1">seed</a>, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> nmax=~(<a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a>) 0) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ac0698386f4f373485fde3a5a2c62469c inherit pro_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Extend a seed candidate to the right. <a href="classCSearch__Base.html#ac0698386f4f373485fde3a5a2c62469c">More...</a><br /></td></tr>
|
||
<tr class="separator:ac0698386f4f373485fde3a5a2c62469c inherit pro_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:acc7b999c38d5eed0cda9b0b41c26c0bb inherit pro_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#acc7b999c38d5eed0cda9b0b41c26c0bb">ComputeSeeds</a> ()</td></tr>
|
||
<tr class="memdesc:acc7b999c38d5eed0cda9b0b41c26c0bb inherit pro_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Compute the seeds after all roots are collected. <a href="classCSearch__Base.html#acc7b999c38d5eed0cda9b0b41c26c0bb">More...</a><br /></td></tr>
|
||
<tr class="separator:acc7b999c38d5eed0cda9b0b41c26c0bb inherit pro_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a877ed8f06744864d1068885fa11e2601 inherit pro_methods_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">unsigned long </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a877ed8f06744864d1068885fa11e2601">ProcessRoot</a> (<a class="el" href="classCSearch__Base.html#ab21f98298eed96cca1c114aab009b741">TTrackedSeeds</a> &seeds, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structSSeedRoot.html">SSeedRoot</a> *root)</td></tr>
|
||
<tr class="memdesc:a877ed8f06744864d1068885fa11e2601 inherit pro_methods_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Process a single root. <a href="classCSearch__Base.html#a877ed8f06744864d1068885fa11e2601">More...</a><br /></td></tr>
|
||
<tr class="separator:a877ed8f06744864d1068885fa11e2601 inherit pro_methods_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pro_methods_classCThread"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classCThread')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classCThread.html">CThread</a></td></tr>
|
||
<tr class="memitem:ga6c85b096316b57cae1be8446a97fc545 inherit pro_methods_classCThread"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#ga6c85b096316b57cae1be8446a97fc545">~CThread</a> (void)</td></tr>
|
||
<tr class="memdesc:ga6c85b096316b57cae1be8446a97fc545 inherit pro_methods_classCThread"><td class="mdescLeft"> </td><td class="mdescRight">To be called only internally! NOTE: destructor of the derived (user-provided) class should be declared "protected", too! <a href="group__Threads.html#ga6c85b096316b57cae1be8446a97fc545">More...</a><br /></td></tr>
|
||
<tr class="separator:ga6c85b096316b57cae1be8446a97fc545 inherit pro_methods_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaf7371892faee363f0869c2b2005852d7 inherit pro_methods_classCThread"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Threads.html#ga4121b90e3cd77993a5bbe314df676b75">TThreadHandle</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#gaf7371892faee363f0869c2b2005852d7">GetThreadHandle</a> ()</td></tr>
|
||
<tr class="separator:gaf7371892faee363f0869c2b2005852d7 inherit pro_methods_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
</table><table class="memberdecls">
|
||
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-static-methods"></a>
|
||
Static Protected Member Functions</h2></td></tr>
|
||
<tr class="memitem:a7f3c57bf8dcdbd2f7f7b4a4e527b18ae"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a7f3c57bf8dcdbd2f7f7b4a4e527b18ae">MakeModString</a> (<a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> &seqstring, <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> &modseqstring, <a class="el" href="classCMSHit.html">CMSHit</a> *MSHit)</td></tr>
|
||
<tr class="memdesc:a7f3c57bf8dcdbd2f7f7b4a4e527b18ae"><td class="mdescLeft"> </td><td class="mdescRight">Makes a string hashed out of the sequence plus mods. <a href="classCSearch.html#a7f3c57bf8dcdbd2f7f7b4a4e527b18ae">More...</a><br /></td></tr>
|
||
<tr class="separator:a7f3c57bf8dcdbd2f7f7b4a4e527b18ae"><td class="memSeparator" colspan="2"> </td></tr>
|
||
</table><table class="memberdecls">
|
||
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-types"></a>
|
||
Private Types</h2></td></tr>
|
||
<tr class="memitem:gad573db5811d949df38bfb39864681a2f"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCSearch__Base.html">CSearch_Base</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gad573db5811d949df38bfb39864681a2f">Tparent</a></td></tr>
|
||
<tr class="separator:gad573db5811d949df38bfb39864681a2f"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr><td colspan="2"><div class="groupHeader">Convenience declarations.</div></td></tr>
|
||
<tr class="memitem:aeb8c0d943e14fc63f6c09a408b742953"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCSearch__Base.html">CSearch_Base</a>< LEGACY, NHITS, <a class="el" href="classCSearch.html">CSearch</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#aeb8c0d943e14fc63f6c09a408b742953">TBase</a></td></tr>
|
||
<tr class="separator:aeb8c0d943e14fc63f6c09a408b742953"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a9431accacfdc77725883ba154caf64b7"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCSearch__Base.html#aec07f7524cf0ec5dc6610b776b3ff4d2">TBase::TIndex_Impl</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a9431accacfdc77725883ba154caf64b7">TIndex_Impl</a></td></tr>
|
||
<tr class="separator:a9431accacfdc77725883ba154caf64b7"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:afb4e78c64195e521cd2e81271d6f544e"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCSearch__Base.html#afd6cb73bb0bbdcdbde5d1f139c6cbc9c">TBase::TSearchOptions</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#afb4e78c64195e521cd2e81271d6f544e">TSearchOptions</a></td></tr>
|
||
<tr class="separator:afb4e78c64195e521cd2e81271d6f544e"><td class="memSeparator" colspan="2"> </td></tr>
|
||
</table><table class="memberdecls">
|
||
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-methods"></a>
|
||
Private Member Functions</h2></td></tr>
|
||
<tr class="memitem:ga264999c3f3e010105d123b417279dcca"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga264999c3f3e010105d123b417279dcca">CSearch</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSearch.html">CSearch</a> &<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="separator:ga264999c3f3e010105d123b417279dcca"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga52e8d7ea461198672027bdec4be74dc4"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCSearch.html">CSearch</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga52e8d7ea461198672027bdec4be74dc4">operator=</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSearch.html">CSearch</a> &<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="separator:ga52e8d7ea461198672027bdec4be74dc4"><td class="memSeparator" colspan="2"> </td></tr>
|
||
</table><table class="memberdecls">
|
||
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-attribs"></a>
|
||
Private Attributes</h2></td></tr>
|
||
<tr class="memitem:a3126e8c4cf573f6b13d90d915a7edeba"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCSeqDB.html">CSeqDB</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a3126e8c4cf573f6b13d90d915a7edeba">rdfp</a></td></tr>
|
||
<tr class="memdesc:a3126e8c4cf573f6b13d90d915a7edeba"><td class="mdescLeft"> </td><td class="mdescRight">blast library <a href="classCSearch.html#a3126e8c4cf573f6b13d90d915a7edeba">More...</a><br /></td></tr>
|
||
<tr class="separator:a3126e8c4cf573f6b13d90d915a7edeba"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a9892817bbb790af0da11bd9241796671"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCMassArray.html">CMassArray</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a9892817bbb790af0da11bd9241796671">MassArray</a></td></tr>
|
||
<tr class="separator:a9892817bbb790af0da11bd9241796671"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a61e60b0813859840f39f0e52dd6623cb"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCMassArray.html">CMassArray</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a61e60b0813859840f39f0e52dd6623cb">PrecursorMassArray</a></td></tr>
|
||
<tr class="separator:a61e60b0813859840f39f0e52dd6623cb"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a069bdebe654ad56719d67336a347ac69"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCMSMod.html">CMSMod</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a069bdebe654ad56719d67336a347ac69">VariableMods</a></td></tr>
|
||
<tr class="separator:a069bdebe654ad56719d67336a347ac69"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a24b7d56cbbdb8c42bf07dbf04503f5ce"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCMSMod.html">CMSMod</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a24b7d56cbbdb8c42bf07dbf04503f5ce">FixedMods</a></td></tr>
|
||
<tr class="separator:a24b7d56cbbdb8c42bf07dbf04503f5ce"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:aca9cf28f5058578a38dabcff76d34d8f"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#aca9cf28f5058578a38dabcff76d34d8f">numseq</a></td></tr>
|
||
<tr class="separator:aca9cf28f5058578a38dabcff76d34d8f"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ae47c14b250cb7077ae9decda48af2241"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCCleave.html">CCleave</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#ae47c14b250cb7077ae9decda48af2241">Enzyme</a></td></tr>
|
||
<tr class="memdesc:ae47c14b250cb7077ae9decda48af2241"><td class="mdescLeft"> </td><td class="mdescRight">the enzyme in use <a href="classCSearch.html#ae47c14b250cb7077ae9decda48af2241">More...</a><br /></td></tr>
|
||
<tr class="separator:ae47c14b250cb7077ae9decda48af2241"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a5bc469e9ba6a7a2a11594be2527a8625"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSRequest.html">CMSRequest</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a5bc469e9ba6a7a2a11594be2527a8625">MyRequest</a></td></tr>
|
||
<tr class="memdesc:a5bc469e9ba6a7a2a11594be2527a8625"><td class="mdescLeft"> </td><td class="mdescRight">Search request. <a href="classCSearch.html#a5bc469e9ba6a7a2a11594be2527a8625">More...</a><br /></td></tr>
|
||
<tr class="separator:a5bc469e9ba6a7a2a11594be2527a8625"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a2a26cd46bb4c00b9cf72d9b05e2914f7"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSResponse.html">CMSResponse</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a2a26cd46bb4c00b9cf72d9b05e2914f7">MyResponse</a></td></tr>
|
||
<tr class="memdesc:a2a26cd46bb4c00b9cf72d9b05e2914f7"><td class="mdescLeft"> </td><td class="mdescRight">Search response. <a href="classCSearch.html#a2a26cd46bb4c00b9cf72d9b05e2914f7">More...</a><br /></td></tr>
|
||
<tr class="separator:a2a26cd46bb4c00b9cf72d9b05e2914f7"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a13a8f4a3aac7c6ae47d3dcfe25037277"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSSearchSettings.html">CMSSearchSettings</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a13a8f4a3aac7c6ae47d3dcfe25037277">MySettings</a></td></tr>
|
||
<tr class="memdesc:a13a8f4a3aac7c6ae47d3dcfe25037277"><td class="mdescLeft"> </td><td class="mdescRight">Search params. <a href="classCSearch.html#a13a8f4a3aac7c6ae47d3dcfe25037277">More...</a><br /></td></tr>
|
||
<tr class="separator:a13a8f4a3aac7c6ae47d3dcfe25037277"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a4238c214c7d1bb8e81e8634bfa534c5e"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCLadderContainer.html">CLadderContainer</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a4238c214c7d1bb8e81e8634bfa534c5e">LadderContainer</a></td></tr>
|
||
<tr class="memdesc:a4238c214c7d1bb8e81e8634bfa534c5e"><td class="mdescLeft"> </td><td class="mdescRight">ion series mass ladders <a href="classCSearch.html#a4238c214c7d1bb8e81e8634bfa534c5e">More...</a><br /></td></tr>
|
||
<tr class="separator:a4238c214c7d1bb8e81e8634bfa534c5e"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a13ca726f5c0b48c3291baa3f6f238938"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classAutoPtr.html">AutoPtr</a>< <a class="el" href="group__Portability.html#gad571e821cdf5dcc936b6beb906ad5a89">Int1</a>, <a class="el" href="structArrayDeleter.html">ArrayDeleter</a>< <a class="el" href="group__Portability.html#gad571e821cdf5dcc936b6beb906ad5a89">Int1</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a13ca726f5c0b48c3291baa3f6f238938">LadderCalc</a></td></tr>
|
||
<tr class="memdesc:a13ca726f5c0b48c3291baa3f6f238938"><td class="mdescLeft"> </td><td class="mdescRight">bool array that indicates if the ladders been calculated <a href="classCSearch.html#a13ca726f5c0b48c3291baa3f6f238938">More...</a><br /></td></tr>
|
||
<tr class="separator:a13ca726f5c0b48c3291baa3f6f238938"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ad2b1eb3f9075259665bb7deeae57e569"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classAutoPtr.html">AutoPtr</a>< <a class="el" href="omssa_8hpp.html#a5742ee0bc8e594f879b5d020791738e4">TMassMask</a>, <a class="el" href="structArrayDeleter.html">ArrayDeleter</a>< <a class="el" href="omssa_8hpp.html#a5742ee0bc8e594f879b5d020791738e4">TMassMask</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#ad2b1eb3f9075259665bb7deeae57e569">MassAndMask</a></td></tr>
|
||
<tr class="memdesc:ad2b1eb3f9075259665bb7deeae57e569"><td class="mdescLeft"> </td><td class="mdescRight">contains bit mask of modifications and resulting mass <a href="classCSearch.html#ad2b1eb3f9075259665bb7deeae57e569">More...</a><br /></td></tr>
|
||
<tr class="separator:ad2b1eb3f9075259665bb7deeae57e569"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ad1185583f34e88e1133cfe4223f22f6b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#ad1185583f34e88e1133cfe4223f22f6b">MaxModPerPep</a></td></tr>
|
||
<tr class="memdesc:ad1185583f34e88e1133cfe4223f22f6b"><td class="mdescLeft"> </td><td class="mdescRight">maximum number of mod combinations per peptide <a href="classCSearch.html#ad1185583f34e88e1133cfe4223f22f6b">More...</a><br /></td></tr>
|
||
<tr class="separator:ad1185583f34e88e1133cfe4223f22f6b"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a3211ebae8e111217dffc840eb0d90c6d"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a3211ebae8e111217dffc840eb0d90c6d">UseRankScore</a></td></tr>
|
||
<tr class="memdesc:a3211ebae8e111217dffc840eb0d90c6d"><td class="mdescLeft"> </td><td class="mdescRight">boolean to turn on rank scoring <a href="classCSearch.html#a3211ebae8e111217dffc840eb0d90c6d">More...</a><br /></td></tr>
|
||
<tr class="separator:a3211ebae8e111217dffc840eb0d90c6d"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:aefe0651422bf8bc0e153fac971e9c5ff"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#aefe0651422bf8bc0e153fac971e9c5ff">PoissonOnly</a></td></tr>
|
||
<tr class="memdesc:aefe0651422bf8bc0e153fac971e9c5ff"><td class="mdescLeft"> </td><td class="mdescRight">boolean to only use Poisson score when using Rank scoring <a href="classCSearch.html#aefe0651422bf8bc0e153fac971e9c5ff">More...</a><br /></td></tr>
|
||
<tr class="separator:aefe0651422bf8bc0e153fac971e9c5ff"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ad27ca236cef55eb917f2db86314cc03b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#ad27ca236cef55eb917f2db86314cc03b">Iterative</a></td></tr>
|
||
<tr class="memdesc:ad27ca236cef55eb917f2db86314cc03b"><td class="mdescLeft"> </td><td class="mdescRight">boolean to turn on iterative search <a href="classCSearch.html#ad27ca236cef55eb917f2db86314cc03b">More...</a><br /></td></tr>
|
||
<tr class="separator:ad27ca236cef55eb917f2db86314cc03b"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ab1e50c269b23c2f0c24b14ac3e5dc5a0"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCMSResponse.html#a10ac4d245cf91be83306cac7793a6377">CMSResponse::TOidSet</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#ab1e50c269b23c2f0c24b14ac3e5dc5a0">OidSet</a></td></tr>
|
||
<tr class="memdesc:ab1e50c269b23c2f0c24b14ac3e5dc5a0"><td class="mdescLeft"> </td><td class="mdescRight">set of oids to be searched <a href="classCSearch.html#ab1e50c269b23c2f0c24b14ac3e5dc5a0">More...</a><br /></td></tr>
|
||
<tr class="separator:ab1e50c269b23c2f0c24b14ac3e5dc5a0"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a2fae93f4e2894bd3f235dad32423142b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a2fae93f4e2894bd3f235dad32423142b">RestrictedSearch</a></td></tr>
|
||
<tr class="memdesc:a2fae93f4e2894bd3f235dad32423142b"><td class="mdescLeft"> </td><td class="mdescRight">is this a oid restricted search <a href="classCSearch.html#a2fae93f4e2894bd3f235dad32423142b">More...</a><br /></td></tr>
|
||
<tr class="separator:a2fae93f4e2894bd3f235dad32423142b"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:af445799f8029ab8f8a942ab78cd8fb6c"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#af445799f8029ab8f8a942ab78cd8fb6c">ThreadNum</a></td></tr>
|
||
<tr class="memdesc:af445799f8029ab8f8a942ab78cd8fb6c"><td class="mdescLeft"> </td><td class="mdescRight">The threadid number. <a href="classCSearch.html#af445799f8029ab8f8a942ab78cd8fb6c">More...</a><br /></td></tr>
|
||
<tr class="separator:af445799f8029ab8f8a942ab78cd8fb6c"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:acb77a8653cb9a52ddeea8705e01a4008"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSRequest.html">CMSRequest</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#acb77a8653cb9a52ddeea8705e01a4008">initRequestIn</a></td></tr>
|
||
<tr class="memdesc:acb77a8653cb9a52ddeea8705e01a4008"><td class="mdescLeft"> </td><td class="mdescRight">These are so <a class="el" href="classCSearch.html#ab0dec8be370a16f7736e36c07841b3f5" title="Derived (user-created) class must provide a real thread function.">CSearch::Main()</a> can call <a class="el" href="classCSearch.html#a5e985bb7e8acd2e85be9e4fe2ee023e6" title="Performs the ms/ms search.">CSearch::Search()</a> in a threaded run, this requires <a class="el" href="classCSearch.html#aaa0a4ed9116b40d1867c12dce88d0dc4" title="Setup the ms/ms search.">CSearch::SetupSearch()</a> to be called before <a class="el" href="group__Threads.html#ga1ca598d60e42a600f8f323c25792042d" title="Run the thread.">CSearch::Run()</a> <a href="classCSearch.html#acb77a8653cb9a52ddeea8705e01a4008">More...</a><br /></td></tr>
|
||
<tr class="separator:acb77a8653cb9a52ddeea8705e01a4008"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:acce6930b2a7bb24c985dc05e60ec675f"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSResponse.html">CMSResponse</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#acce6930b2a7bb24c985dc05e60ec675f">initResponseIn</a></td></tr>
|
||
<tr class="separator:acce6930b2a7bb24c985dc05e60ec675f"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:abae51d52a2c56983a8b0b4bb81b99911"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSModSpecSet.html">CMSModSpecSet</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#abae51d52a2c56983a8b0b4bb81b99911">initModset</a></td></tr>
|
||
<tr class="separator:abae51d52a2c56983a8b0b4bb81b99911"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:af02b5bd6ad91d53341002b4a58d34c71"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSSearchSettings.html">CMSSearchSettings</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#af02b5bd6ad91d53341002b4a58d34c71">initSettingsIn</a></td></tr>
|
||
<tr class="separator:af02b5bd6ad91d53341002b4a58d34c71"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ac5691dd992ecd2ba66b70bb5dcd0400a"><td class="memItemLeft" align="right" valign="top"><a class="el" href="omssa_8hpp.html#a9ffe9cb00c8437193b4225feecd4ab36">TOMSSACallback</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#ac5691dd992ecd2ba66b70bb5dcd0400a">initCallback</a></td></tr>
|
||
<tr class="separator:ac5691dd992ecd2ba66b70bb5dcd0400a"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a248ca093d4fee44de262991748eb7f29"><td class="memItemLeft" align="right" valign="top">void * </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a248ca093d4fee44de262991748eb7f29">initCallbackData</a></td></tr>
|
||
<tr class="separator:a248ca093d4fee44de262991748eb7f29"><td class="memSeparator" colspan="2"> </td></tr>
|
||
</table><table class="memberdecls">
|
||
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-static-attribs"></a>
|
||
Static Private Attributes</h2></td></tr>
|
||
<tr class="memitem:ada7e1d377c5d3784986c7875c273c8e6"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#ada7e1d377c5d3784986c7875c273c8e6">MaxMZ</a> = 0</td></tr>
|
||
<tr class="memdesc:ada7e1d377c5d3784986c7875c273c8e6"><td class="mdescLeft"> </td><td class="mdescRight">maximum m/z value of all spectra precursors used to bound non-specific cleavage searches <a href="classCSearch.html#ada7e1d377c5d3784986c7875c273c8e6">More...</a><br /></td></tr>
|
||
<tr class="separator:ada7e1d377c5d3784986c7875c273c8e6"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a89577321dfd5c014198677bace51721b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch.html#a89577321dfd5c014198677bace51721b">iSearchGlobal</a> = -1</td></tr>
|
||
<tr class="memdesc:a89577321dfd5c014198677bace51721b"><td class="mdescLeft"> </td><td class="mdescRight">Tracks the iSearch number for all search threads. <a href="classCSearch.html#a89577321dfd5c014198677bace51721b">More...</a><br /></td></tr>
|
||
<tr class="separator:a89577321dfd5c014198677bace51721b"><td class="memSeparator" colspan="2"> </td></tr>
|
||
</table><table class="memberdecls">
|
||
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a>
|
||
Additional Inherited Members</h2></td></tr>
|
||
<tr class="inherit_header pub_types_classCSearch__Base"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classCSearch__Base')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="classCSearch__Base.html">CSearch_Base< LEGACY, NHITS, derived_t ></a></td></tr>
|
||
<tr class="memitem:ga962d06a21b7040bbb704b80e9c413972 inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">enum class  </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga962d06a21b7040bbb704b80e9c413972">E_memberIndex</a> { <br />
|
||
  <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gga962d06a21b7040bbb704b80e9c413972ad2c4d82f7037e318e1aa6f58d06bd153">e__allMandatory</a> = 0
|
||
, <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gga962d06a21b7040bbb704b80e9c413972a62948cdb9ceb7cd5f58f4ca140ecefcc">e_query_id</a>
|
||
, <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gga962d06a21b7040bbb704b80e9c413972a04822b1c635a51a0f28cee8e4c2e8d85">e_query_title</a>
|
||
, <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gga962d06a21b7040bbb704b80e9c413972a0fb5810bf046bc2c48c183a0e8d2c379">e_query_len</a>
|
||
, <br />
|
||
  <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gga962d06a21b7040bbb704b80e9c413972a7ea6f5c1267d798c8e10a6f8786a1adb">e_query_masking</a>
|
||
