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2778 lines
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<meta name="generator" content="Doxygen 1.9.0"/>
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<title>NCBI C++ ToolKit: CSeq_align Class Reference</title>
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<link href="tabs.css" rel="stylesheet" type="text/css"/>
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<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
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<div id="titlearea">
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<table cellspacing="0" cellpadding="0">
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<tbody>
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<tr style="height: 56px;">
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<td id="projectalign" style="padding-left: 0.5em;">
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<div id="projectname">NCBI C++ ToolKit
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</div>
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</td>
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</tr>
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</tbody>
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/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&dn=gpl-2.0.txt GPL-v2 */
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$(function() {
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initMenu('',true,true,'/toolkit/','Search');
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/* @license-end */</script>
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<div id="main-nav"></div>
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</div><!-- top -->
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<div class="header">
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<div class="summary">
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<a href="#nested-classes">Classes</a> |
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<a href="#pub-types">Public Types</a> |
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<a href="#pub-methods">Public Member Functions</a> |
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<a href="#pub-static-methods">Static Public Member Functions</a> |
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<a href="#pro-methods">Protected Member Functions</a> |
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<a href="#pri-types">Private Types</a> |
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<a href="#pri-methods">Private Member Functions</a> |
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<a href="classCSeq__align-members.html">List of all members</a> </div>
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<div class="headertitle">
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<div class="title">CSeq_align Class Reference</div> </div>
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</div><!--header-->
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<div class="contents">
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<p>
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<a class="el" href = "https://www.ncbi.nlm.nih.gov/toolkitbookgh/?term=CSeq_align">Search Toolkit Book for <i>CSeq_align</i></a>
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</p>
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<p><code>#include <<a class="el" href="Seq__align_8hpp_source.html">objects/seqalign/Seq_align.hpp</a>></code></p>
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<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
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<img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for CSeq_align:</div>
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<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
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</div>
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<div id="dynsection-0-content" class="dyncontent" style="display:none;">
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<div class="center"><img src="img__inherit__graph/classCSeq__align__inherit__graph.png" border="0" usemap="#aCSeq__align_inherit__map" alt="Inheritance graph"/></div>
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<map name="aCSeq__align_inherit__map" id="aCSeq__align_inherit__map">
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<area shape="rect" title=" " alt="" coords="25,304,115,331"/>
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<area shape="rect" href="classCSeq__align__Base.html" title="CSeq_align_Base –." alt="" coords="7,229,133,256"/>
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<area shape="rect" href="classCSerialObject.html" title="Base class for all serializable objects." alt="" coords="19,155,121,181"/>
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<area shape="rect" href="classCObject.html" title="CObject –." alt="" coords="35,80,105,107"/>
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</map>
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<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center></div>
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<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
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<img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for CSeq_align:</div>
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<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
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</div>
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<div id="dynsection-1-content" class="dyncontent" style="display:none;">
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<div class="center"><img src="img__coll__graph/classCSeq__align__coll__graph.png" border="0" usemap="#aCSeq__align_coll__map" alt="Collaboration graph"/></div>
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<map name="aCSeq__align_coll__map" id="aCSeq__align_coll__map">
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<area shape="rect" title=" " alt="" coords="104,573,193,600"/>
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<area shape="rect" href="classCSeq__align__Base.html" title="CSeq_align_Base –." alt="" coords="85,497,212,524"/>
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<area shape="rect" href="classCSerialObject.html" title="Base class for all serializable objects." alt="" coords="19,401,121,427"/>
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<area shape="rect" href="classCObject.html" title="CObject –." alt="" coords="35,289,105,316"/>
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<area shape="rect" href="classCDebugDumpable.html" title=" " alt="" coords="5,193,135,219"/>