, <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gga962d06a21b7040bbb704b80e9c413972a9aded011e8b4e651957ef0f259eb6788">e_hits</a>
|
||
, <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gga962d06a21b7040bbb704b80e9c413972a7a004bd85e1192849738c975fac3c333">e_stat</a>
|
||
, <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gga962d06a21b7040bbb704b80e9c413972aa456b8c59885679bb286bf8ee9846b4f">e_message</a>
|
||
<br />
|
||
}</td></tr>
|
||
<tr class="separator:ga962d06a21b7040bbb704b80e9c413972 inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga8a4c8e2c3c50387bcbe01b8533c2cbe4 inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga8a4c8e2c3c50387bcbe01b8533c2cbe4">TQuery_id</a></td></tr>
|
||
<tr class="separator:ga8a4c8e2c3c50387bcbe01b8533c2cbe4 inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga6889d230d2397ffe927d232f29566fab inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga6889d230d2397ffe927d232f29566fab">TQuery_title</a></td></tr>
|
||
<tr class="separator:ga6889d230d2397ffe927d232f29566fab inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga8ea8393dbd772563cef38ec2d8abf993 inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga8ea8393dbd772563cef38ec2d8abf993">TQuery_len</a></td></tr>
|
||
<tr class="separator:ga8ea8393dbd772563cef38ec2d8abf993 inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga946dbe57e0dc1cbb265e82ed159fedb8 inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef list< <a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCRange.html">CRange</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga946dbe57e0dc1cbb265e82ed159fedb8">TQuery_masking</a></td></tr>
|
||
<tr class="separator:ga946dbe57e0dc1cbb265e82ed159fedb8 inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaec3ad1ac4ef81a8e040acf64663d0605 inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef list< <a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCHit.html">CHit</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaec3ad1ac4ef81a8e040acf64663d0605">THits</a></td></tr>
|
||
<tr class="separator:gaec3ad1ac4ef81a8e040acf64663d0605 inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga75c7897ec8cbd783c05f6767e298a04a inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCStatistics.html">CStatistics</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga75c7897ec8cbd783c05f6767e298a04a">TStat</a></td></tr>
|
||
<tr class="separator:ga75c7897ec8cbd783c05f6767e298a04a inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga634156ee97752762050d14533d82cd1b inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga634156ee97752762050d14533d82cd1b">TMessage</a></td></tr>
|
||
<tr class="separator:ga634156ee97752762050d14533d82cd1b inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gae288babc0879bfd7f93e109b334790f6 inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCSerialObject_1_1CMemberIndex.html">Tparent::CMemberIndex</a>< <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga962d06a21b7040bbb704b80e9c413972">E_memberIndex</a>, 8 > </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gae288babc0879bfd7f93e109b334790f6">TmemberIndex</a></td></tr>
|
||
<tr class="separator:gae288babc0879bfd7f93e109b334790f6 inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:aec07f7524cf0ec5dc6610b776b3ff4d2 inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCDbIndex__Impl.html">CDbIndex_Impl</a>< LEGACY > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#aec07f7524cf0ec5dc6610b776b3ff4d2">TIndex_Impl</a></td></tr>
|
||
<tr class="separator:aec07f7524cf0ec5dc6610b776b3ff4d2 inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:af09e7fe5e4296ee4e7324def00005f81 inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCDbIndex__Impl.html#a8ec8d9140fad7d0bc48ac86838cc1444">TIndex_Impl::TSubjectMap</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#af09e7fe5e4296ee4e7324def00005f81">TSubjectMap</a></td></tr>
|
||
<tr class="separator:af09e7fe5e4296ee4e7324def00005f81 inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ab21f98298eed96cca1c114aab009b741 inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCTrackedSeeds.html">CTrackedSeeds</a>< NHITS > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#ab21f98298eed96cca1c114aab009b741">TTrackedSeeds</a></td></tr>
|
||
<tr class="separator:ab21f98298eed96cca1c114aab009b741 inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a6672cc315f74ce04ac4cae337a430ec0 inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef derived_t </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a6672cc315f74ce04ac4cae337a430ec0">TDerived</a></td></tr>
|
||
<tr class="separator:a6672cc315f74ce04ac4cae337a430ec0 inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pub_types_classCObject"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classCObject')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="classCObject.html">CObject</a></td></tr>
|
||
<tr class="memitem:ga3cf5f3ac0aef32c4aab1fa66513588cc inherit pub_types_classCObject"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga3cf5f3ac0aef32c4aab1fa66513588cc">EAllocFillMode</a> { <a class="el" href="group__Object.html#gga3cf5f3ac0aef32c4aab1fa66513588cca2b8c59f649cc88eeb7eaeba939e2838d">eAllocFillNone</a> = 1
|
||
, <a class="el" href="group__Object.html#gga3cf5f3ac0aef32c4aab1fa66513588cca336d7ff658b673c2e8fe3aed9b155f04">eAllocFillZero</a>
|
||
, <a class="el" href="group__Object.html#gga3cf5f3ac0aef32c4aab1fa66513588ccab3631bf1c36b77f950d94372290deb76">eAllocFillPattern</a>
|
||
}</td></tr>
|
||
<tr class="memdesc:ga3cf5f3ac0aef32c4aab1fa66513588cc"><td class="mdescLeft"> </td><td class="mdescRight">Control filling of newly allocated memory. <a href="group__Object.html#ga3cf5f3ac0aef32c4aab1fa66513588cc">More...</a><br /></td></tr>
|
||
<tr class="separator:ga3cf5f3ac0aef32c4aab1fa66513588cc inherit pub_types_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga2da943ea997324fcabb60e1a1ed1b71c inherit pub_types_classCObject"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCObjectCounterLocker.html">CObjectCounterLocker</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga2da943ea997324fcabb60e1a1ed1b71c">TLockerType</a></td></tr>
|
||
<tr class="memdesc:ga2da943ea997324fcabb60e1a1ed1b71c inherit pub_types_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Default locker type for <a class="el" href="classCRef.html" title="CRef –.">CRef</a>. <a href="group__Object.html#ga2da943ea997324fcabb60e1a1ed1b71c">More...</a><br /></td></tr>
|
||
<tr class="separator:ga2da943ea997324fcabb60e1a1ed1b71c inherit pub_types_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gad6d6ac3cac6272609b70c101aaaeebf9 inherit pub_types_classCObject"><td class="memItemLeft" align="right" valign="top">typedef atomic< <a class="el" href="group__Portability.html#gacb8f7ba15b8bac46f42c33b22099a6de">Uint8</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#gad6d6ac3cac6272609b70c101aaaeebf9">TCounter</a></td></tr>
|
||
<tr class="memdesc:gad6d6ac3cac6272609b70c101aaaeebf9 inherit pub_types_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Counter type is CAtomiCounter. <a href="group__Object.html#gad6d6ac3cac6272609b70c101aaaeebf9">More...</a><br /></td></tr>
|
||
<tr class="separator:gad6d6ac3cac6272609b70c101aaaeebf9 inherit pub_types_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga2e073b6c5b9c29648510bd99ebe00a5c inherit pub_types_classCObject"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="group__Portability.html#gacb8f7ba15b8bac46f42c33b22099a6de">Uint8</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga2e073b6c5b9c29648510bd99ebe00a5c">TCount</a></td></tr>
|
||
<tr class="memdesc:ga2e073b6c5b9c29648510bd99ebe00a5c inherit pub_types_classCObject"><td class="mdescLeft"> </td><td class="mdescRight">Alias for value type of counter. <a href="group__Object.html#ga2e073b6c5b9c29648510bd99ebe00a5c">More...</a><br /></td></tr>
|
||
<tr class="separator:ga2e073b6c5b9c29648510bd99ebe00a5c inherit pub_types_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pub_types_classCSearch__Base"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classCSearch__Base')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="classCSearch__Base.html">CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > ></a></td></tr>
|
||
<tr class="memitem:ga962d06a21b7040bbb704b80e9c413972 inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">enum class  </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga962d06a21b7040bbb704b80e9c413972">E_memberIndex</a> </td></tr>
|
||
<tr class="separator:ga962d06a21b7040bbb704b80e9c413972 inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga8a4c8e2c3c50387bcbe01b8533c2cbe4 inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga8a4c8e2c3c50387bcbe01b8533c2cbe4">TQuery_id</a></td></tr>
|
||
<tr class="separator:ga8a4c8e2c3c50387bcbe01b8533c2cbe4 inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga6889d230d2397ffe927d232f29566fab inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga6889d230d2397ffe927d232f29566fab">TQuery_title</a></td></tr>
|
||
<tr class="separator:ga6889d230d2397ffe927d232f29566fab inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga8ea8393dbd772563cef38ec2d8abf993 inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga8ea8393dbd772563cef38ec2d8abf993">TQuery_len</a></td></tr>
|
||
<tr class="separator:ga8ea8393dbd772563cef38ec2d8abf993 inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga946dbe57e0dc1cbb265e82ed159fedb8 inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef list< <a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCRange.html">CRange</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga946dbe57e0dc1cbb265e82ed159fedb8">TQuery_masking</a></td></tr>
|
||
<tr class="separator:ga946dbe57e0dc1cbb265e82ed159fedb8 inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gaec3ad1ac4ef81a8e040acf64663d0605 inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef list< <a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCHit.html">CHit</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaec3ad1ac4ef81a8e040acf64663d0605">THits</a></td></tr>
|
||
<tr class="separator:gaec3ad1ac4ef81a8e040acf64663d0605 inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga75c7897ec8cbd783c05f6767e298a04a inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCStatistics.html">CStatistics</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga75c7897ec8cbd783c05f6767e298a04a">TStat</a></td></tr>
|
||
<tr class="separator:ga75c7897ec8cbd783c05f6767e298a04a inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga634156ee97752762050d14533d82cd1b inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga634156ee97752762050d14533d82cd1b">TMessage</a></td></tr>
|
||
<tr class="separator:ga634156ee97752762050d14533d82cd1b inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gae288babc0879bfd7f93e109b334790f6 inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCSerialObject_1_1CMemberIndex.html">Tparent::CMemberIndex</a>< <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga962d06a21b7040bbb704b80e9c413972">E_memberIndex</a>, 8 > </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gae288babc0879bfd7f93e109b334790f6">TmemberIndex</a></td></tr>
|
||
<tr class="separator:gae288babc0879bfd7f93e109b334790f6 inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:aec07f7524cf0ec5dc6610b776b3ff4d2 inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCDbIndex__Impl.html">CDbIndex_Impl</a>< LEGACY > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#aec07f7524cf0ec5dc6610b776b3ff4d2">TIndex_Impl</a></td></tr>
|
||
<tr class="separator:aec07f7524cf0ec5dc6610b776b3ff4d2 inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:af09e7fe5e4296ee4e7324def00005f81 inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCDbIndex__Impl.html#a8ec8d9140fad7d0bc48ac86838cc1444">TIndex_Impl::TSubjectMap</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#af09e7fe5e4296ee4e7324def00005f81">TSubjectMap</a></td></tr>
|
||
<tr class="separator:af09e7fe5e4296ee4e7324def00005f81 inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ab21f98298eed96cca1c114aab009b741 inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCTrackedSeeds.html">CTrackedSeeds</a>< NHITS > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#ab21f98298eed96cca1c114aab009b741">TTrackedSeeds</a></td></tr>
|
||
<tr class="separator:ab21f98298eed96cca1c114aab009b741 inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a6672cc315f74ce04ac4cae337a430ec0 inherit pub_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a6672cc315f74ce04ac4cae337a430ec0">TDerived</a></td></tr>
|
||
<tr class="separator:a6672cc315f74ce04ac4cae337a430ec0 inherit pub_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pub_types_classCThread"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classCThread')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="classCThread.html">CThread</a></td></tr>
|
||
<tr class="memitem:ga473cd5553ed973732c17aee90e193e28 inherit pub_types_classCThread"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#ga473cd5553ed973732c17aee90e193e28">ERunMode</a> { <br />
|
||
  <a class="el" href="group__Threads.html#gga473cd5553ed973732c17aee90e193e28a8ea5c12dd97d39a22b5e848de9221d0e">fRunDefault</a> = 0x00
|
||
, <a class="el" href="group__Threads.html#gga473cd5553ed973732c17aee90e193e28ad38517414d9b9ef7c5113f83cf68a22d">fRunDetached</a> = 0x01
|
||
, <a class="el" href="group__Threads.html#gga473cd5553ed973732c17aee90e193e28a538f51c93aa7f5f6042f45ac5e625efb">fRunBound</a> = 0x10
|
||
, <a class="el" href="group__Threads.html#gga473cd5553ed973732c17aee90e193e28aa2cf219d1d7de740a625e5997608653d">fRunUnbound</a> = 0x20
|
||
, <br />
|
||
  <a class="el" href="group__Threads.html#gga473cd5553ed973732c17aee90e193e28abd779eeaddb15666f4ab6f5ba0a8ceed">fRunNice</a> = 0x40
|
||
, <a class="el" href="group__Threads.html#gga473cd5553ed973732c17aee90e193e28a448e33aba4f70406dac3e739f67c7fa1">fRunAllowST</a> = 0x100
|
||
, <a class="el" href="group__Threads.html#gga473cd5553ed973732c17aee90e193e28a176d6ef550d0711f4c044582172a15f0">fRunCloneRequestContext</a> = 0x200
|
||
<br />
|
||
}</td></tr>
|
||
<tr class="memdesc:ga473cd5553ed973732c17aee90e193e28"><td class="mdescLeft"> </td><td class="mdescRight">Which mode should the thread run in. <a href="group__Threads.html#ga473cd5553ed973732c17aee90e193e28">More...</a><br /></td></tr>
|
||
<tr class="separator:ga473cd5553ed973732c17aee90e193e28 inherit pub_types_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gac3152c5d190b92ef5ebe8cacef8a487e inherit pub_types_classCThread"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#gac3152c5d190b92ef5ebe8cacef8a487e">TRunMode</a></td></tr>
|
||
<tr class="memdesc:gac3152c5d190b92ef5ebe8cacef8a487e inherit pub_types_classCThread"><td class="mdescLeft"> </td><td class="mdescRight">Bitwise OR'd flags for thread creation passed to <a class="el" href="group__Threads.html#ga1ca598d60e42a600f8f323c25792042d" title="Run the thread.">Run()</a>. <a href="group__Threads.html#gac3152c5d190b92ef5ebe8cacef8a487e">More...</a><br /></td></tr>
|
||
<tr class="separator:gac3152c5d190b92ef5ebe8cacef8a487e inherit pub_types_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga839c07ee43332439913a3d84fee9cbb0 inherit pub_types_classCThread"><td class="memItemLeft" align="right" valign="top">typedef unsigned <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Threads.html#ga839c07ee43332439913a3d84fee9cbb0">TID</a></td></tr>
|
||
<tr class="memdesc:ga839c07ee43332439913a3d84fee9cbb0 inherit pub_types_classCThread"><td class="mdescLeft"> </td><td class="mdescRight">Get ID of current thread. <a href="group__Threads.html#ga839c07ee43332439913a3d84fee9cbb0">More...</a><br /></td></tr>
|
||
<tr class="separator:ga839c07ee43332439913a3d84fee9cbb0 inherit pub_types_classCThread"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pro_types_classCSearch__Base"><td colspan="2" onclick="javascript:toggleInherit('pro_types_classCSearch__Base')"><img src="closed.png" alt="-"/> Protected Types inherited from <a class="el" href="classCSearch__Base.html">CSearch_Base< LEGACY, NHITS, derived_t ></a></td></tr>
|
||
<tr class="memitem:afd6cb73bb0bbdcdbde5d1f139c6cbc9c inherit pro_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structCDbIndex_1_1SSearchOptions.html">CDbIndex::SSearchOptions</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#afd6cb73bb0bbdcdbde5d1f139c6cbc9c">TSearchOptions</a></td></tr>
|
||
<tr class="memdesc:afd6cb73bb0bbdcdbde5d1f139c6cbc9c inherit pro_types_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Alias for convenience. <a href="classCSearch__Base.html#afd6cb73bb0bbdcdbde5d1f139c6cbc9c">More...</a><br /></td></tr>
|
||
<tr class="separator:afd6cb73bb0bbdcdbde5d1f139c6cbc9c inherit pro_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a4a4961ff496fcd512762e7eab2636125 inherit pro_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structSTrackedSeed.html">STrackedSeed</a>< NHITS > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a4a4961ff496fcd512762e7eab2636125">TTrackedSeed</a></td></tr>
|
||
<tr class="memdesc:a4a4961ff496fcd512762e7eab2636125 inherit pro_types_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Alias for convenience. <a href="classCSearch__Base.html#a4a4961ff496fcd512762e7eab2636125">More...</a><br /></td></tr>
|
||
<tr class="separator:a4a4961ff496fcd512762e7eab2636125 inherit pro_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a3b66a335f9e1cb938fa6e97943bad17e inherit pro_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef std::vector< <a class="el" href="classCSearch__Base.html#ab21f98298eed96cca1c114aab009b741">TTrackedSeeds</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a3b66a335f9e1cb938fa6e97943bad17e">TTrackedSeedsSet</a></td></tr>
|
||
<tr class="memdesc:a3b66a335f9e1cb938fa6e97943bad17e inherit pro_types_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Representation of the set of currently tracked seeds for all subject sequences. <a href="classCSearch__Base.html#a3b66a335f9e1cb938fa6e97943bad17e">More...</a><br /></td></tr>
|
||
<tr class="separator:a3b66a335f9e1cb938fa6e97943bad17e inherit pro_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pro_types_classCSearch__Base"><td colspan="2" onclick="javascript:toggleInherit('pro_types_classCSearch__Base')"><img src="closed.png" alt="-"/> Protected Types inherited from <a class="el" href="classCSearch__Base.html">CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > ></a></td></tr>
|
||
<tr class="memitem:afd6cb73bb0bbdcdbde5d1f139c6cbc9c inherit pro_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structCDbIndex_1_1SSearchOptions.html">CDbIndex::SSearchOptions</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#afd6cb73bb0bbdcdbde5d1f139c6cbc9c">TSearchOptions</a></td></tr>
|
||
<tr class="memdesc:afd6cb73bb0bbdcdbde5d1f139c6cbc9c inherit pro_types_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Alias for convenience. <a href="classCSearch__Base.html#afd6cb73bb0bbdcdbde5d1f139c6cbc9c">More...</a><br /></td></tr>
|
||
<tr class="separator:afd6cb73bb0bbdcdbde5d1f139c6cbc9c inherit pro_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a4a4961ff496fcd512762e7eab2636125 inherit pro_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structSTrackedSeed.html">STrackedSeed</a>< NHITS > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a4a4961ff496fcd512762e7eab2636125">TTrackedSeed</a></td></tr>
|
||
<tr class="memdesc:a4a4961ff496fcd512762e7eab2636125 inherit pro_types_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Alias for convenience. <a href="classCSearch__Base.html#a4a4961ff496fcd512762e7eab2636125">More...</a><br /></td></tr>
|
||
<tr class="separator:a4a4961ff496fcd512762e7eab2636125 inherit pro_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a3b66a335f9e1cb938fa6e97943bad17e inherit pro_types_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">typedef std::vector< <a class="el" href="classCSearch__Base.html#ab21f98298eed96cca1c114aab009b741">TTrackedSeeds</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a3b66a335f9e1cb938fa6e97943bad17e">TTrackedSeedsSet</a></td></tr>
|
||
<tr class="memdesc:a3b66a335f9e1cb938fa6e97943bad17e inherit pro_types_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Representation of the set of currently tracked seeds for all subject sequences. <a href="classCSearch__Base.html#a3b66a335f9e1cb938fa6e97943bad17e">More...</a><br /></td></tr>
|
||
<tr class="separator:a3b66a335f9e1cb938fa6e97943bad17e inherit pro_types_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pro_attribs_classCSearch__Base"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classCSearch__Base')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classCSearch__Base.html">CSearch_Base< LEGACY, NHITS, derived_t ></a></td></tr>
|
||
<tr class="memitem:aab2ef9eb98b230557992ed9cb7865be2 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSearch__Base.html#aec07f7524cf0ec5dc6610b776b3ff4d2">TIndex_Impl</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#aab2ef9eb98b230557992ed9cb7865be2">index_impl_</a></td></tr>
|
||
<tr class="memdesc:aab2ef9eb98b230557992ed9cb7865be2 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">The index implementation object. <a href="classCSearch__Base.html#aab2ef9eb98b230557992ed9cb7865be2">More...</a><br /></td></tr>
|
||
<tr class="separator:aab2ef9eb98b230557992ed9cb7865be2 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a4c8b02dc1c50f6badab644f459ce90b1 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBLAST__SequenceBlk.html">BLAST_SequenceBlk</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a4c8b02dc1c50f6badab644f459ce90b1">query_</a></td></tr>
|
||
<tr class="memdesc:a4c8b02dc1c50f6badab644f459ce90b1 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">The query sequence encoded in BLASTNA. <a href="classCSearch__Base.html#a4c8b02dc1c50f6badab644f459ce90b1">More...</a><br /></td></tr>
|
||
<tr class="separator:a4c8b02dc1c50f6badab644f459ce90b1 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a14fe15ebc766e7bae05cb2be5ef197f0 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqLoc.html">BlastSeqLoc</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a14fe15ebc766e7bae05cb2be5ef197f0">locs_</a></td></tr>
|
||
<tr class="memdesc:a14fe15ebc766e7bae05cb2be5ef197f0 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Set of query locations to search. <a href="classCSearch__Base.html#a14fe15ebc766e7bae05cb2be5ef197f0">More...</a><br /></td></tr>
|
||
<tr class="separator:a14fe15ebc766e7bae05cb2be5ef197f0 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:acc18a5660da66cdeb55b8fe1c4f7465d inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCSearch__Base.html#afd6cb73bb0bbdcdbde5d1f139c6cbc9c">TSearchOptions</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#acc18a5660da66cdeb55b8fe1c4f7465d">options_</a></td></tr>
|
||
<tr class="memdesc:acc18a5660da66cdeb55b8fe1c4f7465d inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Search options. <a href="classCSearch__Base.html#acc18a5660da66cdeb55b8fe1c4f7465d">More...</a><br /></td></tr>
|
||
<tr class="separator:acc18a5660da66cdeb55b8fe1c4f7465d inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a8f836193bf7d2790477c3450c0954fb3 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCSearch__Base.html#a3b66a335f9e1cb938fa6e97943bad17e">TTrackedSeedsSet</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a8f836193bf7d2790477c3450c0954fb3">seeds_</a></td></tr>
|
||
<tr class="memdesc:a8f836193bf7d2790477c3450c0954fb3 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">The set of currently tracked seeds. <a href="classCSearch__Base.html#a8f836193bf7d2790477c3450c0954fb3">More...</a><br /></td></tr>
|
||
<tr class="separator:a8f836193bf7d2790477c3450c0954fb3 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a90d3087af377156b8cae1f0f97d89639 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="dbindex__sp_8hpp.html#a87f72681bcae3722b02b5cb3844f1cac">TSeqNum</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a90d3087af377156b8cae1f0f97d89639">subject_</a></td></tr>
|
||
<tr class="memdesc:a90d3087af377156b8cae1f0f97d89639 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Logical id of the subject sequence containing the offset value currently being considered. <a href="classCSearch__Base.html#a90d3087af377156b8cae1f0f97d89639">More...</a><br /></td></tr>
|
||
<tr class="separator:a90d3087af377156b8cae1f0f97d89639 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a4a3f4ba895c81cfcec76f0cded121f3a inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="dbindex__sp_8hpp.html#ab24dd73d837409e50d27583ed6f4e273">TWord</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a4a3f4ba895c81cfcec76f0cded121f3a">subj_start_off_</a></td></tr>
|
||
<tr class="memdesc:a4a3f4ba895c81cfcec76f0cded121f3a inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Start offset of subject_. <a href="classCSearch__Base.html#a4a3f4ba895c81cfcec76f0cded121f3a">More...</a><br /></td></tr>
|
||
<tr class="separator:a4a3f4ba895c81cfcec76f0cded121f3a inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:afadd0ab3b1d08d3eb7f07b88fa2b6d9b inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="dbindex__sp_8hpp.html#ab24dd73d837409e50d27583ed6f4e273">TWord</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#afadd0ab3b1d08d3eb7f07b88fa2b6d9b">subj_end_off_</a></td></tr>
|
||
<tr class="memdesc:afadd0ab3b1d08d3eb7f07b88fa2b6d9b inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">End offset of subject_. <a href="classCSearch__Base.html#afadd0ab3b1d08d3eb7f07b88fa2b6d9b">More...</a><br /></td></tr>
|
||
<tr class="separator:afadd0ab3b1d08d3eb7f07b88fa2b6d9b inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a467e56d418d2c05411f586bf5a509567 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="dbindex__sp_8hpp.html#ab24dd73d837409e50d27583ed6f4e273">TWord</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a467e56d418d2c05411f586bf5a509567">subj_start_</a></td></tr>
|
||
<tr class="memdesc:a467e56d418d2c05411f586bf5a509567 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Start position of subject_. <a href="classCSearch__Base.html#a467e56d418d2c05411f586bf5a509567">More...</a><br /></td></tr>
|
||
<tr class="separator:a467e56d418d2c05411f586bf5a509567 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a611599c8d5bf642fa2345912174effb0 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="dbindex__sp_8hpp.html#ab24dd73d837409e50d27583ed6f4e273">TWord</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a611599c8d5bf642fa2345912174effb0">subj_end_</a></td></tr>
|
||
<tr class="memdesc:a611599c8d5bf642fa2345912174effb0 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">One past the end position of subject_. <a href="classCSearch__Base.html#a611599c8d5bf642fa2345912174effb0">More...</a><br /></td></tr>
|
||
<tr class="separator:a611599c8d5bf642fa2345912174effb0 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:aa478b52f11b11e36b509f775b7368844 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#aa478b52f11b11e36b509f775b7368844">qoff_</a></td></tr>
|
||
<tr class="memdesc:aa478b52f11b11e36b509f775b7368844 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Current query offset. <a href="classCSearch__Base.html#aa478b52f11b11e36b509f775b7368844">More...</a><br /></td></tr>
|
||
<tr class="separator:aa478b52f11b11e36b509f775b7368844 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:acc2ef38f0b14c0a13fffe8993e2c19d5 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#acc2ef38f0b14c0a13fffe8993e2c19d5">soff_</a></td></tr>
|
||
<tr class="memdesc:acc2ef38f0b14c0a13fffe8993e2c19d5 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Current subject offset. <a href="classCSearch__Base.html#acc2ef38f0b14c0a13fffe8993e2c19d5">More...</a><br /></td></tr>
|
||
<tr class="separator:acc2ef38f0b14c0a13fffe8993e2c19d5 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ad67d172c3baf63682babcc5b2b8100c2 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#ad67d172c3baf63682babcc5b2b8100c2">qstart_</a></td></tr>
|
||
<tr class="memdesc:ad67d172c3baf63682babcc5b2b8100c2 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Start of the current query segment. <a href="classCSearch__Base.html#ad67d172c3baf63682babcc5b2b8100c2">More...</a><br /></td></tr>
|
||
<tr class="separator:ad67d172c3baf63682babcc5b2b8100c2 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ae997a169c67732a724ebad406444b71b inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#ae997a169c67732a724ebad406444b71b">qstop_</a></td></tr>
|
||
<tr class="memdesc:ae997a169c67732a724ebad406444b71b inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">One past the end of the current query segment. <a href="classCSearch__Base.html#ae997a169c67732a724ebad406444b71b">More...</a><br /></td></tr>
|
||
<tr class="separator:ae997a169c67732a724ebad406444b71b inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a69414cc0fe35b6cec02367f27cb3b697 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCSeedRoots.html">CSeedRoots</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a69414cc0fe35b6cec02367f27cb3b697">roots_</a></td></tr>
|
||
<tr class="memdesc:a69414cc0fe35b6cec02367f27cb3b697 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Collection of initial soff/qoff pairs. <a href="classCSearch__Base.html#a69414cc0fe35b6cec02367f27cb3b697">More...</a><br /></td></tr>
|
||
<tr class="separator:a69414cc0fe35b6cec02367f27cb3b697 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:af1cdc49954776482f041359a254a8474 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">unsigned long </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#af1cdc49954776482f041359a254a8474">code_bits_</a></td></tr>
|
||
<tr class="memdesc:af1cdc49954776482f041359a254a8474 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Number of bits to represent special offset prefix. <a href="classCSearch__Base.html#af1cdc49954776482f041359a254a8474">More...</a><br /></td></tr>
|
||
<tr class="separator:af1cdc49954776482f041359a254a8474 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a01b594886cd899c5624c5935e5c7fd98 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">unsigned long </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a01b594886cd899c5624c5935e5c7fd98">min_offset_</a></td></tr>
|
||
<tr class="memdesc:a01b594886cd899c5624c5935e5c7fd98 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Minumum offset used by the index. <a href="classCSearch__Base.html#a01b594886cd899c5624c5935e5c7fd98">More...</a><br /></td></tr>
|
||
<tr class="separator:a01b594886cd899c5624c5935e5c7fd98 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="inherit_header pro_attribs_classCSearch__Base"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classCSearch__Base')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classCSearch__Base.html">CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > ></a></td></tr>
|
||
<tr class="memitem:aab2ef9eb98b230557992ed9cb7865be2 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSearch__Base.html#aec07f7524cf0ec5dc6610b776b3ff4d2">TIndex_Impl</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#aab2ef9eb98b230557992ed9cb7865be2">index_impl_</a></td></tr>
|
||
<tr class="memdesc:aab2ef9eb98b230557992ed9cb7865be2 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">The index implementation object. <a href="classCSearch__Base.html#aab2ef9eb98b230557992ed9cb7865be2">More...</a><br /></td></tr>
|
||
<tr class="separator:aab2ef9eb98b230557992ed9cb7865be2 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a4c8b02dc1c50f6badab644f459ce90b1 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBLAST__SequenceBlk.html">BLAST_SequenceBlk</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a4c8b02dc1c50f6badab644f459ce90b1">query_</a></td></tr>
|
||
<tr class="memdesc:a4c8b02dc1c50f6badab644f459ce90b1 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">The query sequence encoded in BLASTNA. <a href="classCSearch__Base.html#a4c8b02dc1c50f6badab644f459ce90b1">More...</a><br /></td></tr>
|
||
<tr class="separator:a4c8b02dc1c50f6badab644f459ce90b1 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a14fe15ebc766e7bae05cb2be5ef197f0 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqLoc.html">BlastSeqLoc</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a14fe15ebc766e7bae05cb2be5ef197f0">locs_</a></td></tr>
|
||
<tr class="memdesc:a14fe15ebc766e7bae05cb2be5ef197f0 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Set of query locations to search. <a href="classCSearch__Base.html#a14fe15ebc766e7bae05cb2be5ef197f0">More...</a><br /></td></tr>
|
||
<tr class="separator:a14fe15ebc766e7bae05cb2be5ef197f0 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:acc18a5660da66cdeb55b8fe1c4f7465d inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCSearch__Base.html#afd6cb73bb0bbdcdbde5d1f139c6cbc9c">TSearchOptions</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#acc18a5660da66cdeb55b8fe1c4f7465d">options_</a></td></tr>
|
||
<tr class="memdesc:acc18a5660da66cdeb55b8fe1c4f7465d inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Search options. <a href="classCSearch__Base.html#acc18a5660da66cdeb55b8fe1c4f7465d">More...</a><br /></td></tr>
|
||
<tr class="separator:acc18a5660da66cdeb55b8fe1c4f7465d inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a8f836193bf7d2790477c3450c0954fb3 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCSearch__Base.html#a3b66a335f9e1cb938fa6e97943bad17e">TTrackedSeedsSet</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a8f836193bf7d2790477c3450c0954fb3">seeds_</a></td></tr>
|
||
<tr class="memdesc:a8f836193bf7d2790477c3450c0954fb3 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">The set of currently tracked seeds. <a href="classCSearch__Base.html#a8f836193bf7d2790477c3450c0954fb3">More...</a><br /></td></tr>
|
||
<tr class="separator:a8f836193bf7d2790477c3450c0954fb3 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a90d3087af377156b8cae1f0f97d89639 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="dbindex__sp_8hpp.html#a87f72681bcae3722b02b5cb3844f1cac">TSeqNum</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a90d3087af377156b8cae1f0f97d89639">subject_</a></td></tr>
|
||
<tr class="memdesc:a90d3087af377156b8cae1f0f97d89639 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Logical id of the subject sequence containing the offset value currently being considered. <a href="classCSearch__Base.html#a90d3087af377156b8cae1f0f97d89639">More...</a><br /></td></tr>
|
||
<tr class="separator:a90d3087af377156b8cae1f0f97d89639 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a4a3f4ba895c81cfcec76f0cded121f3a inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="dbindex__sp_8hpp.html#ab24dd73d837409e50d27583ed6f4e273">TWord</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a4a3f4ba895c81cfcec76f0cded121f3a">subj_start_off_</a></td></tr>
|
||
<tr class="memdesc:a4a3f4ba895c81cfcec76f0cded121f3a inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Start offset of subject_. <a href="classCSearch__Base.html#a4a3f4ba895c81cfcec76f0cded121f3a">More...</a><br /></td></tr>
|
||
<tr class="separator:a4a3f4ba895c81cfcec76f0cded121f3a inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:afadd0ab3b1d08d3eb7f07b88fa2b6d9b inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="dbindex__sp_8hpp.html#ab24dd73d837409e50d27583ed6f4e273">TWord</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#afadd0ab3b1d08d3eb7f07b88fa2b6d9b">subj_end_off_</a></td></tr>
|
||
<tr class="memdesc:afadd0ab3b1d08d3eb7f07b88fa2b6d9b inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">End offset of subject_. <a href="classCSearch__Base.html#afadd0ab3b1d08d3eb7f07b88fa2b6d9b">More...</a><br /></td></tr>
|
||
<tr class="separator:afadd0ab3b1d08d3eb7f07b88fa2b6d9b inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a467e56d418d2c05411f586bf5a509567 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="dbindex__sp_8hpp.html#ab24dd73d837409e50d27583ed6f4e273">TWord</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a467e56d418d2c05411f586bf5a509567">subj_start_</a></td></tr>
|
||
<tr class="memdesc:a467e56d418d2c05411f586bf5a509567 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Start position of subject_. <a href="classCSearch__Base.html#a467e56d418d2c05411f586bf5a509567">More...</a><br /></td></tr>
|
||
<tr class="separator:a467e56d418d2c05411f586bf5a509567 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a611599c8d5bf642fa2345912174effb0 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="dbindex__sp_8hpp.html#ab24dd73d837409e50d27583ed6f4e273">TWord</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a611599c8d5bf642fa2345912174effb0">subj_end_</a></td></tr>
|
||
<tr class="memdesc:a611599c8d5bf642fa2345912174effb0 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">One past the end position of subject_. <a href="classCSearch__Base.html#a611599c8d5bf642fa2345912174effb0">More...</a><br /></td></tr>
|
||
<tr class="separator:a611599c8d5bf642fa2345912174effb0 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:aa478b52f11b11e36b509f775b7368844 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#aa478b52f11b11e36b509f775b7368844">qoff_</a></td></tr>
|
||
<tr class="memdesc:aa478b52f11b11e36b509f775b7368844 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Current query offset. <a href="classCSearch__Base.html#aa478b52f11b11e36b509f775b7368844">More...</a><br /></td></tr>
|
||
<tr class="separator:aa478b52f11b11e36b509f775b7368844 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:acc2ef38f0b14c0a13fffe8993e2c19d5 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#acc2ef38f0b14c0a13fffe8993e2c19d5">soff_</a></td></tr>
|
||
<tr class="memdesc:acc2ef38f0b14c0a13fffe8993e2c19d5 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Current subject offset. <a href="classCSearch__Base.html#acc2ef38f0b14c0a13fffe8993e2c19d5">More...</a><br /></td></tr>
|
||
<tr class="separator:acc2ef38f0b14c0a13fffe8993e2c19d5 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ad67d172c3baf63682babcc5b2b8100c2 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#ad67d172c3baf63682babcc5b2b8100c2">qstart_</a></td></tr>
|
||
<tr class="memdesc:ad67d172c3baf63682babcc5b2b8100c2 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Start of the current query segment. <a href="classCSearch__Base.html#ad67d172c3baf63682babcc5b2b8100c2">More...</a><br /></td></tr>
|
||
<tr class="separator:ad67d172c3baf63682babcc5b2b8100c2 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ae997a169c67732a724ebad406444b71b inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#ae997a169c67732a724ebad406444b71b">qstop_</a></td></tr>
|
||
<tr class="memdesc:ae997a169c67732a724ebad406444b71b inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">One past the end of the current query segment. <a href="classCSearch__Base.html#ae997a169c67732a724ebad406444b71b">More...</a><br /></td></tr>
|
||
<tr class="separator:ae997a169c67732a724ebad406444b71b inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a69414cc0fe35b6cec02367f27cb3b697 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCSeedRoots.html">CSeedRoots</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a69414cc0fe35b6cec02367f27cb3b697">roots_</a></td></tr>
|
||
<tr class="memdesc:a69414cc0fe35b6cec02367f27cb3b697 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Collection of initial soff/qoff pairs. <a href="classCSearch__Base.html#a69414cc0fe35b6cec02367f27cb3b697">More...</a><br /></td></tr>
|
||
<tr class="separator:a69414cc0fe35b6cec02367f27cb3b697 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:af1cdc49954776482f041359a254a8474 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">unsigned long </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#af1cdc49954776482f041359a254a8474">code_bits_</a></td></tr>
|
||
<tr class="memdesc:af1cdc49954776482f041359a254a8474 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Number of bits to represent special offset prefix. <a href="classCSearch__Base.html#af1cdc49954776482f041359a254a8474">More...</a><br /></td></tr>
|
||
<tr class="separator:af1cdc49954776482f041359a254a8474 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a01b594886cd899c5624c5935e5c7fd98 inherit pro_attribs_classCSearch__Base"><td class="memItemLeft" align="right" valign="top">unsigned long </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSearch__Base.html#a01b594886cd899c5624c5935e5c7fd98">min_offset_</a></td></tr>
|
||
<tr class="memdesc:a01b594886cd899c5624c5935e5c7fd98 inherit pro_attribs_classCSearch__Base"><td class="mdescLeft"> </td><td class="mdescRight">Minumum offset used by the index. <a href="classCSearch__Base.html#a01b594886cd899c5624c5935e5c7fd98">More...</a><br /></td></tr>
|
||
<tr class="separator:a01b594886cd899c5624c5935e5c7fd98 inherit pro_attribs_classCSearch__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
</table>
|
||
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
|
||
<div class="textblock"><h3>template<bool LEGACY, unsigned long NHITS><br />
|
||
class CSearch< LEGACY, NHITS ></h3>
|
||
|
||
<p><a class="el" href="classCSearch.html" title="CSearch –.">CSearch</a> –. </p>
|
||
<p><a class="el" href="classCSearch.html" title="CSearch –.">CSearch</a> CRTP (to be removed).</p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="Search_8hpp_source.html#l00067">67</a> of file <a class="el" href="Search_8hpp_source.html">Search.hpp</a>.</p>
|
||
</div><h2 class="groupheader">Member Typedef Documentation</h2>
|
||
<a id="aeb8c0d943e14fc63f6c09a408b742953"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#aeb8c0d943e14fc63f6c09a408b742953">◆ </a></span>TBase</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">typedef <a class="el" href="classCSearch__Base.html">CSearch_Base</a>< LEGACY, NHITS, <a class="el" href="classCSearch.html">CSearch</a> > <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::<a class="el" href="classCSearch.html#aeb8c0d943e14fc63f6c09a408b742953">TBase</a></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="dbindex__search_8cpp_source.html#l01359">1359</a> of file <a class="el" href="dbindex__search_8cpp_source.html">dbindex_search.cpp</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a9431accacfdc77725883ba154caf64b7"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a9431accacfdc77725883ba154caf64b7">◆ </a></span>TIndex_Impl</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">typedef <a class="el" href="classCSearch__Base.html#aec07f7524cf0ec5dc6610b776b3ff4d2">TBase::TIndex_Impl</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::<a class="el" href="classCSearch__Base.html#aec07f7524cf0ec5dc6610b776b3ff4d2">TIndex_Impl</a></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="dbindex__search_8cpp_source.html#l01360">1360</a> of file <a class="el" href="dbindex__search_8cpp_source.html">dbindex_search.cpp</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="afb4e78c64195e521cd2e81271d6f544e"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#afb4e78c64195e521cd2e81271d6f544e">◆ </a></span>TSearchOptions</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">typedef <a class="el" href="classCSearch__Base.html#afd6cb73bb0bbdcdbde5d1f139c6cbc9c">TBase::TSearchOptions</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::<a class="el" href="classCSearch__Base.html#afd6cb73bb0bbdcdbde5d1f139c6cbc9c">TSearchOptions</a></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="dbindex__search_8cpp_source.html#l01361">1361</a> of file <a class="el" href="dbindex__search_8cpp_source.html">dbindex_search.cpp</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<h2 class="groupheader">Constructor & Destructor Documentation</h2>
|
||
<a id="ab082f448e7bb480d122bb7f44050bbd6"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#ab082f448e7bb480d122bb7f44050bbd6">◆ </a></span>CSearch() <span class="overload">[1/2]</span></h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::<a class="el" href="classCSearch.html">CSearch</a> </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSearch__Base.html#aec07f7524cf0ec5dc6610b776b3ff4d2">TIndex_Impl</a> & </td>
|
||
<td class="paramname"><em>index_impl</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBLAST__SequenceBlk.html">BLAST_SequenceBlk</a> * </td>
|
||
<td class="paramname"><em>query</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqLoc.html">BlastSeqLoc</a> * </td>
|
||
<td class="paramname"><em>locs</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSearch__Base.html#afd6cb73bb0bbdcdbde5d1f139c6cbc9c">TSearchOptions</a> & </td>
|
||
<td class="paramname"><em>options</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Object constructor. </p>
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">index_impl</td><td>[I] the index implementation object </td></tr>
|
||
<tr><td class="paramname">query</td><td>[I] query data encoded in BLASTNA </td></tr>
|
||
<tr><td class="paramname">locs</td><td>[I] set of query locations to search </td></tr>
|
||
<tr><td class="paramname">options</td><td>[I] search options </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="dbindex__search_8cpp_source.html#l01372">1372</a> of file <a class="el" href="dbindex__search_8cpp_source.html">dbindex_search.cpp</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a2cffda2df314ffc0295a96d819379c64"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a2cffda2df314ffc0295a96d819379c64">◆ </a></span>CSearch() <span class="overload">[2/2]</span></h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::<a class="el" href="classCSearch.html">CSearch</a> </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>tNum</em></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l00412">412</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00634">CSearch< LEGACY, NHITS >::ThreadNum</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="afb321086985371baa64d67d331bfb810"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#afb321086985371baa64d67d331bfb810">◆ </a></span>~CSearch()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::~<a class="el" href="classCSearch.html">CSearch</a> </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