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<area shape="rect" href="classCRef.html" title=" " alt="" coords="145,393,315,435"/>
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<area shape="rect" href="classpair__base__member.html" title=" " alt="" coords="199,185,378,227"/>
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<area shape="rect" href="classCRef.html" title="CRef –." alt="" coords="275,289,409,316"/>
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<area shape="rect" title=" " alt="" coords="193,89,283,115"/>
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<area shape="rect" title=" " alt="" coords="371,5,423,32"/>
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</map>
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<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center></div>
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<table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
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Classes</h2></td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structCSeq__align_1_1SIndel.html">SIndel</a></td></tr>
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<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structCSeq__align_1_1SSeqIdChooser.html">SSeqIdChooser</a></td></tr>
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<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Create a Dense-seg from a Std-seg Used by AlnMgr to handle nucl2prot alignments. <a href="structCSeq__align_1_1SSeqIdChooser.html#details">More...</a><br /></td></tr>
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<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
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</table><table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
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Public Types</h2></td></tr>
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<tr class="memitem:a0a7501fd78111aeea55afdf681847c01"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">EScoreType</a> { <br />
|
||
  <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01a9cde7240e546570379c51fce0d2fdc07">eScore_Score</a>
|
||
, <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01a81436b76d980c991533ea073df6595ac">eScore_Blast</a>
|
||
, <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01aa78693920055c96636e6eb8382547bd2">eScore_BitScore</a>
|
||
, <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01a8e7cb4abab8e31d273ab7ac7cebe904f">eScore_EValue</a>
|
||
, <br />
|
||
  <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01a8b206034192680e97bec91a259fa2e66">eScore_AlignLength</a>
|
||
, <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01aebeed46a10702323f38954054bf2d75d">eScore_IdentityCount</a>
|
||
, <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01ad014ecd153a9d12cd7d4bcd729ef6f99">eScore_PositiveCount</a>
|
||
, <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01aa82e92f460d31775cbaedf2601241f0a">eScore_NegativeCount</a>
|
||
, <br />
|
||
  <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01afedb2a5a1a642865bc91d97ae7cc115b">eScore_MismatchCount</a>
|
||
, <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01a0e2e5d80919920444278e60f374adf03">eScore_GapCount</a>
|
||
, <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01a1dac2a7e5759c0c4e0f4006794beb216">eScore_PercentIdentity_Gapped</a>
|
||
, <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01aa2d67a9fda6e715efc9880152d362dfe">eScore_PercentIdentity_Ungapped</a>
|
||
, <br />
|
||
  <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01a1c87d321a8d2c8f6f67e63deab8e6cfc">eScore_PercentIdentity_GapOpeningOnly</a>
|
||
, <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01ad4f7605cad81bd97a04504a4c63fbd27">eScore_PercentCoverage</a>
|
||
, <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01a8685247b6667ac4a0eda08c5d6ea24d9">eScore_SumEValue</a>
|
||
, <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01aea89e39c3219df67ffdc6afdd53e657f">eScore_CompAdjMethod</a>
|
||
, <br />
|
||
  <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01adb8117f24d2dfa30ec95a8348b350a57">eScore_HighQualityPercentCoverage</a>
|
||
, <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01afcb9e5d9011e7b58357044c2eb9457c6">eScore_Matches</a>
|
||
, <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01a3db9aec8bf5278e428a88c0908963ad0">eScore_OverallIdentity</a>
|
||
, <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01ae9ca67a00f22300eea1b4711626d3cb7">eScore_Splices</a>
|
||
, <br />
|
||
  <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01a316a91ecb5510dbf7db981d470bb0a18">eScore_ConsensusSplices</a>
|
||
, <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01ae85897f7a9a6dc10da39bc906fb151b5">eScore_ProductCoverage</a>
|
||
, <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01acaa810a22045f0235fc0ec9d9ac76b59">eScore_ExonIdentity</a>
|
||
, <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01afadc41286b7a24bcb46403235ee3fd0a">eScore_PercentIdentity</a> = eScore_PercentIdentity_Gapped
|
||
<br />
|
||
}</td></tr>
|
||
<tr class="memdesc:a0a7501fd78111aeea55afdf681847c01"><td class="mdescLeft"> </td><td class="mdescRight">enum controlling known named scores <a href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">More...</a><br /></td></tr>
|
||
<tr class="separator:a0a7501fd78111aeea55afdf681847c01"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:ae8447af5653b27fa09d886821029a4c7"><td class="memItemLeft" align="right" valign="top">typedef pair< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a>, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#ae8447af5653b27fa09d886821029a4c7">TLengthRange</a></td></tr>
|
||
<tr class="separator:ae8447af5653b27fa09d886821029a4c7"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:a59b599d4d23745a6ff33afb1bcbf0417"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classmap.html">map</a>< <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a>, <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">EScoreType</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a59b599d4d23745a6ff33afb1bcbf0417">TScoreNameMap</a></td></tr>
|
||
<tr class="separator:a59b599d4d23745a6ff33afb1bcbf0417"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="inherit_header pub_types_classCSeq__align__Base"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classCSeq__align__Base')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="classCSeq__align__Base.html">CSeq_align_Base</a></td></tr>
|
||
<tr class="memitem:gac180c46e798d862f504865299b627f3b inherit pub_types_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#gac180c46e798d862f504865299b627f3b">EType</a> { <br />
|
||
  <a class="el" href="group__dataspec__NCBI__Seqalign.html#ggac180c46e798d862f504865299b627f3bafedcafc96a3eeeb32f16d5297747b740">eType_not_set</a> = 0