</div>
|
||
</div>
|
||
<h2 class="groupheader">Member Function Documentation</h2>
|
||
<a id="a700db5bb0d32f23cb372df1128aa220b"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a700db5bb0d32f23cb372df1128aa220b">◆ </a></span>AddIonsToHit()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::AddIonsToHit </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="classCMSHits.html">CMSHits</a> * </td>
|
||
<td class="paramname"><em>Hit</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCMSHit.html">CMSHit</a> * </td>
|
||
<td class="paramname"><em>MSHit</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Adds ion information to hitset. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l01465">1465</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="msscore_8hpp_source.html#l00244">CMSBasicMatchedPeak::GetCharge()</a>, <a class="el" href="msscore_8hpp_source.html#l00906">CMSSpectrumMatch::GetHitInfo()</a>, <a class="el" href="msscore_8hpp_source.html#l00894">CMSSpectrumMatch::GetHits()</a>, <a class="el" href="msscore_8hpp_source.html#l00232">CMSBasicMatchedPeak::GetIonSeries()</a>, <a class="el" href="msscore_8hpp_source.html#l00145">CMSBasicPeak::GetMZ()</a>, <a class="el" href="msscore_8hpp_source.html#l00256">CMSBasicMatchedPeak::GetNumber()</a>, <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>, and <a class="el" href="MSHits___8hpp_source.html#l00906">CMSHits_Base::SetMzhits()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l01508">CSearch< LEGACY, NHITS >::SetResult()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a1ba3ebe55f67dfd66295d574128c087f"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a1ba3ebe55f67dfd66295d574128c087f">◆ </a></span>AddModsToHit()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::AddModsToHit </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="classCMSHits.html">CMSHits</a> * </td>
|
||
<td class="paramname"><em>Hit</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCMSHit.html">CMSHit</a> * </td>
|
||
<td class="paramname"><em>MSHit</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Adds modification information to hitset. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l01447">1447</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="mspeak_8hpp_source.html#l00152">CMSModInfo::GetIsFixed()</a>, <a class="el" href="mspeak_8hpp_source.html#l00127">CMSModInfo::GetModEnum()</a>, <a class="el" href="mspeak_8hpp_source.html#l00407">CMSHit::GetModInfo()</a>, <a class="el" href="mspeak_8hpp_source.html#l00413">CMSHit::GetNumModInfo()</a>, <a class="el" href="mspeak_8hpp_source.html#l00139">CMSModInfo::GetSite()</a>, <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>, and <a class="el" href="MSHits___8hpp_source.html#l01025">CMSHits_Base::SetMods()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l01508">CSearch< LEGACY, NHITS >::SetResult()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a23d70f957aafb37b5aee39174630f305"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a23d70f957aafb37b5aee39174630f305">◆ </a></span>CalcModIndex()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::CalcModIndex </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> * </td>
|
||
<td class="paramname"><em>ModIndex</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> & </td>
|
||
<td class="paramname"><em>iMod</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> & </td>
|
||
<td class="paramname"><em>NumMod</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>NumFixed</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>NumModSites</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCMod.html">CMod</a> </td>
|
||
<td class="paramname"><em>CModList</em>[] </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00715">715</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="msms_8hpp_source.html#l00343">CMod::GetSite()</a>, and <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00774">CSearch< LEGACY, NHITS >::CreateModCombinations()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="abc4645a96133b78f3d16fff99b169852"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#abc4645a96133b78f3d16fff99b169852">◆ </a></span>CalcNSort()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::CalcNSort </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="omssa_8hpp.html#ad8a34208f6d4d5bfff7322ac0a82f9a4">TScoreList</a> & </td>
|
||
<td class="paramname"><em>ScoreList</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype">double </td>
|
||
<td class="paramname"><em>Threshold</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCMSPeak.html">CMSPeak</a> * </td>
|
||
<td class="paramname"><em>Peaks</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>calculate the evalues of the top hits and sort </p>
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">Threshold</td><td>the noise threshold to apply to the peaks </td></tr>
|
||
<tr><td class="paramname">Peaks</td><td>the spectrum to be scored </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l01889">1889</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="ncbidbg_8hpp_source.html#l00122">_TRACE</a>, <a class="el" href="ncbi__localip_8c_source.html#l00102">a</a>, <a class="el" href="msscore_8cpp_source.html#l00509">CMSSpectrumMatch::CalcNormalTopHit()</a>, <a class="el" href="msscore_8cpp_source.html#l00452">CMSSpectrumMatch::CalcPoissonMean()</a>, <a class="el" href="msscore_8cpp_source.html#l00526">CMSSpectrumMatch::CalcPvalue()</a>, <a class="el" href="msscore_8cpp_source.html#l00554">CMSSpectrumMatch::CalcPvalueTopHit()</a>, <a class="el" href="msscore_8cpp_source.html#l00585">CMSSpectrumMatch::CalcRankProb()</a>, <a class="el" href="mspeak_8cpp_source.html#l00182">CMSHit::CountHits()</a>, <a class="el" href="omssa_8cpp_source.html#l01869">CSearch< LEGACY, NHITS >::DoubleCompare()</a>, <a class="el" href="ncbidiag_8hpp_source.html#l00186">ERR_POST</a>, <a class="el" href="ncbifloat_8h_source.html#l00103">finite</a>, <a class="el" href="msscore_8hpp_source.html#l00846">CMSSpectrumMatch::GetCharge()</a>, <a class="el" href="mspeak_8hpp_source.html#l01238">CMSPeak::GetConsiderMult()</a>, <a class="el" href="omssa_8hpp_source.html#l00892">CSearch< LEGACY, NHITS >::GetEnzyme()</a>, <a class="el" href="msscore_8hpp_source.html#l00822">CMSSpectrumMatch::GetExpMass()</a>, <a class="el" href="mspeak_8hpp_source.html#l01189">CMSPeak::GetHitList()</a>, <a class="el" href="mspeak_8hpp_source.html#l01195">CMSPeak::GetHitListIndex()</a>, <a class="el" href="Search___8hpp_source.html#l00587">CSearch_Base< LEGACY, NHITS, derived_t >::GetHits()</a>, <a class="el" href="msscore_8cpp_source.html#l00629">CMSSpectrumMatch::GetMaxDelta()</a>, <a class="el" href="mspeak_8cpp_source.html#l01216">CMSPeak::GetMaxI()</a>, <a class="el" href="mspeak_8hpp_source.html#l01317">CMSPeak::GetNumCharges()</a>, <a class="el" href="mspeak_8hpp_source.html#l01213">CMSPeak::GetPeptidesExamined()</a>, <a class="el" href="omssa_8hpp_source.html#l00802">CSearch< LEGACY, NHITS >::GetPoissonOnly()</a>, <a class="el" href="msladder_8hpp_source.html#l00557">CLadderContainer::GetSeriesChargePairList()</a>, <a class="el" href="omssa_8hpp_source.html#l00826">CSearch< LEGACY, NHITS >::GetSettings()</a>, <a class="el" href="mspeak_8hpp_source.html#l01305">CMSPeak::GetWhich()</a>, <a class="el" href="mspeak_8cpp_source.html#l01137">CMSPeak::HighLow()</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l01185">Info()</a>, <a class="el" href="map_8hpp_source.html#l00305">multimap_checker< Container >::insert()</a>, <a class="el" href="ncbifloat_8h_source.html#l00092">isnan</a>, <a class="el" href="omssa_8cpp_source.html#l01844">CSearch< LEGACY, NHITS >::MatchAndSort()</a>, <a class="el" href="MSMod_8hpp_source.html#l00064">MSSCALE2INT</a>, <a class="el" href="zlib_2crc32_8c_source.html#l00057">N</a>, <a class="el" href="omssa_8hpp_source.html#l00899">CSearch< LEGACY, NHITS >::SetLadderContainer()</a>, and <a class="el" href="omssa_8hpp_source.html#l00604">CSearch< LEGACY, NHITS >::UseRankScore</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l01508">CSearch< LEGACY, NHITS >::SetResult()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a372b2bcc105eb0b6efd9d01cb02fe6d8"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a372b2bcc105eb0b6efd9d01cb02fe6d8">◆ </a></span>CheckFixed()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::CheckFixed </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>i</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>NumFixed</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCMod.html">CMod</a> </td>
|
||
<td class="paramname"><em>ModList</em>[], </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> * </td>
|
||
<td class="paramname"><em>ModIndex</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Checks to see that given modindex points to a site shared by a fixed mod. </p>
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">i</td><td>index into ModIndex </td></tr>
|
||
<tr><td class="paramname">NumFixed</td><td>number of fixed mods in ModIndex </td></tr>
|
||
<tr><td class="paramname">ModList</td><td>modification information </td></tr>
|
||
<tr><td class="paramname">ModIndex</td><td>array of iterators pointing to mod ordinals </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
<dl class="section return"><dt>Returns</dt><dd>true if shared </dd></dl>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a5f3558924cdf0e9e64444cff2bad31a1"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a5f3558924cdf0e9e64444cff2bad31a1">◆ </a></span>ClearLadderCalc()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::ClearLadderCalc </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>Max</em></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Clear the ladder calc array up to max index. </p>
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">Max</td><td>the number of indices to clear </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00778">778</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="ncbimisc_8hpp_source.html#l00469">AutoPtr< X, Del >::get()</a>, and <a class="el" href="omssa_8hpp_source.html#l00583">CSearch< LEGACY, NHITS >::LadderCalc</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a5c9a98b50a19cfd4f4b36f4cf74e3467"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a5c9a98b50a19cfd4f4b36f4cf74e3467">◆ </a></span>CompareLadders()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::CompareLadders </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>iMod</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCMSPeak.html">CMSPeak</a> * </td>
|
||
<td class="paramname"><em>Peaks</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td>
|
||
<td class="paramname"><em>OrLadders</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="mspeak_8hpp.html#a390bf355505d5e3cd42686bd76a67042">TMassPeak</a> * </td>
|
||
<td class="paramname"><em>MassPeak</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>compare ladders to experiment </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l00483">483</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="msladder_8cpp_source.html#l00324">CLadderContainer::Begin()</a>, <a class="el" href="mspeak_8hpp_source.html#l01342">_MassPeak::Charge</a>, <a class="el" href="mspeak_8cpp_source.html#l00443">CMSPeak::CompareSortedRank()</a>, <a class="el" href="mspeak_8hpp_source.html#l01238">CMSPeak::GetConsiderMult()</a>, <a class="el" href="mspeak_8hpp_source.html#l01305">CMSPeak::GetWhich()</a>, <a class="el" href="msladder_8cpp_source.html#l00310">CLadderContainer::Next()</a>, <a class="el" href="omssa_8hpp_source.html#l00899">CSearch< LEGACY, NHITS >::SetLadderContainer()</a>, and <a class="el" href="mspeak_8hpp_source.html#l01171">CMSPeak::SetPeakLists()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a9a257aad48c39a9680af16f5ffc3ff82"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a9a257aad48c39a9680af16f5ffc3ff82">◆ </a></span>CompareLaddersTop()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::CompareLaddersTop </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>iMod</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCMSPeak.html">CMSPeak</a> * </td>
|
||
<td class="paramname"><em>Peaks</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="mspeak_8hpp.html#a390bf355505d5e3cd42686bd76a67042">TMassPeak</a> * </td>
|
||
<td class="paramname"><em>MassPeak</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l00514">514</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="msladder_8cpp_source.html#l00324">CLadderContainer::Begin()</a>, <a class="el" href="mspeak_8hpp_source.html#l01342">_MassPeak::Charge</a>, <a class="el" href="mspeak_8cpp_source.html#l00503">CMSPeak::CompareTop()</a>, <a class="el" href="mspeak_8hpp_source.html#l01238">CMSPeak::GetConsiderMult()</a>, <a class="el" href="msladder_8cpp_source.html#l00310">CLadderContainer::Next()</a>, and <a class="el" href="omssa_8hpp_source.html#l00899">CSearch< LEGACY, NHITS >::SetLadderContainer()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a5d6e9641c571ad98ffdca0ae950e5d0d"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a5d6e9641c571ad98ffdca0ae950e5d0d">◆ </a></span>CopySettings()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::CopySettings </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS > > </td>
|
||
<td class="paramname"><em>fromObj</em></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l00970">970</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00644">CSearch< LEGACY, NHITS >::initCallback</a>, <a class="el" href="omssa_8hpp_source.html#l00645">CSearch< LEGACY, NHITS >::initCallbackData</a>, <a class="el" href="omssa_8hpp_source.html#l00642">CSearch< LEGACY, NHITS >::initModset</a>, <a class="el" href="omssa_8hpp_source.html#l00640">CSearch< LEGACY, NHITS >::initRequestIn</a>, <a class="el" href="omssa_8hpp_source.html#l00641">CSearch< LEGACY, NHITS >::initResponseIn</a>, <a class="el" href="omssa_8hpp_source.html#l00643">CSearch< LEGACY, NHITS >::initSettingsIn</a>, <a class="el" href="omssa_8hpp_source.html#l00614">CSearch< LEGACY, NHITS >::Iterative</a>, <a class="el" href="omssa_8hpp_source.html#l00553">CSearch< LEGACY, NHITS >::numseq</a>, <a class="el" href="omssa_8hpp_source.html#l00546">CSearch< LEGACY, NHITS >::rdfp</a>, and <a class="el" href="omssa_8hpp_source.html#l00604">CSearch< LEGACY, NHITS >::UseRankScore</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssaapp_8cpp_source.html#l00528">COMSSABase::RunSearch()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a97552a0ba34fd079fa3ae704450448fa"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a97552a0ba34fd079fa3ae704450448fa">◆ </a></span>CountModSites()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::CountModSites </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> & </td>
|
||
<td class="paramname"><em>NumModSites</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>NumMod</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCMod.html">CMod</a> </td>
|
||
<td class="paramname"><em>ModList</em>[] </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>count the number of unique sites modified </p>
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">NumModSites</td><td>the number of unique mod sites </td></tr>
|
||
<tr><td class="paramname">NumMod</td><td>the number of mods </td></tr>
|
||
<tr><td class="paramname">ModList</td><td>modification information </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l00755">755</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="msms_8hpp_source.html#l00343">CMod::GetSite()</a>, and <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="aa59a3ac07d68a71a67d820344a92101a"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#aa59a3ac07d68a71a67d820344a92101a">◆ </a></span>CreateLadders()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::CreateLadders </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> char * </td>
|
||
<td class="paramname"><em>Sequence</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>iSearch</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>position</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>endposition</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> * </td>
|
||
<td class="paramname"><em>Masses</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>iMissed</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCAA.html">CAA</a> & </td>
|
||
<td class="paramname"><em>AA</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>iMod</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCMod.html">CMod</a> </td>
|
||
<td class="paramname"><em>ModList</em>[], </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>NumMod</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>create the ladders from sequence </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l00441">441</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="msladder_8cpp_source.html#l00324">CLadderContainer::Begin()</a>, <a class="el" href="omssa_8hpp_source.html#l00826">CSearch< LEGACY, NHITS >::GetSettings()</a>, <a class="el" href="msscore_8cpp_source.html#l00234">CMSMatchedPeakSetMap::Key2Charge()</a>, <a class="el" href="msscore_8cpp_source.html#l00240">CMSMatchedPeakSetMap::Key2Series()</a>, <a class="el" href="omssa_8hpp_source.html#l00549">CSearch< LEGACY, NHITS >::MassArray</a>, <a class="el" href="msladder_8cpp_source.html#l00310">CLadderContainer::Next()</a>, <a class="el" href="omssa_8hpp_source.html#l00899">CSearch< LEGACY, NHITS >::SetLadderContainer()</a>, <a class="el" href="omssa_8hpp_source.html#l00784">CSearch< LEGACY, NHITS >::SetMassAndMask()</a>, and <a class="el" href="omssa_8hpp_source.html#l00820">CSearch< LEGACY, NHITS >::SetSettings()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a595bed291dc6ca4685397e914b05cdc3"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a595bed291dc6ca4685397e914b05cdc3">◆ </a></span>CreateModCombinations()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::CreateModCombinations </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>Missed</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> char * </td>
|
||
<td class="paramname"><em>PepStart</em>[], </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>Masses</em>[], </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>EndMasses</em>[], </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>NumMod</em>[], </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>NumMassAndMask</em>[], </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>NumModSites</em>[], </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCMod.html">CMod</a> </td>
|
||
<td class="paramname"><em>ModList</em>[][32] </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l00774">774</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00715">CSearch< LEGACY, NHITS >::CalcModIndex()</a>, <a class="el" href="MSSearchType___8hpp_source.html#l00068">eMSSearchType_exact</a>, <a class="el" href="omssa_8hpp_source.html#l00826">CSearch< LEGACY, NHITS >::GetSettings()</a>, <a class="el" href="omssa_8hpp_source.html#l00654">CSearch< LEGACY, NHITS >::InitModIndex()</a>, <a class="el" href="msms_8hpp_source.html#l00070">kNeutron</a>, <a class="el" href="omssa_8hpp_source.html#l00694">CSearch< LEGACY, NHITS >::MakeBoolMask()</a>, <a class="el" href="omssa_8hpp_source.html#l00097">_MassMask::Mask</a>, <a class="el" href="omssa_8hpp_source.html#l00097">_MassMask::Mass</a>, <a class="el" href="omssa_8hpp_source.html#l00588">CSearch< LEGACY, NHITS >::MassAndMask</a>, <a class="el" href="omssa_8hpp_source.html#l00075">MAXMOD</a>, <a class="el" href="omssa_8hpp_source.html#l00593">CSearch< LEGACY, NHITS >::MaxModPerPep</a>, <a class="el" href="MSMod_8hpp_source.html#l00064">MSSCALE2INT</a>, <a class="el" href="omssa_8hpp_source.html#l00784">CSearch< LEGACY, NHITS >::SetMassAndMask()</a>, <a class="el" href="omssa_8hpp_source.html#l00820">CSearch< LEGACY, NHITS >::SetSettings()</a>, and <a class="el" href="compile__time_8hpp_source.html#l00173">ct::sort()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="aaf1ea6b0a864974e1f42f7f45af6f9b1"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#aaf1ea6b0a864974e1f42f7f45af6f9b1">◆ </a></span>CreateSequence()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::CreateSequence </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>Start</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>Stop</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> & </td>
|
||
<td class="paramname"><em>seqstring</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCSeqDBSequence.html">CSeqDBSequence</a> & </td>
|
||
<td class="paramname"><em>Sequence</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Generate a peptide sequence. </p>
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">Start</td><td>start of sequence </td></tr>
|
||
<tr><td class="paramname">Stop</td><td>stop of sequence </td></tr>
|
||
<tr><td class="paramname">seqstring</td><td>sequence string </td></tr>
|
||
<tr><td class="paramname"><a class="el" href="classSequence.html">Sequence</a></td><td>sequence object </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l01494">1494</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="MSMod_8hpp_source.html#l00058">UniqueAA</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l01750">CSearch< LEGACY, NHITS >::PepCharge()</a>, and <a class="el" href="omssa_8cpp_source.html#l01508">CSearch< LEGACY, NHITS >::SetResult()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="aec515d80a97b58deecf3a14f3d2c9ce6"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#aec515d80a97b58deecf3a14f3d2c9ce6">◆ </a></span>DecodeOffset()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::DecodeOffset </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="dbindex__sp_8hpp.html#ab24dd73d837409e50d27583ed6f4e273">TWord</a> </td>
|
||
<td class="paramname"><em>offset</em></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Decode offset value into subject position. </p>
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">offset</td><td>Offset value.</td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
<dl class="section return"><dt>Returns</dt><dd>Corresponding position in the subject. </dd></dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="dbindex__search_8cpp_source.html#l01397">1397</a> of file <a class="el" href="dbindex__search_8cpp_source.html">dbindex_search.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="dbindex_8hpp_source.html#l01149">CSubjectMap::DecodeOffset()</a>, <a class="el" href="dbindex__sp_8hpp_source.html#l00400">CDbIndex_Impl< LEGACY >::GetSubjectMap()</a>, <a class="el" href="dbindex__search_8cpp_source.html#l00952">CSearch_Base< LEGACY, NHITS, derived_t >::index_impl_</a>, <a class="el" href="ftds100_2freetds_2replacements_8h_source.html#l00160">offset</a>, <a class="el" href="dbindex__search_8cpp_source.html#l01382">CSearch< LEGACY, NHITS >::SetSubjInfo()</a>, and <a class="el" href="dbindex__search_8cpp_source.html#l00958">CSearch_Base< LEGACY, NHITS, derived_t >::subject_</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a0b96efd3650fe192a63b9f36cb6f1861"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a0b96efd3650fe192a63b9f36cb6f1861">◆ </a></span>DeleteVariableOverlap()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::DeleteVariableOverlap </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> & </td>
|
||
<td class="paramname"><em>NumMod</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCMod.html">CMod</a> </td>
|
||
<td class="paramname"><em>ModList</em>[] </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>delete variable mods that overlap with fixed mods </p>
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">NumMod</td><td>the number of modifications </td></tr>
|
||
<tr><td class="paramname">ModList</td><td>modification information </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l00627">627</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>, and <a class="el" href="msms_8hpp_source.html#l00424">CMod::SetFixed()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a74da212c53668b580dd0d6784e4c99cd"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a74da212c53668b580dd0d6784e4c99cd">◆ </a></span>DoubleCompare()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::DoubleCompare </td>
|
||
<td>(</td>
|
||
<td class="paramtype">list< <a class="el" href="classCMSMatchedPeakSet.html">CMSMatchedPeakSet</a> * > & </td>
|
||
<td class="paramname"><em>SingleForward</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype">list< <a class="el" href="classCMSMatchedPeakSet.html">CMSMatchedPeakSet</a> * > & </td>
|
||
<td class="paramname"><em>SingleBackward</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype">list< <a class="el" href="classCMSMatchedPeakSet.html">CMSMatchedPeakSet</a> * > & </td>
|
||
<td class="paramname"><em>Double</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td>
|
||
<td class="paramname"><em>DoubleForward</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">SingleForward</td><td>singly charged NC ions </td></tr>
|
||
<tr><td class="paramname">SingleBackward</td><td>singly charged CN ions </td></tr>
|
||
<tr><td class="paramname">Double</td><td>double charged product ions </td></tr>
|
||
<tr><td class="paramname">DoubleForward</td><td>is the double series a forward series? </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l01869">1869</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l01889">CSearch< LEGACY, NHITS >::CalcNSort()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a6585a6b9070686c7ecb0242b379c1e6d"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a6585a6b9070686c7ecb0242b379c1e6d">◆ </a></span>GetEnzyme()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCConstRef.html">CConstRef</a>< <a class="el" href="classCCleave.html">CCleave</a> > <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::GetEnzyme </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td> const</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Get search enzyme. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00892">892</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00558">CSearch< LEGACY, NHITS >::Enzyme</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l01889">CSearch< LEGACY, NHITS >::CalcNSort()</a>, <a class="el" href="omssa_8cpp_source.html#l01750">CSearch< LEGACY, NHITS >::PepCharge()</a>, and <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a116591c2917d62d1ffea2b178e5a7485"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a116591c2917d62d1ffea2b178e5a7485">◆ </a></span>GetIterative()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::GetIterative </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td> const</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Gets iterate search. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00814">814</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00614">CSearch< LEGACY, NHITS >::Iterative</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssacl_8cpp_source.html#l00106">COMSSA::Run()</a>, <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>, <a class="el" href="omssa_8cpp_source.html#l01508">CSearch< LEGACY, NHITS >::SetResult()</a>, and <a class="el" href="omssa_8cpp_source.html#l00564">CSearch< LEGACY, NHITS >::Spectrum2Peak()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a4abbe6dc72e495a4595ffd7ba0a7d912"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a4abbe6dc72e495a4595ffd7ba0a7d912">◆ </a></span>GetLadderCalc()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="group__Portability.html#gad571e821cdf5dcc936b6beb906ad5a89">Int1</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::GetLadderCalc </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>i</em></td><td>)</td>
|
||
<td> const</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Get the bit that indicates whether a ladder was calculated. </p>
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">i</td><td>the index of the ladder </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00766">766</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="ncbimisc_8hpp_source.html#l00469">AutoPtr< X, Del >::get()</a>, <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>, and <a class="el" href="omssa_8hpp_source.html#l00583">CSearch< LEGACY, NHITS >::LadderCalc</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a0fd54889c5ae97be8b5e942d275db348"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a0fd54889c5ae97be8b5e942d275db348">◆ </a></span>GetLadderContainer()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCLadderContainer.html">CLadderContainer</a> & <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::GetLadderContainer </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td> const</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>get the ladder container </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00906">906</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00578">CSearch< LEGACY, NHITS >::LadderContainer</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="ac59e5496b857452d021b63a6fdcdf009"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#ac59e5496b857452d021b63a6fdcdf009">◆ </a></span>Getnumseq()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::Getnumseq </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td> const</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00868">868</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00553">CSearch< LEGACY, NHITS >::numseq</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>, and <a class="el" href="omssa_8cpp_source.html#l01508">CSearch< LEGACY, NHITS >::SetResult()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a858463feb06dac70536f85ea51b67a11"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a858463feb06dac70536f85ea51b67a11">◆ </a></span>GetOidSet()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCMSResponse.html#a10ac4d245cf91be83306cac7793a6377">CMSResponse::TOidSet</a> & <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::GetOidSet </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td> const</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>get the oidset </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00862">862</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00619">CSearch< LEGACY, NHITS >::OidSet</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l01736">CSearch< LEGACY, NHITS >::WriteBioseqs()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a833f4a13658de188ea0a461fd2419b90"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a833f4a13658de188ea0a461fd2419b90">◆ </a></span>GetPoissonOnly()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::GetPoissonOnly </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td> const</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Gets the scoring to use rank statistics only with Poisson. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00802">802</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00609">CSearch< LEGACY, NHITS >::PoissonOnly</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l01889">CSearch< LEGACY, NHITS >::CalcNSort()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a38cc1279d2c040a2354f0ac02036bb62"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a38cc1279d2c040a2354f0ac02036bb62">◆ </a></span>GetRequest()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCConstRef.html">CConstRef</a>< <a class="el" href="classCMSRequest.html">CMSRequest</a> > <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::GetRequest </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td> const</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Get search request. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00838">838</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00563">CSearch< LEGACY, NHITS >::MyRequest</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00564">CSearch< LEGACY, NHITS >::Spectrum2Peak()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a6ea4e23a8ab44c7938979d0b6f134f6b"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a6ea4e23a8ab44c7938979d0b6f134f6b">◆ </a></span>GetResponse()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCConstRef.html">CConstRef</a>< <a class="el" href="classCMSResponse.html">CMSResponse</a> > <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::GetResponse </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td> const</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Get search response. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00850">850</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00568">CSearch< LEGACY, NHITS >::MyResponse</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00921">CSearch< LEGACY, NHITS >::MakeOidSet()</a>, <a class="el" href="omssa_8cpp_source.html#l00541">CSearch< LEGACY, NHITS >::ReSearch()</a>, and <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a867076b42b583d945df34ae8fc65f8a7"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a867076b42b583d945df34ae8fc65f8a7">◆ </a></span>GetRestrictedSearch()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::GetRestrictedSearch </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td> const</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>is this search restricted to the oid set? </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00880">880</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00624">CSearch< LEGACY, NHITS >::RestrictedSearch</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a6cde243e25dd495d88c213c29bbceeaf"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a6cde243e25dd495d88c213c29bbceeaf">◆ </a></span>GetSettings()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCConstRef.html">CConstRef</a>< <a class="el" href="classCMSSearchSettings.html">CMSSearchSettings</a> > <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::GetSettings </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td> const</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Get search settings. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00826">826</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00573">CSearch< LEGACY, NHITS >::MySettings</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l01889">CSearch< LEGACY, NHITS >::CalcNSort()</a>, <a class="el" href="omssa_8cpp_source.html#l00441">CSearch< LEGACY, NHITS >::CreateLadders()</a>, <a class="el" href="omssa_8cpp_source.html#l00774">CSearch< LEGACY, NHITS >::CreateModCombinations()</a>, <a class="el" href="omssa_8cpp_source.html#l00901">CSearch< LEGACY, NHITS >::InitLadders()</a>, <a class="el" href="omssa_8cpp_source.html#l00921">CSearch< LEGACY, NHITS >::MakeOidSet()</a>, <a class="el" href="omssa_8cpp_source.html#l01844">CSearch< LEGACY, NHITS >::MatchAndSort()</a>, <a class="el" href="omssa_8cpp_source.html#l01750">CSearch< LEGACY, NHITS >::PepCharge()</a>, <a class="el" href="omssa_8cpp_source.html#l00541">CSearch< LEGACY, NHITS >::ReSearch()</a>, <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>, <a class="el" href="omssa_8cpp_source.html#l00888">CSearch< LEGACY, NHITS >::SetIons()</a>, <a class="el" href="omssa_8cpp_source.html#l01508">CSearch< LEGACY, NHITS >::SetResult()</a>, and <a class="el" href="omssa_8cpp_source.html#l00564">CSearch< LEGACY, NHITS >::Spectrum2Peak()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a4b038a63bf625bb3d7a94e3a7a9179b5"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a4b038a63bf625bb3d7a94e3a7a9179b5">◆ </a></span>InitBlast()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::InitBlast </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> char * </td>
|
||
<td class="paramname"><em>blastdb</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td>
|
||
<td class="paramname"><em>use_mmap</em> = <code><a class="el" href="ftds14_2freetds_2freetds_2bool_8h.html#a65e9886d74aaee76545e83dd09011727">false</a></code> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>init blast databases. </p>
|
||
<p>stream thru db if InitDB true</p>
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">blastdb</td><td>name of blast database </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l00429">429</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="seqdb_8hpp_source.html#l00174">CSeqDB::eProtein</a>, <a class="el" href="seqdb_8cpp_source.html#l00680">CSeqDB::GetNumOIDs()</a>, <a class="el" href="omssa_8hpp_source.html#l00553">CSearch< LEGACY, NHITS >::numseq</a>, <a class="el" href="omssa_8hpp_source.html#l00546">CSearch< LEGACY, NHITS >::rdfp</a>, and <a class="el" href="ncbiobj_8hpp_source.html#l00773">CRef< C, Locker >::Reset()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssacl_8cpp_source.html#l00106">COMSSA::Run()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="aa4b35edf347f79e7f05cea071e3c6a19"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#aa4b35edf347f79e7f05cea071e3c6a19">◆ </a></span>InitLadders()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::InitLadders </td>
|
||
<td>(</td>
|
||
<td class="paramtype">std::list< <a class="el" href="msscore_8hpp.html#ac70bf0eb50fe802a40d5cd4495516b03">EMSIonSeries</a> > & </td>
|
||
<td class="paramname"><em>Ions</em></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>initialize mass ladders </p>
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">Ions</td><td>list of ion types </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l00901">901</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="msladder_8cpp_source.html#l00271">CLadderContainer::CreateLadderArrays()</a>, <a class="el" href="omssa_8hpp_source.html#l00826">CSearch< LEGACY, NHITS >::GetSettings()</a>, <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>, <a class="el" href="msladder_8hpp_source.html#l00056">kMSLadderMax</a>, <a class="el" href="omssa_8hpp_source.html#l00593">CSearch< LEGACY, NHITS >::MaxModPerPep</a>, <a class="el" href="omssa_8hpp_source.html#l00899">CSearch< LEGACY, NHITS >::SetLadderContainer()</a>, and <a class="el" href="msladder_8hpp_source.html#l00550">CLadderContainer::SetSeriesChargePairList()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a6a3db8e4323473dd503c595154253420"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a6a3db8e4323473dd503c595154253420">◆ </a></span>InitModIndex()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::InitModIndex </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> * </td>
|
||
<td class="paramname"><em>ModIndex</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> & </td>
|
||
<td class="paramname"><em>iMod</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>NumMod</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>NumModSites</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCMod.html">CMod</a> </td>
|
||
<td class="paramname"><em>ModList</em>[] </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00654">654</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="msms_8hpp_source.html#l00343">CMod::GetSite()</a>, and <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00774">CSearch< LEGACY, NHITS >::CreateModCombinations()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="ab0dec8be370a16f7736e36c07841b3f5"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#ab0dec8be370a16f7736e36c07841b3f5">◆ </a></span>Main()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void * <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::Main </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Derived (user-created) class must provide a real thread function. </p>
|
||
|
||
<p>Implements <a class="el" href="group__Threads.html#gab129643bde65500cf09299898b9b7e49">CThread</a>.</p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l00955">955</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="ftds100_2freetds_2freetds_2bool_8h_source.html#l00034">bool</a>, <a class="el" href="omssa_8hpp_source.html#l00644">CSearch< LEGACY, NHITS >::initCallback</a>, <a class="el" href="omssa_8hpp_source.html#l00642">CSearch< LEGACY, NHITS >::initModset</a>, <a class="el" href="omssa_8hpp_source.html#l00640">CSearch< LEGACY, NHITS >::initRequestIn</a>, <a class="el" href="omssa_8hpp_source.html#l00641">CSearch< LEGACY, NHITS >::initResponseIn</a>, <a class="el" href="omssa_8hpp_source.html#l00643">CSearch< LEGACY, NHITS >::initSettingsIn</a>, and <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a2630407c949d7b0b3136af103d74897c"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a2630407c949d7b0b3136af103d74897c">◆ </a></span>MakeBoolMap()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::MakeBoolMap </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> * </td>
|
||
<td class="paramname"><em>ModMask</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> * </td>
|
||
<td class="paramname"><em>ModIndex</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> & </td>
|
||
<td class="paramname"><em>iMod</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> & </td>
|
||
<td class="paramname"><em>NumMod</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00682">682</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a016929b10fdf9e5b016113de9d3e32e4"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a016929b10fdf9e5b016113de9d3e32e4">◆ </a></span>MakeBoolMask()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">unsigned <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::MakeBoolMask </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> * </td>
|
||
<td class="paramname"><em>ModIndex</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>iMod</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00694">694</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00774">CSearch< LEGACY, NHITS >::CreateModCombinations()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a5012de4013ae530046aa163e174f835b"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a5012de4013ae530046aa163e174f835b">◆ </a></span>MakeIntFromBoolMap()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">unsigned <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::MakeIntFromBoolMap </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> * </td>
|
||
<td class="paramname"><em>ModMask</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> & </td>
|
||
<td class="paramname"><em>NumMod</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00705">705</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a7f3c57bf8dcdbd2f7f7b4a4e527b18ae"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a7f3c57bf8dcdbd2f7f7b4a4e527b18ae">◆ </a></span>MakeModString()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::MakeModString </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> & </td>
|
||
<td class="paramname"><em>seqstring</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> & </td>
|
||
<td class="paramname"><em>modseqstring</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCMSHit.html">CMSHit</a> * </td>
|
||
<td class="paramname"><em>MSHit</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">static</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Makes a string hashed out of the sequence plus mods. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l01483">1483</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="mspeak_8hpp_source.html#l00127">CMSModInfo::GetModEnum()</a>, <a class="el" href="mspeak_8hpp_source.html#l00407">CMSHit::GetModInfo()</a>, <a class="el" href="mspeak_8hpp_source.html#l00413">CMSHit::GetNumModInfo()</a>, <a class="el" href="mspeak_8hpp_source.html#l00139">CMSModInfo::GetSite()</a>, <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>, and <a class="el" href="corelib_2ncbistr_8hpp_source.html#l05078">NStr::IntToString()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l01508">CSearch< LEGACY, NHITS >::SetResult()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="abe8b6214346549d5a66db282e79e52e1"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#abe8b6214346549d5a66db282e79e52e1">◆ </a></span>MakeOidSet()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::MakeOidSet </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>makes map of oid from previous search used in iterative searching </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l00921">921</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="util_2debug_2set_8hpp_source.html#l00153">set< Key, Compare >::clear()</a>, <a class="el" href="omssa_8hpp_source.html#l00850">CSearch< LEGACY, NHITS >::GetResponse()</a>, <a class="el" href="omssa_8hpp_source.html#l00826">CSearch< LEGACY, NHITS >::GetSettings()</a>, <a class="el" href="omssa_8hpp_source.html#l00856">CSearch< LEGACY, NHITS >::SetOidSet()</a>, and <a class="el" href="omssa_8hpp_source.html#l00874">CSearch< LEGACY, NHITS >::SetRestrictedSearch()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a5b43109372a8440c837e70afe74271cd"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a5b43109372a8440c837e70afe74271cd">◆ </a></span>MatchAndSort()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::MatchAndSort </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="classCMSPeak.html">CMSPeak</a> * </td>
|
||
<td class="paramname"><em>Peaks</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCMSHit.html">CMSHit</a> & </td>
|
||
<td class="paramname"><em>Hit</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="mspeak_8hpp.html#a96730e665542e37f1b3da213391525cf">EMSPeakListTypes</a> </td>
|
||
<td class="paramname"><em>Which</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>minintensity</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> TSeriesChargePairList::const_iterator & </td>