|
||
, <a class="el" href="group__dataspec__NCBI__Seqalign.html#ggac180c46e798d862f504865299b627f3baa8cdfe71cb8414809ff25418f197ff21">eType_global</a> = 1
|
||
, <a class="el" href="group__dataspec__NCBI__Seqalign.html#ggac180c46e798d862f504865299b627f3ba919b0c5d525642ca0e35d400f15ea084">eType_diags</a> = 2
|
||
, <a class="el" href="group__dataspec__NCBI__Seqalign.html#ggac180c46e798d862f504865299b627f3ba104823bc3212b44749897e915e361dcc">eType_partial</a> = 3
|
||
, <br />
|
||
  <a class="el" href="group__dataspec__NCBI__Seqalign.html#ggac180c46e798d862f504865299b627f3babb20e653dae63280a1589eacc7ebeeba">eType_disc</a> = 4
|
||
, <a class="el" href="group__dataspec__NCBI__Seqalign.html#ggac180c46e798d862f504865299b627f3ba39197272e248ea03ce44c50a586e3780">eType_other</a> = 255
|
||
<br />
|
||
}</td></tr>
|
||
<tr class="separator:gac180c46e798d862f504865299b627f3b inherit pub_types_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga96c37ea021b33766f9eb2d76dd12d1ca inherit pub_types_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top">enum class  </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga96c37ea021b33766f9eb2d76dd12d1ca">E_memberIndex</a> { <br />
|
||
  <a class="el" href="group__dataspec__NCBI__Seqalign.html#gga96c37ea021b33766f9eb2d76dd12d1caad2c4d82f7037e318e1aa6f58d06bd153">e__allMandatory</a> = 0
|
||
, <a class="el" href="group__dataspec__NCBI__Seqalign.html#gga96c37ea021b33766f9eb2d76dd12d1caad7a4adc15efe8d9eb513672c61274a25">e_type</a>
|
||
, <a class="el" href="group__dataspec__NCBI__Seqalign.html#gga96c37ea021b33766f9eb2d76dd12d1caa45275be29706b9877c6a4ebff91ec126">e_dim</a>
|
||
, <a class="el" href="group__dataspec__NCBI__Seqalign.html#gga96c37ea021b33766f9eb2d76dd12d1caacdb2436e3dc2499a4dd53fb68df17d9c">e_score</a>
|
||
, <br />
|
||
  <a class="el" href="group__dataspec__NCBI__Seqalign.html#gga96c37ea021b33766f9eb2d76dd12d1caa39eacff1918e61cca4dd48f23f93891f">e_segs</a>
|
||
, <a class="el" href="group__dataspec__NCBI__Seqalign.html#gga96c37ea021b33766f9eb2d76dd12d1caa50a0f78e0b9c701f8eb146ccde317ece">e_bounds</a>
|
||
, <a class="el" href="group__dataspec__NCBI__Seqalign.html#gga96c37ea021b33766f9eb2d76dd12d1caa71d0735f755f8f34960e4a40ab86a368">e_id</a>
|
||
, <a class="el" href="group__dataspec__NCBI__Seqalign.html#gga96c37ea021b33766f9eb2d76dd12d1caa01c3adbb514070ea7b63bec93d63fd2e">e_ext</a>
|
||
<br />
|
||
}</td></tr>
|
||
<tr class="separator:ga96c37ea021b33766f9eb2d76dd12d1ca inherit pub_types_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga9e03b4ccdbe94fe477e133b8933f7fda inherit pub_types_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="group__dataspec__NCBI__Seqalign.html#gac180c46e798d862f504865299b627f3b">EType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga9e03b4ccdbe94fe477e133b8933f7fda">TType</a></td></tr>
|
||
<tr class="separator:ga9e03b4ccdbe94fe477e133b8933f7fda inherit pub_types_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga54ad0aeb1e6312f218c88b223d3b7890 inherit pub_types_classCSeq__align__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__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a></td></tr>
|
||
<tr class="separator:ga54ad0aeb1e6312f218c88b223d3b7890 inherit pub_types_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga31490879f6caded03bb483742739611f inherit pub_types_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top">typedef vector< <a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCScore.html">CScore</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga31490879f6caded03bb483742739611f">TScore</a></td></tr>
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<tr class="separator:ga31490879f6caded03bb483742739611f inherit pub_types_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga8389ef87dff253dde4df333567562e19 inherit pub_types_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCSeq__align__Base_1_1C__Segs.html">C_Segs</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga8389ef87dff253dde4df333567562e19">TSegs</a></td></tr>
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||
<tr class="separator:ga8389ef87dff253dde4df333567562e19 inherit pub_types_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga8b1d61f3811d85be053524abb0e963d3 inherit pub_types_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top">typedef list< <a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCSeq__loc.html">CSeq_loc</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga8b1d61f3811d85be053524abb0e963d3">TBounds</a></td></tr>
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||
<tr class="separator:ga8b1d61f3811d85be053524abb0e963d3 inherit pub_types_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:ga72648ee97d4103c54633f45cb6fb9537 inherit pub_types_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top">typedef list< <a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCObject__id.html">CObject_id</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga72648ee97d4103c54633f45cb6fb9537">TId</a></td></tr>
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||
<tr class="separator:ga72648ee97d4103c54633f45cb6fb9537 inherit pub_types_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:ga73cb7c9e275783e84681fbc2a320b850 inherit pub_types_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top">typedef list< <a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCUser__object.html">CUser_object</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga73cb7c9e275783e84681fbc2a320b850">TExt</a></td></tr>
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||
<tr class="separator:ga73cb7c9e275783e84681fbc2a320b850 inherit pub_types_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga965d4ee634a7d44a419183e663029571 inherit pub_types_classCSeq__align__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__Seqalign.html#ga96c37ea021b33766f9eb2d76dd12d1ca">E_memberIndex</a>, 8 > </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga965d4ee634a7d44a419183e663029571">TmemberIndex</a></td></tr>
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||
<tr class="separator:ga965d4ee634a7d44a419183e663029571 inherit pub_types_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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||
<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>
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||
<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>
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||
<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>
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||
<tr class="separator:ga2da943ea997324fcabb60e1a1ed1b71c inherit pub_types_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
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||
<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>
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||
<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>
|
||
</table><table class="memberdecls">
|
||
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
|
||
Public Member Functions</h2></td></tr>
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||
<tr class="memitem:a2e40ec368f73515d029efb850d7aa483"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a2e40ec368f73515d029efb850d7aa483">CSeq_align</a> (void)</td></tr>
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||
<tr class="memdesc:a2e40ec368f73515d029efb850d7aa483"><td class="mdescLeft"> </td><td class="mdescRight">constructor <a href="classCSeq__align.html#a2e40ec368f73515d029efb850d7aa483">More...</a><br /></td></tr>
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||
<tr class="separator:a2e40ec368f73515d029efb850d7aa483"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:ac873ad1fe8db9ed40f098ca730040e1d"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#ac873ad1fe8db9ed40f098ca730040e1d">~CSeq_align</a> (void)</td></tr>
|
||
<tr class="memdesc:ac873ad1fe8db9ed40f098ca730040e1d"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="classCSeq__align.html#ac873ad1fe8db9ed40f098ca730040e1d">More...</a><br /></td></tr>
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||
<tr class="separator:ac873ad1fe8db9ed40f098ca730040e1d"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:a75181a63597ffedae193a1f9c7d3a2f1"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a75181a63597ffedae193a1f9c7d3a2f1">CheckNumRows</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:a75181a63597ffedae193a1f9c7d3a2f1"><td class="mdescLeft"> </td><td class="mdescRight">Validatiors. <a href="classCSeq__align.html#a75181a63597ffedae193a1f9c7d3a2f1">More...</a><br /></td></tr>
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||
<tr class="separator:a75181a63597ffedae193a1f9c7d3a2f1"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:ad6c982af80b7728ad3777a1d0a26f89d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#ad6c982af80b7728ad3777a1d0a26f89d">Validate</a> (<a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> full_test=<a class="el" href="ftds14_2freetds_2freetds_2bool_8h.html#a65e9886d74aaee76545e83dd09011727">false</a>) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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||
<tr class="separator:ad6c982af80b7728ad3777a1d0a26f89d"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:a4a8a8b945db67efbe59e74fe8c03593d"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRange.html">CRange</a>< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a4a8a8b945db67efbe59e74fe8c03593d">GetSeqRange</a> (<a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:a4a8a8b945db67efbe59e74fe8c03593d"><td class="mdescLeft"> </td><td class="mdescRight">GetSeqRange <a class="el" href="classNB.html">NB</a>: On a Spliced-seg, in case the product-type is protein, these only return the amin part of Prot-pos. <a href="classCSeq__align.html#a4a8a8b945db67efbe59e74fe8c03593d">More...</a><br /></td></tr>
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||
<tr class="separator:a4a8a8b945db67efbe59e74fe8c03593d"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:a9d9970a4214c3b03f879e5d439f1b74d"><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="classCSeq__align.html#a9d9970a4214c3b03f879e5d439f1b74d">GetSeqStart</a> (<a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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||
<tr class="separator:a9d9970a4214c3b03f879e5d439f1b74d"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:a6e0fe43fbf04caafc3f808e5ce35c75f"><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="classCSeq__align.html#a6e0fe43fbf04caafc3f808e5ce35c75f">GetSeqStop</a> (<a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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||
<tr class="separator:a6e0fe43fbf04caafc3f808e5ce35c75f"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:aaf45eabbfe89cfc16dced0bceb9b0cea"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__Seqloc.html#ga2d4d48fde1d3f62563eac193a3b5afae">ENa_strand</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#aaf45eabbfe89cfc16dced0bceb9b0cea">GetSeqStrand</a> (<a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:aaf45eabbfe89cfc16dced0bceb9b0cea"><td class="mdescLeft"> </td><td class="mdescRight">Get strand (the first one if segments have different strands). <a href="classCSeq__align.html#aaf45eabbfe89cfc16dced0bceb9b0cea">More...</a><br /></td></tr>
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||
<tr class="separator:aaf45eabbfe89cfc16dced0bceb9b0cea"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:a801ec9a68d0cb752aea142758dc1532d"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSeq__id.html">CSeq_id</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a801ec9a68d0cb752aea142758dc1532d">GetSeq_id</a> (<a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:a801ec9a68d0cb752aea142758dc1532d"><td class="mdescLeft"> </td><td class="mdescRight">Get seq-id (the first one if segments have different ids). <a href="classCSeq__align.html#a801ec9a68d0cb752aea142758dc1532d">More...</a><br /></td></tr>
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<tr class="separator:a801ec9a68d0cb752aea142758dc1532d"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a2511741b3a06c6e995e135d134f48083"><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="classCSeq__align.html#a2511741b3a06c6e995e135d134f48083">GetTotalGapCount</a> (<a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>=-1) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:a2511741b3a06c6e995e135d134f48083"><td class="mdescLeft"> </td><td class="mdescRight">Retrieves the total number of gaps in the given row an alignment; all gaps by default. <a href="classCSeq__align.html#a2511741b3a06c6e995e135d134f48083">More...</a><br /></td></tr>
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<tr class="separator:a2511741b3a06c6e995e135d134f48083"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a9aa843619a79e4bbd532d9920f0aef8d"><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="classCSeq__align.html#a9aa843619a79e4bbd532d9920f0aef8d">GetTotalGapCountWithinRange</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__RangeSupport.html#gabb457385e479479764dd959a1d182765">TSeqRange</a> &range, <a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>=-1) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="separator:a9aa843619a79e4bbd532d9920f0aef8d"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a8315dc19cc8a8386d64a96ea0709353f"><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="classCSeq__align.html#a8315dc19cc8a8386d64a96ea0709353f">GetTotalGapCountWithinRanges</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCRangeCollection.html">CRangeCollection</a>< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > &ranges, <a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>=-1) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="separator:a8315dc19cc8a8386d64a96ea0709353f"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:af7a953721b2c699a28cd5ae12f7fd49c"><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="classCSeq__align.html#af7a953721b2c699a28cd5ae12f7fd49c">GetNumGapOpenings</a> (<a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>=-1) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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||