|
||
<td class="paramname"><em>iPairList</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype">list< <a class="el" href="classCMSMatchedPeakSet.html">CMSMatchedPeakSet</a> * > & </td>
|
||
<td class="paramname"><em>SingleForward</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype">list< <a class="el" href="classCMSMatchedPeakSet.html">CMSMatchedPeakSet</a> * > & </td>
|
||
<td class="paramname"><em>SingleBackward</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Creates match ion match lists. </p>
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">Peaks</td><td>peak list </td></tr>
|
||
<tr><td class="paramname">Hit</td><td>the hit </td></tr>
|
||
<tr><td class="paramname">Which</td><td>which peak list to use </td></tr>
|
||
<tr><td class="paramname">minintensity</td><td>minimum intensity </td></tr>
|
||
<tr><td class="paramname">iPairList</td><td></td></tr>
|
||
<tr><td class="paramname">Forward</td><td>NC ions </td></tr>
|
||
<tr><td class="paramname">Backward</td><td>CN ions </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l01844">1844</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00826">CSearch< LEGACY, NHITS >::GetSettings()</a>, <a class="el" href="msscore_8hpp_source.html#l00086">kIonDirection</a>, and <a class="el" href="omssa_8cpp_source.html#l01750">CSearch< LEGACY, NHITS >::PepCharge()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l01889">CSearch< LEGACY, NHITS >::CalcNSort()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a41bbf21492f67c93eff4235396d56443"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a41bbf21492f67c93eff4235396d56443">◆ </a></span>OnExit()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::OnExit </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Override this to execute finalization code. </p>
|
||
<p>Unlike destructor, this code will be executed before thread termination and as a part of the thread. </p>
|
||
|
||
<p>Reimplemented from <a class="el" href="group__Threads.html#ga6b4a213a07c902cfced97b03f16751bb">CThread</a>.</p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l00966">966</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a7c92570f5a6ab9ff8a1e2bdadc373969"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a7c92570f5a6ab9ff8a1e2bdadc373969">◆ </a></span>PepCharge()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCMSMatchedPeakSet.html">CMSMatchedPeakSet</a> * <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::PepCharge </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="classCMSHit.html">CMSHit</a> & </td>
|
||
<td class="paramname"><em>Hit</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>SeriesCharge</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>Ion</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>MinIntensity</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>Which</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCMSPeak.html">CMSPeak</a> * </td>
|
||
<td class="paramname"><em>Peaks</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>Maxproductions</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>fill out MatchedPeakSet </p>
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">Hit</td><td>the match being evaluated </td></tr>
|
||
<tr><td class="paramname">SeriesCharge</td><td>charge of ion series </td></tr>
|
||
<tr><td class="paramname">Ion</td><td>which ion series </td></tr>
|
||
<tr><td class="paramname">MinIntensity</td><td>the minimum intensity to consider </td></tr>
|
||
<tr><td class="paramname">Which</td><td>which version of experimental peaks to use </td></tr>
|
||
<tr><td class="paramname">Peaks</td><td>experimental peaks </td></tr>
|
||
<tr><td class="paramname">Maxproductions</td><td>the number of ions in each series actually searched </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
<dl class="section return"><dt>Returns</dt><dd>MatchedPeakSet that was filled out </dd></dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l01750">1750</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="mspeak_8cpp_source.html#l00595">CMSPeak::CountMZRange()</a>, <a class="el" href="omssa_8cpp_source.html#l01494">CSearch< LEGACY, NHITS >::CreateSequence()</a>, <a class="el" href="msscore_8hpp_source.html#l00554">eMSBothTerminalBias</a>, <a class="el" href="msscore_8hpp_source.html#l00553">eMSCTerminalBias</a>, <a class="el" href="msscore_8hpp_source.html#l00551">eMSNoTerminalBias</a>, <a class="el" href="msscore_8hpp_source.html#l00552">eMSNTerminalBias</a>, <a class="el" href="msscore_8cpp_source.html#l00287">CMSSpectrumMatch::FillMatchedPeaks()</a>, <a class="el" href="omssa_8hpp_source.html#l00892">CSearch< LEGACY, NHITS >::GetEnzyme()</a>, <a class="el" href="msscore_8hpp_source.html#l00822">CMSSpectrumMatch::GetExpMass()</a>, <a class="el" href="ncbiobj_8hpp_source.html#l00998">CRef< C, Locker >::GetPointer()</a>, <a class="el" href="mspeak_8hpp_source.html#l00389">CMSHit::GetSeqIndex()</a>, <a class="el" href="omssa_8hpp_source.html#l00826">CSearch< LEGACY, NHITS >::GetSettings()</a>, <a class="el" href="mspeak_8hpp_source.html#l00365">CMSHit::GetStart()</a>, <a class="el" href="mspeak_8hpp_source.html#l00377">CMSHit::GetStop()</a>, <a class="el" href="mspeak_8hpp_source.html#l01286">CMSPeak::GetTol()</a>, <a class="el" href="msladder_8hpp_source.html#l00056">kMSLadderMax</a>, <a class="el" href="ftds100_2freetds_2freetds_2dlist_8tmpl_8h_source.html#l00056">next()</a>, <a class="el" href="ftds100_2freetds_2freetds_2dlist_8tmpl_8h_source.html#l00061">prev()</a>, <a class="el" href="omssa_8hpp_source.html#l00546">CSearch< LEGACY, NHITS >::rdfp</a>, <a class="el" href="msscore_8hpp_source.html#l00924">CMSSpectrumMatch::SetIonSeriesMatchMap()</a>, <a class="el" href="msscore_8hpp_source.html#l00442">CMSMatchedPeakSet::SetMatchedPeakSet()</a>, and <a class="el" href="msscore_8cpp_source.html#l00213">CMSMatchedPeakSetMap::SetSeries()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l01844">CSearch< LEGACY, NHITS >::MatchAndSort()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="ad9ddeebd9a5f9835d465ce7e306c697f"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#ad9ddeebd9a5f9835d465ce7e306c697f">◆ </a></span>ReSearch()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::ReSearch </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>Number</em></td><td>)</td>
|
||
<td> const</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>examines a hitset to see if any good hits </p>
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">Number</td><td>the spectrum number of the hitset </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
<dl class="section return"><dt>Returns</dt><dd>true if no good hits </dd></dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l00541">541</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00850">CSearch< LEGACY, NHITS >::GetResponse()</a>, <a class="el" href="omssa_8hpp_source.html#l00826">CSearch< LEGACY, NHITS >::GetSettings()</a>, and <a class="el" href="ncbiobj_8hpp_source.html#l00735">CRef< C, Locker >::IsNull()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00564">CSearch< LEGACY, NHITS >::Spectrum2Peak()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="ac066a9f07f05ae02f3dc47e114cd4c29"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#ac066a9f07f05ae02f3dc47e114cd4c29">◆ </a></span>ResetGlobals()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::ResetGlobals </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">static</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Reset global parameters used in threaded search. </p>
|
||
<p>Call whenever rerunning a search. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l00421">421</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00629">CSearch< LEGACY, NHITS >::iSearchGlobal</a>, <a class="el" href="omssa_8hpp_source.html#l00599">CSearch< LEGACY, NHITS >::MaxMZ</a>, <a class="el" href="ncbiobj_8hpp_source.html#l00773">CRef< C, Locker >::Reset()</a>, and <a class="el" href="omssa_8hpp_source.html#l00225">CSearch< LEGACY, NHITS >::SharedPeakSet</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a5e985bb7e8acd2e85be9e4fe2ee023e6"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a5e985bb7e8acd2e85be9e4fe2ee023e6">◆ </a></span>Search()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::Search </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSRequest.html">CMSRequest</a> > </td>
|
||
<td class="paramname"><em>MyRequestIn</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSResponse.html">CMSResponse</a> > </td>
|
||
<td class="paramname"><em>MyResponseIn</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSModSpecSet.html">CMSModSpecSet</a> > </td>
|
||
<td class="paramname"><em>Modset</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSSearchSettings.html">CMSSearchSettings</a> > </td>
|
||
<td class="paramname"><em>SettingsIn</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="omssa_8hpp.html#a9ffe9cb00c8437193b4225feecd4ab36">TOMSSACallback</a> </td>
|
||
<td class="paramname"><em>Callback</em> = <code>0</code>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype">void * </td>
|
||
<td class="paramname"><em>CallbackData</em> = <code>0</code> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Performs the ms/ms search. </p>
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">MyRequestIn</td><td>the user search params and spectra </td></tr>
|
||
<tr><td class="paramname">MyResponseIn</td><td>the results of the search </td></tr>
|
||
<tr><td class="paramname">Modset</td><td>list of modifications </td></tr>
|
||
<tr><td class="paramname">SettingsIn</td><td>the search settings </td></tr>
|
||
<tr><td class="paramname">Callback</td><td>callback function for progress meter </td></tr>
|
||
<tr><td class="paramname">CallbackData</td><td>data passed back to callback fcn </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l00985">985</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="mspeak_8cpp_source.html#l00349">CMSPeak::AddHit()</a>, <a class="el" href="group__IntervalTree.html#gaae69387898421b5f068b36bc7e539390">CIntervalTree::AllIntervals()</a>, <a class="el" href="msladder_8cpp_source.html#l00324">CLadderContainer::Begin()</a>, <a class="el" href="msms_8cpp_source.html#l00116">CCleave::CalcAndCut()</a>, <a class="el" href="mspeak_8hpp_source.html#l01342">_MassPeak::Charge</a>, <a class="el" href="msms_8hpp_source.html#l00720">CCleave::CheckCleaveChar()</a>, <a class="el" href="seqdb_8cpp_source.html#l00728">CSeqDB::CheckOrFindOID()</a>, <a class="el" href="omssa_8hpp_source.html#l00778">CSearch< LEGACY, NHITS >::ClearLadderCalc()</a>, <a class="el" href="msms_8cpp_source.html#l00545">CCleaveFactory::CleaveFactory()</a>, <a class="el" href="omssa_8cpp_source.html#l00483">CSearch< LEGACY, NHITS >::CompareLadders()</a>, <a class="el" href="omssa_8cpp_source.html#l00514">CSearch< LEGACY, NHITS >::CompareLaddersTop()</a>, <a class="el" href="omssa_8cpp_source.html#l00755">CSearch< LEGACY, NHITS >::CountModSites()</a>, <a class="el" href="omssa_8cpp_source.html#l00441">CSearch< LEGACY, NHITS >::CreateLadders()</a>, <a class="el" href="omssa_8cpp_source.html#l00774">CSearch< LEGACY, NHITS >::CreateModCombinations()</a>, <a class="el" href="omssa_8cpp_source.html#l00627">CSearch< LEGACY, NHITS >::DeleteVariableOverlap()</a>, <a class="el" href="MSModType___8hpp_source.html#l00072">eMSModType_modcp</a>, <a class="el" href="MSModType___8hpp_source.html#l00073">eMSModType_modcpaa</a>, <a class="el" href="ncbidiag_8hpp_source.html#l00186">ERR_POST</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l01209">Fatal()</a>, <a class="el" href="omssa_8hpp_source.html#l00552">CSearch< LEGACY, NHITS >::FixedMods</a>, <a class="el" href="msms_8hpp_source.html#l00878">CCleave::GetCleaveNum()</a>, <a class="el" href="msms_8hpp_source.html#l00397">CMod::GetEnum()</a>, <a class="el" href="omssa_8hpp_source.html#l00892">CSearch< LEGACY, NHITS >::GetEnzyme()</a>, <a class="el" href="msms_8hpp_source.html#l00415">CMod::GetFixed()</a>, <a class="el" href="msms_8hpp_source.html#l00127">CMassArray::GetIntMass()</a>, <a class="el" href="omssa_8hpp_source.html#l00814">CSearch< LEGACY, NHITS >::GetIterative()</a>, <a class="el" href="omssa_8hpp_source.html#l00766">CSearch< LEGACY, NHITS >::GetLadderCalc()</a>, <a class="el" href="msms_8hpp_source.html#l00160">CAA::GetMap()</a>, <a class="el" href="MSSearchSettings___8hpp_source.html#l03714">CMSSearchSettings_Base::GetMinnoenzyme()</a>, <a class="el" href="MSModSpecSet_8hpp_source.html#l00230">CMSModSpecSet::GetModType()</a>, <a class="el" href="MSSearchSettings___8hpp_source.html#l04114">CMSSearchSettings_Base::GetNmethionine()</a>, <a class="el" href="msms_8hpp_source.html#l00860">CCleave::GetNonSpecific()</a>, <a class="el" href="omssa_8hpp_source.html#l00868">CSearch< LEGACY, NHITS >::Getnumseq()</a>, <a class="el" href="ncbiobj_8hpp_source.html#l00998">CRef< C, Locker >::GetPointer()</a>, <a class="el" href="omssa_8hpp_source.html#l00850">CSearch< LEGACY, NHITS >::GetResponse()</a>, <a class="el" href="omssa_8hpp_source.html#l00880">CSearch< LEGACY, NHITS >::GetRestrictedSearch()</a>, <a class="el" href="omssa_8hpp_source.html#l00826">CSearch< LEGACY, NHITS >::GetSettings()</a>, <a class="el" href="msms_8hpp_source.html#l00343">CMod::GetSite()</a>, <a class="el" href="seq__loc__util_8cpp_source.html#l00525">GetStop()</a>, <a class="el" href="msms_8hpp_source.html#l00866">CCleave::GetStop()</a>, <a class="el" href="seqdb_8cpp_source.html#l00441">CSeqDB::GetTaxIDs()</a>, <a class="el" href="group__IntervalTree.html#gaff19b423d84bc63a6adfc47a45813ee9">CIntervalTreeIterator< Traits >::GetValue()</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l01185">Info()</a>, <a class="el" href="msms_8cpp_source.html#l00641">CMassArray::Init()</a>, <a class="el" href="Mod_8cpp_source.html#l00056">CMSMod::Init()</a>, <a class="el" href="omssa_8cpp_source.html#l00901">CSearch< LEGACY, NHITS >::InitLadders()</a>, <a class="el" href="group__IntervalTree.html#gab9c8e7a37bc69e3af0e4091ceadc2d29">CIntervalTree::IntervalsContaining()</a>, <a class="el" href="omssa_8hpp_source.html#l00629">CSearch< LEGACY, NHITS >::iSearchGlobal</a>, <a class="el" href="omssa_8hpp_source.html#l00583">CSearch< LEGACY, NHITS >::LadderCalc</a>, <a class="el" href="omssa_8cpp_source.html#l00921">CSearch< LEGACY, NHITS >::MakeOidSet()</a>, <a class="el" href="mspeak_8hpp_source.html#l01337">_MassPeak::Mass</a>, <a class="el" href="omssa_8hpp_source.html#l00097">_MassMask::Mass</a>, <a class="el" href="omssa_8hpp_source.html#l00588">CSearch< LEGACY, NHITS >::MassAndMask</a>, <a class="el" href="omssa_8hpp_source.html#l00549">CSearch< LEGACY, NHITS >::MassArray</a>, <a class="el" href="omssa_8hpp_source.html#l00072">MAXMISSEDCLEAVE</a>, <a class="el" href="omssa_8hpp_source.html#l00075">MAXMOD</a>, <a class="el" href="omssa_8hpp_source.html#l00077">MAXMOD2</a>, <a class="el" href="omssa_8hpp_source.html#l00593">CSearch< LEGACY, NHITS >::MaxModPerPep</a>, <a class="el" href="omssa_8hpp_source.html#l00599">CSearch< LEGACY, NHITS >::MaxMZ</a>, <a class="el" href="MSMod_8hpp_source.html#l00063">MSSCALE</a>, <a class="el" href="msladder_8cpp_source.html#l00310">CLadderContainer::Next()</a>, <a class="el" href="mspeak_8hpp_source.html#l01343">_MassPeak::Peak</a>, <a class="el" href="omssa_8hpp_source.html#l00550">CSearch< LEGACY, NHITS >::PrecursorMassArray</a>, <a class="el" href="omssa_8hpp_source.html#l00546">CSearch< LEGACY, NHITS >::rdfp</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00480">AutoPtr< X, Del >::reset()</a>, <a class="el" href="ncbiobj_8hpp_source.html#l00773">CRef< C, Locker >::Reset()</a>, <a class="el" href="msms_8hpp_source.html#l00306">CMod::Reset()</a>, <a class="el" href="msscore_8hpp_source.html#l00852">CMSSpectrumMatch::SetCharge()</a>, <a class="el" href="MSSearchSettings___8hpp_source.html#l02915">CMSSearchSettings_Base::SetDoublenum()</a>, <a class="el" href="omssa_8hpp_source.html#l00886">CSearch< LEGACY, NHITS >::SetEnzyme()</a>, <a class="el" href="msscore_8hpp_source.html#l00828">CMSSpectrumMatch::SetExpMass()</a>, <a class="el" href="msscore_8hpp_source.html#l00900">CMSSpectrumMatch::SetHits()</a>, <a class="el" href="mspeak_8hpp_source.html#l01397">CMSPeakSet::SetIntervalTree()</a>, <a class="el" href="omssa_8cpp_source.html#l00888">CSearch< LEGACY, NHITS >::SetIons()</a>, <a class="el" href="omssa_8hpp_source.html#l00772">CSearch< LEGACY, NHITS >::SetLadderCalc()</a>, <a class="el" href="omssa_8hpp_source.html#l00899">CSearch< LEGACY, NHITS >::SetLadderContainer()</a>, <a class="el" href="omssa_8hpp_source.html#l00784">CSearch< LEGACY, NHITS >::SetMassAndMask()</a>, <a class="el" href="msms_8hpp_source.html#l00897">CCleave::SetNMethionine()</a>, <a class="el" href="omssa_8hpp_source.html#l00856">CSearch< LEGACY, NHITS >::SetOidSet()</a>, <a class="el" href="mspeak_8hpp_source.html#l01219">CMSPeak::SetPeptidesExamined()</a>, <a class="el" href="omssa_8hpp_source.html#l00832">CSearch< LEGACY, NHITS >::SetRequest()</a>, <a class="el" href="omssa_8hpp_source.html#l00844">CSearch< LEGACY, NHITS >::SetResponse()</a>, <a class="el" href="MSResponse___8hpp_source.html#l00510">CMSResponse_Base::SetScale()</a>, <a class="el" href="MSSearchSettings___8hpp_source.html#l03353">CMSSearchSettings_Base::SetScale()</a>, <a class="el" href="mspeak_8hpp_source.html#l00395">CMSHit::SetSeqIndex()</a>, <a class="el" href="omssa_8hpp_source.html#l00820">CSearch< LEGACY, NHITS >::SetSettings()</a>, <a class="el" href="MSSearchSettings___8hpp_source.html#l02868">CMSSearchSettings_Base::SetSinglenum()</a>, <a class="el" href="mspeak_8hpp_source.html#l00371">CMSHit::SetStart()</a>, <a class="el" href="msms_8hpp_source.html#l00872">CCleave::SetStop()</a>, <a class="el" href="mspeak_8hpp_source.html#l00383">CMSHit::SetStop()</a>, <a class="el" href="omssa_8hpp_source.html#l00225">CSearch< LEGACY, NHITS >::SharedPeakSet</a>, <a class="el" href="omssa_8cpp_source.html#l00564">CSearch< LEGACY, NHITS >::Spectrum2Peak()</a>, <a class="el" href="omssa_8cpp_source.html#l00663">CSearch< LEGACY, NHITS >::UpdateWithNewPep()</a>, <a class="el" href="omssa_8hpp_source.html#l00604">CSearch< LEGACY, NHITS >::UseRankScore</a>, <a class="el" href="omssa_8hpp_source.html#l00551">CSearch< LEGACY, NHITS >::VariableMods</a>, and <a class="el" href="ncbiexpt_8hpp_source.html#l01191">Warning()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00955">CSearch< LEGACY, NHITS >::Main()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a8caa7e28ab2f6e799a45cca224aef58b"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a8caa7e28ab2f6e799a45cca224aef58b">◆ </a></span>SetEnzyme()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCCleave.html">CCleave</a> > & <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::SetEnzyme </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Set search enzyme. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00886">886</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00558">CSearch< LEGACY, NHITS >::Enzyme</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="aa719dd5213417bea90158e151546b4b3"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#aa719dd5213417bea90158e151546b4b3">◆ </a></span>SetIons()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::SetIons </td>
|
||
<td>(</td>
|
||
<td class="paramtype">list< <a class="el" href="msscore_8hpp.html#ac70bf0eb50fe802a40d5cd4495516b03">EMSIonSeries</a> > & </td>
|
||
<td class="paramname"><em>Ions</em></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>set up the ions to use </p>
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">Ions</td><td>list of ions to be set up </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l00888">888</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="ncbidiag_8hpp_source.html#l00186">ERR_POST</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l01209">Fatal()</a>, <a class="el" href="omssa_8hpp_source.html#l00826">CSearch< LEGACY, NHITS >::GetSettings()</a>, <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>, and <a class="el" href="namespacencbi_1_1grid_1_1netcache_1_1search_1_1fields.html#a0f3896dcec83a75496951b513af45a54">ncbi::grid::netcache::search::fields::size</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a07e07ceccdb937756560dfcd245fb328"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a07e07ceccdb937756560dfcd245fb328">◆ </a></span>SetIterative()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> & <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::SetIterative </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Sets iterate search. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00808">808</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00614">CSearch< LEGACY, NHITS >::Iterative</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssacl_8cpp_source.html#l00106">COMSSA::Run()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a1207c6c341781f4b9a3cc95a75ccd158"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a1207c6c341781f4b9a3cc95a75ccd158">◆ </a></span>SetLadderCalc()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="group__Portability.html#gad571e821cdf5dcc936b6beb906ad5a89">Int1</a> & <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::SetLadderCalc </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>i</em></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Set the bit that indicates whether a ladder was calculated. </p>
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">i</td><td>the index of the ladder </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00772">772</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="ncbimisc_8hpp_source.html#l00469">AutoPtr< X, Del >::get()</a>, <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>, and <a class="el" href="omssa_8hpp_source.html#l00583">CSearch< LEGACY, NHITS >::LadderCalc</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a225222f019e481ef0c9b21df51d9fea3"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a225222f019e481ef0c9b21df51d9fea3">◆ </a></span>SetLadderContainer()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCLadderContainer.html">CLadderContainer</a> & <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::SetLadderContainer </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>set the ladder container </p>
|
||