<tr class="memdesc:af7a953721b2c699a28cd5ae12f7fd49c"><td class="mdescLeft"> </td><td class="mdescRight">Retrieves the number of gap openings in a given row in an alignment (ignoring how many gaps are in the gapped region); all gaps by default. <a href="classCSeq__align.html#af7a953721b2c699a28cd5ae12f7fd49c">More...</a><br /></td></tr>
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<tr class="separator:af7a953721b2c699a28cd5ae12f7fd49c"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a40feccb2adfcbdf6ee99dbe290b1e2d0"><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="classCSeq__align.html#a40feccb2adfcbdf6ee99dbe290b1e2d0">GetNumGapOpeningsWithinRange</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__RangeSupport.html#gabb457385e479479764dd959a1d182765">TSeqRange</a> &range, <a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>=-1) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="separator:a40feccb2adfcbdf6ee99dbe290b1e2d0"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a1dd42a36ca228931b0f4db55caa0e802"><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="classCSeq__align.html#a1dd42a36ca228931b0f4db55caa0e802">GetNumGapOpeningsWithinRanges</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCRangeCollection.html">CRangeCollection</a>< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > &ranges, <a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>=-1) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="separator:a1dd42a36ca228931b0f4db55caa0e802"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ac4dcd004970024f04f0aede4cb678fd4"><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="classCSeq__align.html#ac4dcd004970024f04f0aede4cb678fd4">GetNumFrameshifts</a> (<a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>=-1) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memdesc:ac4dcd004970024f04f0aede4cb678fd4"><td class="mdescLeft"> </td><td class="mdescRight">Retrieves the number of times a given row shifts frames; i.e. <a href="classCSeq__align.html#ac4dcd004970024f04f0aede4cb678fd4">More...</a><br /></td></tr>
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<tr class="separator:ac4dcd004970024f04f0aede4cb678fd4"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:abc9277371560e91505524972298d1e95"><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="classCSeq__align.html#abc9277371560e91505524972298d1e95">GetNumFrameshiftsWithinRange</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__RangeSupport.html#gabb457385e479479764dd959a1d182765">TSeqRange</a> &range, <a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>=-1) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="separator:abc9277371560e91505524972298d1e95"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a69513924865028222e35f58234a95106"><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="classCSeq__align.html#a69513924865028222e35f58234a95106">GetNumFrameshiftsWithinRanges</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCRangeCollection.html">CRangeCollection</a>< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > &ranges, <a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>=-1) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="separator:a69513924865028222e35f58234a95106"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ac01cbd2f42d297bf8129c8bdb40d31bf"><td class="memItemLeft" align="right" valign="top">vector< <a class="el" href="structCSeq__align_1_1SIndel.html">SIndel</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#ac01cbd2f42d297bf8129c8bdb40d31bf">GetIndels</a> (<a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>=-1) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memdesc:ac01cbd2f42d297bf8129c8bdb40d31bf"><td class="mdescLeft"> </td><td class="mdescRight">Retrieves descriptions of all indels on a given row. <a href="classCSeq__align.html#ac01cbd2f42d297bf8129c8bdb40d31bf">More...</a><br /></td></tr>
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<tr class="separator:ac01cbd2f42d297bf8129c8bdb40d31bf"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a98b8b94878c00a567c5b45494ceb34d7"><td class="memItemLeft" align="right" valign="top">vector< <a class="el" href="structCSeq__align_1_1SIndel.html">SIndel</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a98b8b94878c00a567c5b45494ceb34d7">GetIndelsWithinRange</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__RangeSupport.html#gabb457385e479479764dd959a1d182765">TSeqRange</a> &range, <a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>=-1) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="separator:a98b8b94878c00a567c5b45494ceb34d7"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a2acb690a377c462a9a9db3c528b2c22b"><td class="memItemLeft" align="right" valign="top">vector< <a class="el" href="structCSeq__align_1_1SIndel.html">SIndel</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a2acb690a377c462a9a9db3c528b2c22b">GetIndelsWithinRanges</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCRangeCollection.html">CRangeCollection</a>< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > &ranges, <a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>=-1) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="separator:a2acb690a377c462a9a9db3c528b2c22b"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ab63468109dc5871caa430d34fe7dfba8"><td class="memItemLeft" align="right" valign="top">vector< <a class="el" href="structCSeq__align_1_1SIndel.html">SIndel</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#ab63468109dc5871caa430d34fe7dfba8">GetFrameshifts</a> (<a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>=-1) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memdesc:ab63468109dc5871caa430d34fe7dfba8"><td class="mdescLeft"> </td><td class="mdescRight">Retrieves descriptions of all frameshifts on a given row; i.e. <a href="classCSeq__align.html#ab63468109dc5871caa430d34fe7dfba8">More...</a><br /></td></tr>
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<tr class="separator:ab63468109dc5871caa430d34fe7dfba8"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a8968c122b97da0f9cd320fc941c8a43d"><td class="memItemLeft" align="right" valign="top">vector< <a class="el" href="structCSeq__align_1_1SIndel.html">SIndel</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a8968c122b97da0f9cd320fc941c8a43d">GetFrameshiftsWithinRange</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__RangeSupport.html#gabb457385e479479764dd959a1d182765">TSeqRange</a> &range, <a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>=-1) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="separator:a8968c122b97da0f9cd320fc941c8a43d"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ac9542ed1bee82529e62ba6fc4d87e81e"><td class="memItemLeft" align="right" valign="top">vector< <a class="el" href="structCSeq__align_1_1SIndel.html">SIndel</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#ac9542ed1bee82529e62ba6fc4d87e81e">GetFrameshiftsWithinRanges</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCRangeCollection.html">CRangeCollection</a>< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > &ranges, <a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>=-1) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="separator:ac9542ed1bee82529e62ba6fc4d87e81e"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a5acb629f0eeddc050c5e93de4f14d3ca"><td class="memItemLeft" align="right" valign="top">vector< <a class="el" href="structCSeq__align_1_1SIndel.html">SIndel</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a5acb629f0eeddc050c5e93de4f14d3ca">GetNonFrameshifts</a> (<a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>=-1) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memdesc:a5acb629f0eeddc050c5e93de4f14d3ca"><td class="mdescLeft"> </td><td class="mdescRight">Retrieves descriptions of all non-frameshift indels on a given row; i.e. <a href="classCSeq__align.html#a5acb629f0eeddc050c5e93de4f14d3ca">More...</a><br /></td></tr>
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<tr class="separator:a5acb629f0eeddc050c5e93de4f14d3ca"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a2fd557f3bb33caa1612ad80f130fb8b4"><td class="memItemLeft" align="right" valign="top">vector< <a class="el" href="structCSeq__align_1_1SIndel.html">SIndel</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a2fd557f3bb33caa1612ad80f130fb8b4">GetNonFrameshiftsWithinRange</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__RangeSupport.html#gabb457385e479479764dd959a1d182765">TSeqRange</a> &range, <a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>=-1) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="separator:a2fd557f3bb33caa1612ad80f130fb8b4"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:abba500351271d04d8e09f393049f21e3"><td class="memItemLeft" align="right" valign="top">vector< <a class="el" href="structCSeq__align_1_1SIndel.html">SIndel</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#abba500351271d04d8e09f393049f21e3">GetNonFrameshiftsWithinRanges</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCRangeCollection.html">CRangeCollection</a>< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > &ranges, <a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>=-1) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="separator:abba500351271d04d8e09f393049f21e3"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a2d99ace5e945d611a25e6150279a7e25"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRangeCollection.html">CRangeCollection</a>< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a2d99ace5e945d611a25e6150279a7e25">GetAlignedBases</a> (<a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memdesc:a2d99ace5e945d611a25e6150279a7e25"><td class="mdescLeft"> </td><td class="mdescRight">Retrieves the locations of aligned bases in the given row, excluding gaps and incontinuities. <a href="classCSeq__align.html#a2d99ace5e945d611a25e6150279a7e25">More...</a><br /></td></tr>
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<tr class="separator:a2d99ace5e945d611a25e6150279a7e25"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ab212b5bf2e03db11215dc938646d484a"><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="classCSeq__align.html#ab212b5bf2e03db11215dc938646d484a">GetAlignLength</a> (<a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> include_gaps=<a class="el" href="ftds14_2freetds_2freetds_2bool_8h.html#a41f9c5fb8b08eb5dc3edce4dcb37fee7">true</a>) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memdesc:ab212b5bf2e03db11215dc938646d484a"><td class="mdescLeft"> </td><td class="mdescRight">Get the length of this alignment. <a href="classCSeq__align.html#ab212b5bf2e03db11215dc938646d484a">More...</a><br /></td></tr>
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<tr class="separator:ab212b5bf2e03db11215dc938646d484a"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a87c8ad395ebf1b07fbfa4cff17a159f5"><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="classCSeq__align.html#a87c8ad395ebf1b07fbfa4cff17a159f5">GetAlignLengthWithinRange</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__RangeSupport.html#gabb457385e479479764dd959a1d182765">TSeqRange</a> &range, <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> include_gaps=<a class="el" href="ftds14_2freetds_2freetds_2bool_8h.html#a41f9c5fb8b08eb5dc3edce4dcb37fee7">true</a>) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memdesc:a87c8ad395ebf1b07fbfa4cff17a159f5"><td class="mdescLeft"> </td><td class="mdescRight">Get the length of this alignment within a specified range By default, this function computes an alignment length including all gap segments. <a href="classCSeq__align.html#a87c8ad395ebf1b07fbfa4cff17a159f5">More...</a><br /></td></tr>
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<tr class="separator:a87c8ad395ebf1b07fbfa4cff17a159f5"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ac5128aef39a4ea6e8c676154beb6c0ed"><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="classCSeq__align.html#ac5128aef39a4ea6e8c676154beb6c0ed">GetAlignLengthWithinRanges</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCRangeCollection.html">CRangeCollection</a>< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > &ranges, <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> include_gaps=<a class="el" href="ftds14_2freetds_2freetds_2bool_8h.html#a41f9c5fb8b08eb5dc3edce4dcb37fee7">true</a>) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memdesc:ac5128aef39a4ea6e8c676154beb6c0ed"><td class="mdescLeft"> </td><td class="mdescRight">Get the length of this alignment within a specified range By default, this function computes an alignment length including all gap segments. <a href="classCSeq__align.html#ac5128aef39a4ea6e8c676154beb6c0ed">More...</a><br /></td></tr>