<p>this container holds theoretical mass ladders sorted by charge and series type </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00899">899</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00578">CSearch< LEGACY, NHITS >::LadderContainer</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l01889">CSearch< LEGACY, NHITS >::CalcNSort()</a>, <a class="el" href="omssa_8cpp_source.html#l00483">CSearch< LEGACY, NHITS >::CompareLadders()</a>, <a class="el" href="omssa_8cpp_source.html#l00514">CSearch< LEGACY, NHITS >::CompareLaddersTop()</a>, <a class="el" href="omssa_8cpp_source.html#l00441">CSearch< LEGACY, NHITS >::CreateLadders()</a>, <a class="el" href="omssa_8cpp_source.html#l00901">CSearch< LEGACY, NHITS >::InitLadders()</a>, and <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a5e21827850070f3805984a8ec22f7ca2"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a5e21827850070f3805984a8ec22f7ca2">◆ </a></span>SetMassAndMask()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="omssa_8hpp.html#a5742ee0bc8e594f879b5d020791738e4">TMassMask</a> & <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::SetMassAndMask </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>i</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>j</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Set the mask and mass of mod bit array. </p>
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">i</td><td>the index for missed cleavages </td></tr>
|
||
<tr><td class="paramname">j</td><td>the index for modification combinations </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00784">784</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>, <a class="el" href="omssa_8hpp_source.html#l00588">CSearch< LEGACY, NHITS >::MassAndMask</a>, and <a class="el" href="omssa_8hpp_source.html#l00593">CSearch< LEGACY, NHITS >::MaxModPerPep</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00441">CSearch< LEGACY, NHITS >::CreateLadders()</a>, <a class="el" href="omssa_8cpp_source.html#l00774">CSearch< LEGACY, NHITS >::CreateModCombinations()</a>, and <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a089138cdcb2856ca6603948a408e194c"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a089138cdcb2856ca6603948a408e194c">◆ </a></span>SetOidSet()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCMSResponse.html#a10ac4d245cf91be83306cac7793a6377">CMSResponse::TOidSet</a> & <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::SetOidSet </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>get the oidset </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00856">856</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00619">CSearch< LEGACY, NHITS >::OidSet</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00921">CSearch< LEGACY, NHITS >::MakeOidSet()</a>, <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>, and <a class="el" href="omssa_8cpp_source.html#l01508">CSearch< LEGACY, NHITS >::SetResult()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="ad6568eb8d7547a6af3a8b5ca303ed000"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#ad6568eb8d7547a6af3a8b5ca303ed000">◆ </a></span>SetPoissonOnly()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> & <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::SetPoissonOnly </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Sets the scoring to use rank statistics only with Poisson. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00796">796</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00609">CSearch< LEGACY, NHITS >::PoissonOnly</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssacl_8cpp_source.html#l00106">COMSSA::Run()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a0029addacfa8c89a9eb3e94df3dd6e63"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a0029addacfa8c89a9eb3e94df3dd6e63">◆ </a></span>SetRankScore()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> & <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::SetRankScore </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Sets the scoring to use rank statistics. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00790">790</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00604">CSearch< LEGACY, NHITS >::UseRankScore</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssacl_8cpp_source.html#l00106">COMSSA::Run()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a69c302b985e6fbbc4743cae6528b2459"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a69c302b985e6fbbc4743cae6528b2459">◆ </a></span>SetRequest()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSRequest.html">CMSRequest</a> > & <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::SetRequest </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Set search request. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00832">832</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00563">CSearch< LEGACY, NHITS >::MyRequest</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a2a7af7c803ecb9d836edee6a96bc0f66"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a2a7af7c803ecb9d836edee6a96bc0f66">◆ </a></span>SetResponse()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSResponse.html">CMSResponse</a> > & <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::SetResponse </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Set search response. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00844">844</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00568">CSearch< LEGACY, NHITS >::MyResponse</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>, <a class="el" href="omssa_8cpp_source.html#l01508">CSearch< LEGACY, NHITS >::SetResult()</a>, and <a class="el" href="omssa_8cpp_source.html#l01736">CSearch< LEGACY, NHITS >::WriteBioseqs()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a6725f89bb3ad2921ba45315d9c5fbbdb"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a6725f89bb3ad2921ba45315d9c5fbbdb">◆ </a></span>SetRestrictedSearch()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> & <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::SetRestrictedSearch </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>is this search restricted to the oid set? </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00874">874</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00624">CSearch< LEGACY, NHITS >::RestrictedSearch</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00921">CSearch< LEGACY, NHITS >::MakeOidSet()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a096b35d0875e07b62218b8ff95760d06"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a096b35d0875e07b62218b8ff95760d06">◆ </a></span>SetResult()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::SetResult </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSPeakSet.html">CMSPeakSet</a> > </td>
|
||
<td class="paramname"><em>PeakSet</em></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l01508">1508</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="ncbidbg_8hpp_source.html#l00122">_TRACE</a>, <a class="el" href="omssa_8cpp_source.html#l01465">CSearch< LEGACY, NHITS >::AddIonsToHit()</a>, <a class="el" href="omssa_8cpp_source.html#l01447">CSearch< LEGACY, NHITS >::AddModsToHit()</a>, <a class="el" href="map_8hpp_source.html#l00291">multimap_checker< Container >::begin()</a>, <a class="el" href="omssa_8cpp_source.html#l01889">CSearch< LEGACY, NHITS >::CalcNSort()</a>, <a class="el" href="map_8hpp_source.html#l00309">multimap_checker< Container >::clear()</a>, <a class="el" href="util_2debug_2set_8hpp_source.html#l00153">set< Key, Compare >::clear()</a>, <a class="el" href="omssa_8cpp_source.html#l01494">CSearch< LEGACY, NHITS >::CreateSequence()</a>, <a class="el" href="map_8hpp_source.html#l00289">multimap_checker< Container >::empty()</a>, <a class="el" href="MSHitError___8hpp_source.html#l00068">eMSHitError_notenuffpeaks</a>, <a class="el" href="map_8hpp_source.html#l00152">map_checker< Container >::end()</a>, <a class="el" href="map_8hpp_source.html#l00292">multimap_checker< Container >::end()</a>, <a class="el" href="ncbidiag_8hpp_source.html#l00186">ERR_POST</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l01197">Error()</a>, <a class="el" href="map_8hpp_source.html#l00153">map_checker< Container >::find()</a>, <a class="el" href="ncbiutil_8hpp_source.html#l00250">FindBestChoice()</a>, <a class="el" href="MSResponse_8cpp_source.html#l00148">CMSResponse::FindHitSet()</a>, <a class="el" href="ncbifloat_8h_source.html#l00103">finite</a>, <a class="el" href="Blast__def__line__set___8hpp_source.html#l00165">CBlast_def_line_set_Base::Get()</a>, <a class="el" href="style__manager_8cpp_source.html#l00563">GetCharge()</a>, <a class="el" href="msscore_8hpp_source.html#l00846">CMSSpectrumMatch::GetCharge()</a>, <a class="el" href="mspeak_8hpp_source.html#l01244">CMSPeak::GetError()</a>, <a class="el" href="msscore_8hpp_source.html#l00822">CMSSpectrumMatch::GetExpMass()</a>, <a class="el" href="seqdb_8cpp_source.html#l00418">CSeqDB::GetHdr()</a>, <a class="el" href="omssa_8hpp_source.html#l00814">CSearch< LEGACY, NHITS >::GetIterative()</a>, <a class="el" href="mspeak_8hpp_source.html#l01262">CMSPeak::GetName()</a>, <a class="el" href="mspeak_8hpp_source.html#l01274">CMSPeak::GetNumber()</a>, <a class="el" href="omssa_8hpp_source.html#l00868">CSearch< LEGACY, NHITS >::Getnumseq()</a>, <a class="el" href="mspeak_8hpp_source.html#l01403">CMSPeakSet::GetPeaks()</a>, <a class="el" href="ncbiobj_8hpp_source.html#l00998">CRef< C, Locker >::GetPointer()</a>, <a class="el" href="compartp_8cpp_source.html#l00100">GetSeqIdString()</a>, <a class="el" href="mspeak_8hpp_source.html#l00389">CMSHit::GetSeqIndex()</a>, <a class="el" href="omssa_8hpp_source.html#l00826">CSearch< LEGACY, NHITS >::GetSettings()</a>, <a class="el" href="mspeak_8hpp_source.html#l00365">CMSHit::GetStart()</a>, <a class="el" href="mspeak_8hpp_source.html#l00377">CMSHit::GetStop()</a>, <a class="el" href="msscore_8hpp_source.html#l00834">CMSSpectrumMatch::GetTheoreticalMass()</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l01185">Info()</a>, <a class="el" href="util_2debug_2set_8hpp_source.html#l00149">set< Key, Compare >::insert()</a>, <a class="el" href="ncbifloat_8h_source.html#l00092">isnan</a>, <a class="el" href="ncbiobj_8hpp_source.html#l00735">CRef< C, Locker >::IsNull()</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00815">ITERATE</a>, <a class="el" href="omssa_8hpp_source.html#l00083">kHighEval</a>, <a class="el" href="omssa_8cpp_source.html#l01483">CSearch< LEGACY, NHITS >::MakeModString()</a>, <a class="el" href="omssa_8hpp_source.html#l00546">CSearch< LEGACY, NHITS >::rdfp</a>, <a class="el" href="Seq__id_8hpp_source.html#l00772">CSeq_id::Score()</a>, <a class="el" href="MSPepHit___8hpp_source.html#l00696">CMSPepHit_Base::SetAccession()</a>, <a class="el" href="MSHits___8hpp_source.html#l00844">CMSHits_Base::SetCharge()</a>, <a class="el" href="MSResponse___8hpp_source.html#l00745">CMSResponse_Base::SetDbversion()</a>, <a class="el" href="MSPepHit___8hpp_source.html#l00743">CMSPepHit_Base::SetDefline()</a>, <a class="el" href="MSHits___8hpp_source.html#l00750">CMSHits_Base::SetEvalue()</a>, <a class="el" href="MSPepHit___8hpp_source.html#l00656">CMSPepHit_Base::SetGi()</a>, <a class="el" href="MSResponse___8hpp_source.html#l00472">CMSResponse_Base::SetHitsets()</a>, <a class="el" href="MSHits___8hpp_source.html#l00988">CMSHits_Base::SetMass()</a>, <a class="el" href="MSPepHit___8hpp_source.html#l00844">CMSPepHit_Base::SetOid()</a>, <a class="el" href="omssa_8hpp_source.html#l00856">CSearch< LEGACY, NHITS >::SetOidSet()</a>, <a class="el" href="MSHits___8hpp_source.html#l00881">CMSHits_Base::SetPephits()</a>, <a class="el" href="MSHits___8hpp_source.html#l01053">CMSHits_Base::SetPepstart()</a>, <a class="el" href="MSHits___8hpp_source.html#l01100">CMSHits_Base::SetPepstop()</a>, <a class="el" href="MSHits___8hpp_source.html#l00934">CMSHits_Base::SetPepstring()</a>, <a class="el" href="MSPepHit___8hpp_source.html#l00797">CMSPepHit_Base::SetProtlength()</a>, <a class="el" href="MSHits___8hpp_source.html#l00797">CMSHits_Base::SetPvalue()</a>, <a class="el" href="omssa_8hpp_source.html#l00844">CSearch< LEGACY, NHITS >::SetResponse()</a>, <a class="el" href="MSPepHit___8hpp_source.html#l00562">CMSPepHit_Base::SetStart()</a>, <a class="el" href="MSPepHit___8hpp_source.html#l00609">CMSPepHit_Base::SetStop()</a>, <a class="el" href="MSHits___8hpp_source.html#l01201">CMSHits_Base::SetTheomass()</a>, <a class="el" href="MSMod_8hpp_source.html#l00058">UniqueAA</a>, <a class="el" href="omssa_8hpp_source.html#l00604">CSearch< LEGACY, NHITS >::UseRankScore</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l01191">Warning()</a>, and <a class="el" href="omssa_8cpp_source.html#l01736">CSearch< LEGACY, NHITS >::WriteBioseqs()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="ab379f3355f0dc89c0d50ef135b59133a"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#ab379f3355f0dc89c0d50ef135b59133a">◆ </a></span>SetSettings()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSSearchSettings.html">CMSSearchSettings</a> > & <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::SetSettings </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Set search settings. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00820">820</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00573">CSearch< LEGACY, NHITS >::MySettings</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00441">CSearch< LEGACY, NHITS >::CreateLadders()</a>, <a class="el" href="omssa_8cpp_source.html#l00774">CSearch< LEGACY, NHITS >::CreateModCombinations()</a>, and <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="af30e25b14d759f030a00231ed6b22ce6"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#af30e25b14d759f030a00231ed6b22ce6">◆ </a></span>SetSubjInfo()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::SetSubjInfo </td>
|
||
<td>(</td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Set the parameters of the current subject sequence. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="dbindex__search_8cpp_source.html#l01382">1382</a> of file <a class="el" href="dbindex__search_8cpp_source.html">dbindex_search.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="dbindex__sp_8hpp_source.html#l00400">CDbIndex_Impl< LEGACY >::GetSubjectMap()</a>, <a class="el" href="dbindex__search_8cpp_source.html#l00952">CSearch_Base< LEGACY, NHITS, derived_t >::index_impl_</a>, <a class="el" href="dbindex_8hpp_source.html#l01164">CSubjectMap::SetSubjInfo()</a>, <a class="el" href="dbindex__search_8cpp_source.html#l00963">CSearch_Base< LEGACY, NHITS, derived_t >::subj_end_</a>, <a class="el" href="dbindex__search_8cpp_source.html#l00962">CSearch_Base< LEGACY, NHITS, derived_t >::subj_start_</a>, and <a class="el" href="dbindex__search_8cpp_source.html#l00958">CSearch_Base< LEGACY, NHITS, derived_t >::subject_</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="dbindex__search_8cpp_source.html#l01397">CSearch< LEGACY, NHITS >::DecodeOffset()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="aaa0a4ed9116b40d1867c12dce88d0dc4"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#aaa0a4ed9116b40d1867c12dce88d0dc4">◆ </a></span>SetupSearch()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::SetupSearch </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSRequest.html">CMSRequest</a> > </td>
|
||
<td class="paramname"><em>MyRequestIn</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSResponse.html">CMSResponse</a> > </td>
|
||
<td class="paramname"><em>MyResponseIn</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSModSpecSet.html">CMSModSpecSet</a> > </td>
|
||
<td class="paramname"><em>Modset</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSSearchSettings.html">CMSSearchSettings</a> > </td>
|
||
<td class="paramname"><em>SettingsIn</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="omssa_8hpp.html#a9ffe9cb00c8437193b4225feecd4ab36">TOMSSACallback</a> </td>
|
||
<td class="paramname"><em>Callback</em> = <code>0</code>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype">void * </td>
|
||
<td class="paramname"><em>CallbackData</em> = <code>0</code> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Setup the ms/ms search. </p>
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">MyRequestIn</td><td>the user search params and spectra </td></tr>
|
||
<tr><td class="paramname">MyResponseIn</td><td>the results of the search </td></tr>
|
||
<tr><td class="paramname">Modset</td><td>list of modifications </td></tr>
|
||
<tr><td class="paramname">SettingsIn</td><td>the search settings </td></tr>
|
||
<tr><td class="paramname">Callback</td><td>callback function for progress meter </td></tr>
|
||
<tr><td class="paramname">CallbackData</td><td>data passed back to callback fcn </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l00940">940</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="omssa_8hpp_source.html#l00644">CSearch< LEGACY, NHITS >::initCallback</a>, <a class="el" href="omssa_8hpp_source.html#l00645">CSearch< LEGACY, NHITS >::initCallbackData</a>, <a class="el" href="omssa_8hpp_source.html#l00642">CSearch< LEGACY, NHITS >::initModset</a>, <a class="el" href="omssa_8hpp_source.html#l00640">CSearch< LEGACY, NHITS >::initRequestIn</a>, <a class="el" href="omssa_8hpp_source.html#l00641">CSearch< LEGACY, NHITS >::initResponseIn</a>, and <a class="el" href="omssa_8hpp_source.html#l00643">CSearch< LEGACY, NHITS >::initSettingsIn</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssacl_8cpp_source.html#l00106">COMSSA::Run()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a2a897d5d32fb118ab2270b410cb1d309"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a2a897d5d32fb118ab2270b410cb1d309">◆ </a></span>Spectrum2Peak()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::Spectrum2Peak </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSPeakSet.html">CMSPeakSet</a> > </td>
|
||
<td class="paramname"><em>PeakSet</em></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l00564">564</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="mspeak_8hpp_source.html#l01391">CMSPeakSet::AddPeak()</a>, <a class="el" href="mspeak_8hpp_source.html#l00066">eMSPeakListCharge1</a>, <a class="el" href="MSSpectrumFileType___8hpp_source.html#l00064">eMSSpectrumFileType_dta</a>, <a class="el" href="ncbidiag_8hpp_source.html#l00186">ERR_POST</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l01197">Error()</a>, <a class="el" href="omssa_8hpp_source.html#l00814">CSearch< LEGACY, NHITS >::GetIterative()</a>, <a class="el" href="omssa_8hpp_source.html#l00838">CSearch< LEGACY, NHITS >::GetRequest()</a>, <a class="el" href="omssa_8hpp_source.html#l00826">CSearch< LEGACY, NHITS >::GetSettings()</a>, <a class="el" href="omssa_8hpp_source.html#l00599">CSearch< LEGACY, NHITS >::MaxMZ</a>, <a class="el" href="MSMod_8hpp_source.html#l00064">MSSCALE2INT</a>, <a class="el" href="omssa_8cpp_source.html#l00557">PositiveSign()</a>, <a class="el" href="mspeak_8cpp_source.html#l00548">CMSPeak::ReadAndProcess()</a>, <a class="el" href="omssa_8cpp_source.html#l00541">CSearch< LEGACY, NHITS >::ReSearch()</a>, <a class="el" href="mspeak_8cpp_source.html#l01253">CMSPeakSet::SortPeaks()</a>, <a class="el" href="chainer_8hpp_source.html#l00086">transform()</a>, and <a class="el" href="mspeak_8cpp_source.html#l00757">CMSPeak::Write()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a637f77ccd43f042285819109df4b4aa0"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a637f77ccd43f042285819109df4b4aa0">◆ </a></span>TestPersist()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::TestPersist </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00219">219</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a0fcf525f5779fa355036968974bf0716"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a0fcf525f5779fa355036968974bf0716">◆ </a></span>UpdateWithNewPep()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::UpdateWithNewPep </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>Missed</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> char * </td>
|
||
<td class="paramname"><em>PepStart</em>[], </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> char * </td>
|
||
<td class="paramname"><em>PepEnd</em>[], </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>NumMod</em>[], </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCMod.html">CMod</a> </td>
|
||
<td class="paramname"><em>ModList</em>[][32], </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>Masses</em>[], </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>EndMasses</em>[], </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>NumModSites</em>[], </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSModSpecSet.html">CMSModSpecSet</a> > & </td>
|
||
<td class="paramname"><em>Modset</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>update sites and masses for new peptide </p>
|
||
<dl class="params"><dt>Parameters</dt><dd>
|
||
<table class="params">
|
||
<tr><td class="paramname">Missed</td><td>how many missed cleavages </td></tr>
|
||
<tr><td class="paramname">PepStart</td><td>array of peptide starts </td></tr>
|
||
<tr><td class="paramname">PepEnd</td><td>array of peptide ends </td></tr>
|
||
<tr><td class="paramname">NumMod</td><td>array of the number of mods </td></tr>
|
||
<tr><td class="paramname">ModList</td><td>modification info </td></tr>
|
||
<tr><td class="paramname">Masses</td><td>peptide masses </td></tr>
|
||
<tr><td class="paramname">EndMasses</td><td>peptide end masses </td></tr>
|
||
<tr><td class="paramname">NumModSites</td><td>array of number of unfixed mod sites </td></tr>
|
||
<tr><td class="paramname">Modset</td><td>modification specifications </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l00663">663</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="MSModType___8hpp_source.html#l00066">eMSModType_modn</a>, <a class="el" href="MSModType___8hpp_source.html#l00067">eMSModType_modnaa</a>, <a class="el" href="MSModType___8hpp_source.html#l00070">eMSModType_modnp</a>, <a class="el" href="MSModType___8hpp_source.html#l00071">eMSModType_modnpaa</a>, <a class="el" href="MSModSpecSet_8hpp_source.html#l00230">CMSModSpecSet::GetModType()</a>, and <a class="el" href="omssa_8hpp_source.html#l00075">MAXMOD</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a4a3fb267ab67ccd78b2b3a7200c3821a"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a4a3fb267ab67ccd78b2b3a7200c3821a">◆ </a></span>WriteBioseqs()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::WriteBioseqs </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>write oidset to result </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8cpp_source.html#l01736">1736</a> of file <a class="el" href="omssa_8cpp_source.html">omssa.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="seqdb_8cpp_source.html#l00504">CSeqDB::GetBioseq()</a>, <a class="el" href="omssa_8hpp_source.html#l00862">CSearch< LEGACY, NHITS >::GetOidSet()</a>, <a class="el" href="ncbiobj_8hpp_source.html#l01401">CConstRef< C, Locker >::IsNull()</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00815">ITERATE</a>, <a class="el" href="omssa_8hpp_source.html#l00546">CSearch< LEGACY, NHITS >::rdfp</a>, <a class="el" href="MSResponse___8cpp_source.html#l00081">CMSResponse_Base::SetBioseqs()</a>, and <a class="el" href="omssa_8hpp_source.html#l00844">CSearch< LEGACY, NHITS >::SetResponse()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l01508">CSearch< LEGACY, NHITS >::SetResult()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<h2 class="groupheader">Member Data Documentation</h2>