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<tr class="memitem:a8dfa02516df3b7e99f392c053a962ed4"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a8dfa02516df3b7e99f392c053a962ed4">AlignLengthRatio</a> () <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memitem:a80224af23d990db9de01aa7b8a3e9c06"><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="classCSeq__align.html#a80224af23d990db9de01aa7b8a3e9c06">GetNamedScore</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> &id, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> &score) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memdesc:a80224af23d990db9de01aa7b8a3e9c06"><td class="mdescLeft"> </td><td class="mdescRight">Get score. <a href="classCSeq__align.html#a80224af23d990db9de01aa7b8a3e9c06">More...</a><br /></td></tr>
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<tr class="memitem:a64a1edcedc36bba2e8d554d2a2b2708c"><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="classCSeq__align.html#a64a1edcedc36bba2e8d554d2a2b2708c">GetNamedScore</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> &id, double &score) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memdesc:a64a1edcedc36bba2e8d554d2a2b2708c"><td class="mdescLeft"> </td><td class="mdescRight">--------------------------------------------------------------------------- PRE : name of score to return POST: whether or not we found that score; score converted to double <a href="classCSeq__align.html#a64a1edcedc36bba2e8d554d2a2b2708c">More...</a><br /></td></tr>
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<tr class="memitem:a179f3a1e25383a6343f481c8221e4a00"><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="classCSeq__align.html#a179f3a1e25383a6343f481c8221e4a00">GetNamedScore</a> (<a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">EScoreType</a> <a class="el" href="structtype.html">type</a>, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> &score) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memitem:ac73daf82c97fb571b266a09a9eb81ade"><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="classCSeq__align.html#ac73daf82c97fb571b266a09a9eb81ade">GetNamedScore</a> (<a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">EScoreType</a> <a class="el" href="structtype.html">type</a>, double &score) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memitem:a731dda257ee388ccb949ef71c394916f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a731dda257ee388ccb949ef71c394916f">SetNamedScore</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> &id, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> score)</td></tr>
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<tr class="memitem:ab341f680226edd9c4d6c60520b80f6a8"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#ab341f680226edd9c4d6c60520b80f6a8">SetNamedScore</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> &id, double score)</td></tr>
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<tr class="memitem:a6171d9165ae21c54d89e2144f7cb99b5"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a6171d9165ae21c54d89e2144f7cb99b5">SetNamedScore</a> (<a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">EScoreType</a> <a class="el" href="structtype.html">type</a>, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> score)</td></tr>
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<tr class="memitem:ac83f06633e6c67f200244622627617f9"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#ac83f06633e6c67f200244622627617f9">SetNamedScore</a> (<a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">EScoreType</a> <a class="el" href="structtype.html">type</a>, double score)</td></tr>
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<tr class="memitem:a8345d5f956b4ddc58976e8f4115f8db8"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a8345d5f956b4ddc58976e8f4115f8db8">ResetNamedScore</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> &name)</td></tr>
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<tr class="memitem:a67b6cc4b7e39f1e59ba3e51d1f6dca5e"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a67b6cc4b7e39f1e59ba3e51d1f6dca5e">ResetNamedScore</a> (<a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">EScoreType</a> <a class="el" href="structtype.html">type</a>)</td></tr>
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<tr class="memitem:a302e1860f81ea4eed8f968111801e8a7"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a302e1860f81ea4eed8f968111801e8a7">Reverse</a> (void)</td></tr>
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<tr class="memdesc:a302e1860f81ea4eed8f968111801e8a7"><td class="mdescLeft"> </td><td class="mdescRight">Reverse the segments' orientation NOTE: currently *only* works for dense-seg. <a href="classCSeq__align.html#a302e1860f81ea4eed8f968111801e8a7">More...</a><br /></td></tr>
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<tr class="memitem:a7c073ec76fa340c940566afd99f7ba00"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a7c073ec76fa340c940566afd99f7ba00">SwapRows</a> (<a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> row1, <a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> row2)</td></tr>
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<tr class="memdesc:a7c073ec76fa340c940566afd99f7ba00"><td class="mdescLeft"> </td><td class="mdescRight">Swap the position of two rows in the alignment NOTE: currently *only* works for dense-seg & disc. <a href="classCSeq__align.html#a7c073ec76fa340c940566afd99f7ba00">More...</a><br /></td></tr>
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<tr class="memitem:a1e3f25b2b080d97a62de8ab154c44f4f"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCSeq__align.html">CSeq_align</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a1e3f25b2b080d97a62de8ab154c44f4f">CreateDensegFromStdseg</a> (<a class="el" href="structCSeq__align_1_1SSeqIdChooser.html">SSeqIdChooser</a> *SeqIdChooser=0) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memdesc:a1e3f25b2b080d97a62de8ab154c44f4f"><td class="mdescLeft"> </td><td class="mdescRight">---------------------------------------------------------------------------- PRE : the Seq-align has StdSeg segs POST: Seq_align of type Dense-seg is created with m_Widths if necessary <a href="classCSeq__align.html#a1e3f25b2b080d97a62de8ab154c44f4f">More...</a><br /></td></tr>
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<tr class="separator:a1e3f25b2b080d97a62de8ab154c44f4f"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a0d093ea51ad07028965a50434b7c9fa9"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCSeq__align.html">CSeq_align</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a0d093ea51ad07028965a50434b7c9fa9">CreateDensegFromDisc</a> (<a class="el" href="structCSeq__align_1_1SSeqIdChooser.html">SSeqIdChooser</a> *SeqIdChooser=0) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memitem:a01fd58c2eeecadeac3fae344bf46dab2"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCSeq__align.html">CSeq_align</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a01fd58c2eeecadeac3fae344bf46dab2">CreateTranslatedDensegFromNADenseg</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memdesc:a01fd58c2eeecadeac3fae344bf46dab2"><td class="mdescLeft"> </td><td class="mdescRight">Create a Dense-seg with widths from Dense-seg of nucleotides Used by AlnMgr to handle translated nucl2nucl alignments IMPORTANT NOTE: Do *NOT* use for alignments containing proteins; the code will not check for this. <a href="classCSeq__align.html#a01fd58c2eeecadeac3fae344bf46dab2">More...</a><br /></td></tr>