|
||
<a id="ae47c14b250cb7077ae9decda48af2241"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#ae47c14b250cb7077ae9decda48af2241">◆ </a></span>Enzyme</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCRef.html">CRef</a><<a class="el" href="classCCleave.html">CCleave</a>> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::Enzyme</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>the enzyme in use </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00558">558</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8hpp_source.html#l00892">CSearch< LEGACY, NHITS >::GetEnzyme()</a>, and <a class="el" href="omssa_8hpp_source.html#l00886">CSearch< LEGACY, NHITS >::SetEnzyme()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a24b7d56cbbdb8c42bf07dbf04503f5ce"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a24b7d56cbbdb8c42bf07dbf04503f5ce">◆ </a></span>FixedMods</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCMSMod.html">CMSMod</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::FixedMods</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00552">552</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="ac5691dd992ecd2ba66b70bb5dcd0400a"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#ac5691dd992ecd2ba66b70bb5dcd0400a">◆ </a></span>initCallback</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="omssa_8hpp.html#a9ffe9cb00c8437193b4225feecd4ab36">TOMSSACallback</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::initCallback</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00644">644</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00970">CSearch< LEGACY, NHITS >::CopySettings()</a>, <a class="el" href="omssa_8cpp_source.html#l00955">CSearch< LEGACY, NHITS >::Main()</a>, and <a class="el" href="omssa_8cpp_source.html#l00940">CSearch< LEGACY, NHITS >::SetupSearch()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a248ca093d4fee44de262991748eb7f29"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a248ca093d4fee44de262991748eb7f29">◆ </a></span>initCallbackData</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void* <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::initCallbackData</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00645">645</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00970">CSearch< LEGACY, NHITS >::CopySettings()</a>, and <a class="el" href="omssa_8cpp_source.html#l00940">CSearch< LEGACY, NHITS >::SetupSearch()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="abae51d52a2c56983a8b0b4bb81b99911"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#abae51d52a2c56983a8b0b4bb81b99911">◆ </a></span>initModset</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCRef.html">CRef</a><<a class="el" href="classCMSModSpecSet.html">CMSModSpecSet</a>> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::initModset</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00642">642</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00970">CSearch< LEGACY, NHITS >::CopySettings()</a>, <a class="el" href="omssa_8cpp_source.html#l00955">CSearch< LEGACY, NHITS >::Main()</a>, and <a class="el" href="omssa_8cpp_source.html#l00940">CSearch< LEGACY, NHITS >::SetupSearch()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="acb77a8653cb9a52ddeea8705e01a4008"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#acb77a8653cb9a52ddeea8705e01a4008">◆ </a></span>initRequestIn</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCRef.html">CRef</a><<a class="el" href="classCMSRequest.html">CMSRequest</a>> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::initRequestIn</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>These are so <a class="el" href="classCSearch.html#ab0dec8be370a16f7736e36c07841b3f5" title="Derived (user-created) class must provide a real thread function.">CSearch::Main()</a> can call <a class="el" href="classCSearch.html#a5e985bb7e8acd2e85be9e4fe2ee023e6" title="Performs the ms/ms search.">CSearch::Search()</a> in a threaded run, this requires <a class="el" href="classCSearch.html#aaa0a4ed9116b40d1867c12dce88d0dc4" title="Setup the ms/ms search.">CSearch::SetupSearch()</a> to be called before <a class="el" href="group__Threads.html#ga1ca598d60e42a600f8f323c25792042d" title="Run the thread.">CSearch::Run()</a> </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00640">640</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00970">CSearch< LEGACY, NHITS >::CopySettings()</a>, <a class="el" href="omssa_8cpp_source.html#l00955">CSearch< LEGACY, NHITS >::Main()</a>, and <a class="el" href="omssa_8cpp_source.html#l00940">CSearch< LEGACY, NHITS >::SetupSearch()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="acce6930b2a7bb24c985dc05e60ec675f"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#acce6930b2a7bb24c985dc05e60ec675f">◆ </a></span>initResponseIn</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCRef.html">CRef</a><<a class="el" href="classCMSResponse.html">CMSResponse</a>> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::initResponseIn</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00641">641</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00970">CSearch< LEGACY, NHITS >::CopySettings()</a>, <a class="el" href="omssa_8cpp_source.html#l00955">CSearch< LEGACY, NHITS >::Main()</a>, and <a class="el" href="omssa_8cpp_source.html#l00940">CSearch< LEGACY, NHITS >::SetupSearch()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="af02b5bd6ad91d53341002b4a58d34c71"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#af02b5bd6ad91d53341002b4a58d34c71">◆ </a></span>initSettingsIn</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCRef.html">CRef</a><<a class="el" href="classCMSSearchSettings.html">CMSSearchSettings</a>> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::initSettingsIn</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00643">643</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00970">CSearch< LEGACY, NHITS >::CopySettings()</a>, <a class="el" href="omssa_8cpp_source.html#l00955">CSearch< LEGACY, NHITS >::Main()</a>, and <a class="el" href="omssa_8cpp_source.html#l00940">CSearch< LEGACY, NHITS >::SetupSearch()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a89577321dfd5c014198677bace51721b"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a89577321dfd5c014198677bace51721b">◆ </a></span>iSearchGlobal</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::iSearchGlobal = -1</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">static</span><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Tracks the iSearch number for all search threads. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00629">629</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00421">CSearch< LEGACY, NHITS >::ResetGlobals()</a>, and <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="ad27ca236cef55eb917f2db86314cc03b"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#ad27ca236cef55eb917f2db86314cc03b">◆ </a></span>Iterative</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::Iterative</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>boolean to turn on iterative search </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00614">614</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00970">CSearch< LEGACY, NHITS >::CopySettings()</a>, <a class="el" href="omssa_8hpp_source.html#l00814">CSearch< LEGACY, NHITS >::GetIterative()</a>, and <a class="el" href="omssa_8hpp_source.html#l00808">CSearch< LEGACY, NHITS >::SetIterative()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a13ca726f5c0b48c3291baa3f6f238938"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a13ca726f5c0b48c3291baa3f6f238938">◆ </a></span>LadderCalc</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classAutoPtr.html">AutoPtr</a><<a class="el" href="group__Portability.html#gad571e821cdf5dcc936b6beb906ad5a89">Int1</a>, <a class="el" href="structArrayDeleter.html">ArrayDeleter</a><<a class="el" href="group__Portability.html#gad571e821cdf5dcc936b6beb906ad5a89">Int1</a>> > <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::LadderCalc</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>bool array that indicates if the ladders been calculated </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00583">583</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8hpp_source.html#l00778">CSearch< LEGACY, NHITS >::ClearLadderCalc()</a>, <a class="el" href="omssa_8hpp_source.html#l00766">CSearch< LEGACY, NHITS >::GetLadderCalc()</a>, <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>, and <a class="el" href="omssa_8hpp_source.html#l00772">CSearch< LEGACY, NHITS >::SetLadderCalc()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a4238c214c7d1bb8e81e8634bfa534c5e"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a4238c214c7d1bb8e81e8634bfa534c5e">◆ </a></span>LadderContainer</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCLadderContainer.html">CLadderContainer</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::LadderContainer</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>ion series mass ladders </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00578">578</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8hpp_source.html#l00906">CSearch< LEGACY, NHITS >::GetLadderContainer()</a>, and <a class="el" href="omssa_8hpp_source.html#l00899">CSearch< LEGACY, NHITS >::SetLadderContainer()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="ad2b1eb3f9075259665bb7deeae57e569"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#ad2b1eb3f9075259665bb7deeae57e569">◆ </a></span>MassAndMask</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classAutoPtr.html">AutoPtr</a><<a class="el" href="omssa_8hpp.html#a5742ee0bc8e594f879b5d020791738e4">TMassMask</a>, <a class="el" href="structArrayDeleter.html">ArrayDeleter</a><<a class="el" href="omssa_8hpp.html#a5742ee0bc8e594f879b5d020791738e4">TMassMask</a>> > <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::MassAndMask</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>contains bit mask of modifications and resulting mass </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00588">588</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00774">CSearch< LEGACY, NHITS >::CreateModCombinations()</a>, <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>, and <a class="el" href="omssa_8hpp_source.html#l00784">CSearch< LEGACY, NHITS >::SetMassAndMask()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a9892817bbb790af0da11bd9241796671"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a9892817bbb790af0da11bd9241796671">◆ </a></span>MassArray</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCMassArray.html">CMassArray</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::MassArray</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00549">549</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00441">CSearch< LEGACY, NHITS >::CreateLadders()</a>, and <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="ad1185583f34e88e1133cfe4223f22f6b"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#ad1185583f34e88e1133cfe4223f22f6b">◆ </a></span>MaxModPerPep</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::MaxModPerPep</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>maximum number of mod combinations per peptide </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00593">593</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00774">CSearch< LEGACY, NHITS >::CreateModCombinations()</a>, <a class="el" href="omssa_8cpp_source.html#l00901">CSearch< LEGACY, NHITS >::InitLadders()</a>, <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>, and <a class="el" href="omssa_8hpp_source.html#l00784">CSearch< LEGACY, NHITS >::SetMassAndMask()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="ada7e1d377c5d3784986c7875c273c8e6"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#ada7e1d377c5d3784986c7875c273c8e6">◆ </a></span>MaxMZ</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::MaxMZ = 0</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">static</span><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>maximum m/z value of all spectra precursors used to bound non-specific cleavage searches </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00599">599</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00421">CSearch< LEGACY, NHITS >::ResetGlobals()</a>, <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>, and <a class="el" href="omssa_8cpp_source.html#l00564">CSearch< LEGACY, NHITS >::Spectrum2Peak()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a5bc469e9ba6a7a2a11594be2527a8625"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a5bc469e9ba6a7a2a11594be2527a8625">◆ </a></span>MyRequest</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCRef.html">CRef</a><<a class="el" href="classCMSRequest.html">CMSRequest</a>> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::MyRequest</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Search request. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00563">563</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8hpp_source.html#l00838">CSearch< LEGACY, NHITS >::GetRequest()</a>, and <a class="el" href="omssa_8hpp_source.html#l00832">CSearch< LEGACY, NHITS >::SetRequest()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a2a26cd46bb4c00b9cf72d9b05e2914f7"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a2a26cd46bb4c00b9cf72d9b05e2914f7">◆ </a></span>MyResponse</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCRef.html">CRef</a><<a class="el" href="classCMSResponse.html">CMSResponse</a>> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::MyResponse</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Search response. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00568">568</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8hpp_source.html#l00850">CSearch< LEGACY, NHITS >::GetResponse()</a>, and <a class="el" href="omssa_8hpp_source.html#l00844">CSearch< LEGACY, NHITS >::SetResponse()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a13a8f4a3aac7c6ae47d3dcfe25037277"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a13a8f4a3aac7c6ae47d3dcfe25037277">◆ </a></span>MySettings</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCRef.html">CRef</a><<a class="el" href="classCMSSearchSettings.html">CMSSearchSettings</a>> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::MySettings</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Search params. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00573">573</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8hpp_source.html#l00826">CSearch< LEGACY, NHITS >::GetSettings()</a>, and <a class="el" href="omssa_8hpp_source.html#l00820">CSearch< LEGACY, NHITS >::SetSettings()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="aca9cf28f5058578a38dabcff76d34d8f"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#aca9cf28f5058578a38dabcff76d34d8f">◆ </a></span>numseq</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::numseq</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00553">553</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00970">CSearch< LEGACY, NHITS >::CopySettings()</a>, <a class="el" href="omssa_8hpp_source.html#l00868">CSearch< LEGACY, NHITS >::Getnumseq()</a>, and <a class="el" href="omssa_8cpp_source.html#l00429">CSearch< LEGACY, NHITS >::InitBlast()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="ab1e50c269b23c2f0c24b14ac3e5dc5a0"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#ab1e50c269b23c2f0c24b14ac3e5dc5a0">◆ </a></span>OidSet</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCMSResponse.html#a10ac4d245cf91be83306cac7793a6377">CMSResponse::TOidSet</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::OidSet</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>set of oids to be searched </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00619">619</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8hpp_source.html#l00862">CSearch< LEGACY, NHITS >::GetOidSet()</a>, and <a class="el" href="omssa_8hpp_source.html#l00856">CSearch< LEGACY, NHITS >::SetOidSet()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="aefe0651422bf8bc0e153fac971e9c5ff"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#aefe0651422bf8bc0e153fac971e9c5ff">◆ </a></span>PoissonOnly</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::PoissonOnly</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>boolean to only use Poisson score when using Rank scoring </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00609">609</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8hpp_source.html#l00802">CSearch< LEGACY, NHITS >::GetPoissonOnly()</a>, and <a class="el" href="omssa_8hpp_source.html#l00796">CSearch< LEGACY, NHITS >::SetPoissonOnly()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a61e60b0813859840f39f0e52dd6623cb"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a61e60b0813859840f39f0e52dd6623cb">◆ </a></span>PrecursorMassArray</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCMassArray.html">CMassArray</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::PrecursorMassArray</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00550">550</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a3126e8c4cf573f6b13d90d915a7edeba"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a3126e8c4cf573f6b13d90d915a7edeba">◆ </a></span>rdfp</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCRef.html">CRef</a><<a class="el" href="classCSeqDB.html">CSeqDB</a>> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::rdfp</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>blast library </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00546">546</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00970">CSearch< LEGACY, NHITS >::CopySettings()</a>, <a class="el" href="omssa_8cpp_source.html#l00429">CSearch< LEGACY, NHITS >::InitBlast()</a>, <a class="el" href="omssa_8cpp_source.html#l01750">CSearch< LEGACY, NHITS >::PepCharge()</a>, <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>, <a class="el" href="omssa_8cpp_source.html#l01508">CSearch< LEGACY, NHITS >::SetResult()</a>, and <a class="el" href="omssa_8cpp_source.html#l01736">CSearch< LEGACY, NHITS >::WriteBioseqs()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a2fae93f4e2894bd3f235dad32423142b"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a2fae93f4e2894bd3f235dad32423142b">◆ </a></span>RestrictedSearch</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::RestrictedSearch</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>is this a oid restricted search </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00624">624</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8hpp_source.html#l00880">CSearch< LEGACY, NHITS >::GetRestrictedSearch()</a>, and <a class="el" href="omssa_8hpp_source.html#l00874">CSearch< LEGACY, NHITS >::SetRestrictedSearch()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="adb2d68ee893f402a1f1520a25ada487b"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#adb2d68ee893f402a1f1520a25ada487b">◆ </a></span>SharedPeakSet</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCMSPeakSet.html">CMSPeakSet</a> > <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::SharedPeakSet = <a class="el" href="group__AppFramework.html#ggae62facd370a837a6e56086869977621baf9a713ed26dee661a259730e650987e4">null</a></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">static</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00225">225</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00421">CSearch< LEGACY, NHITS >::ResetGlobals()</a>, and <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="af445799f8029ab8f8a942ab78cd8fb6c"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#af445799f8029ab8f8a942ab78cd8fb6c">◆ </a></span>ThreadNum</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::ThreadNum</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>The threadid number. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00634">634</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00412">CSearch< LEGACY, NHITS >::CSearch()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a3211ebae8e111217dffc840eb0d90c6d"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a3211ebae8e111217dffc840eb0d90c6d">◆ </a></span>UseRankScore</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::UseRankScore</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>boolean to turn on rank scoring </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00604">604</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l01889">CSearch< LEGACY, NHITS >::CalcNSort()</a>, <a class="el" href="omssa_8cpp_source.html#l00970">CSearch< LEGACY, NHITS >::CopySettings()</a>, <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>, <a class="el" href="omssa_8hpp_source.html#l00790">CSearch< LEGACY, NHITS >::SetRankScore()</a>, and <a class="el" href="omssa_8cpp_source.html#l01508">CSearch< LEGACY, NHITS >::SetResult()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a069bdebe654ad56719d67336a347ac69"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a069bdebe654ad56719d67336a347ac69">◆ </a></span>VariableMods</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<div class="memtemplate">
|
||
template<bool LEGACY, unsigned long NHITS> </div>
|
||
<table class="mlabels">
|
||
<tr>
|
||
<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="classCMSMod.html">CMSMod</a> <a class="el" href="classCSearch.html">CSearch</a>< LEGACY, NHITS >::VariableMods</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="omssa_8hpp_source.html#l00551">551</a> of file <a class="el" href="omssa_8hpp_source.html">omssa.hpp</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="omssa_8cpp_source.html#l00985">CSearch< LEGACY, NHITS >::Search()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<hr/>The documentation for this class was generated from the following files:<ul>
|
||
<li>include/objects/blastxml2/<a class="el" href="Search_8hpp_source.html">Search.hpp</a></li>
|
||
<li>src/algo/blast/dbindex/<a class="el" href="dbindex__search_8cpp_source.html">dbindex_search.cpp</a></li>
|
||
<li>src/algo/ms/omssa/<a class="el" href="omssa_8hpp_source.html">omssa.hpp</a></li>
|
||
<li>src/algo/ms/omssa/<a class="el" href="omssa_8cpp_source.html">omssa.cpp</a></li>
|
||
<li>src/objects/blastxml2/<a class="el" href="Search_8cpp_source.html">Search.cpp</a></li>
|
||
</ul>
|
||
</div><!-- contents -->
|
||
<!-- start footer part -->
|
||
<hr class="footer"/><address class="footer"><small>
|
||
Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.9.0
|
||
</small></address>
|
||
<address style="align: right;"><small>Modified on Fri Sep 20 14:56:58 2024 by modify_doxy.py rev. 669887</small></address>
|
||
</body>
|
||
</html>
|