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<tr class="memitem:a87ed9d4eac3797922458bf943b5b8112"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a87ed9d4eac3797922458bf943b5b8112">SplitOnLongDiscontinuity</a> (list< <a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCSeq__align.html">CSeq_align</a> > > &aligns, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> discontinuity_threshold) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memdesc:a87ed9d4eac3797922458bf943b5b8112"><td class="mdescLeft"> </td><td class="mdescRight">Split the alignment at any discontinuity greater than threshold; populate aligns list with new alignments. <a href="classCSeq__align.html#a87ed9d4eac3797922458bf943b5b8112">More...</a><br /></td></tr>
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<tr class="memitem:a2ccc4265d1325463617fde3a586319da"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a2ccc4265d1325463617fde3a586319da">OffsetRow</a> (<a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>, <a class="el" href="group__AppFramework.html#ga92c3033316f74e84da312174e871d85c">TSignedSeqPos</a> <a class="el" href="url__tooltip__handler_8cpp.html#af1a7c6ddf735b32939485fddbaec4e75">offset</a>)</td></tr>
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<tr class="memdesc:a2ccc4265d1325463617fde3a586319da"><td class="mdescLeft"> </td><td class="mdescRight">Offset row's coords. <a href="classCSeq__align.html#a2ccc4265d1325463617fde3a586319da">More...</a><br /></td></tr>
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<tr class="memitem:a83652f375f028ffd6deffc15ca945d4b"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a83652f375f028ffd6deffc15ca945d4b">RemapToLoc</a> (<a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSeq__loc.html">CSeq_loc</a> &dst_loc, <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> ignore_strand=<a class="el" href="ftds14_2freetds_2freetds_2bool_8h.html#a65e9886d74aaee76545e83dd09011727">false</a>)</td></tr>
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<tr class="memitem:a718ea26ead4d345db111595705e26b04"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCSeq__loc.html">CSeq_loc</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a718ea26ead4d345db111595705e26b04">CreateRowSeq_loc</a> (<a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="string__bind_8c.html#a2715889d5feef62a0535c302cf093382">row</a>) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memitem:adb3adece65b714acf63aab32a3a1ee56"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCSeq__align.html#ae8447af5653b27fa09d886821029a4c7">TLengthRange</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#adb3adece65b714acf63aab32a3a1ee56">GapLengthRange</a> () <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memitem:a49565489afe3881528c9017803c9f68b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCSeq__align.html#ae8447af5653b27fa09d886821029a4c7">TLengthRange</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a49565489afe3881528c9017803c9f68b">IntronLengthRange</a> () <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memitem:a2816ade4f70cd458a8e7d9916be35518"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCSeq__align.html#ae8447af5653b27fa09d886821029a4c7">TLengthRange</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a2816ade4f70cd458a8e7d9916be35518">ExonLengthRange</a> () <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memitem:ae3d3081b4316011a7ee6b248f2f46f86"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCConstRef.html">CConstRef</a>< <a class="el" href="classCUser__object.html">CUser_object</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#ae3d3081b4316011a7ee6b248f2f46f86">FindExt</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> &ext_type) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memdesc:ae3d3081b4316011a7ee6b248f2f46f86"><td class="mdescLeft"> </td><td class="mdescRight">Find extension by type in ext container. <a href="classCSeq__align.html#ae3d3081b4316011a7ee6b248f2f46f86">More...</a><br /></td></tr>
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<tr class="separator:ae3d3081b4316011a7ee6b248f2f46f86"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:adf3fc863310039e51c5e63b575104f4f"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCUser__object.html">CUser_object</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#adf3fc863310039e51c5e63b575104f4f">FindExt</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> &ext_type)</td></tr>
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<tr class="memdesc:adf3fc863310039e51c5e63b575104f4f"><td class="mdescLeft"> </td><td class="mdescRight">Non-const version of <a class="el" href="classCSeq__align.html#ae3d3081b4316011a7ee6b248f2f46f86" title="Find extension by type in ext container.">FindExt()</a>. <a href="classCSeq__align.html#adf3fc863310039e51c5e63b575104f4f">More...</a><br /></td></tr>
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<tr class="separator:adf3fc863310039e51c5e63b575104f4f"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="inherit_header pub_methods_classCSeq__align__Base"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classCSeq__align__Base')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classCSeq__align__Base.html">CSeq_align_Base</a></td></tr>
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<tr class="memitem:gae981bf58e38f8f22619d29bc62411b16 inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#gae981bf58e38f8f22619d29bc62411b16">CSeq_align_Base</a> (void)</td></tr>
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<tr class="separator:gae981bf58e38f8f22619d29bc62411b16 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga451096137eca0656708c5c76ad479018 inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga451096137eca0656708c5c76ad479018">~CSeq_align_Base</a> (void)</td></tr>
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<tr class="separator:ga451096137eca0656708c5c76ad479018 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga982a8492b756d4aff8cd9007742abfd8 inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga982a8492b756d4aff8cd9007742abfd8">DECLARE_INTERNAL_TYPE_INFO</a> ()</td></tr>
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<tr class="separator:ga982a8492b756d4aff8cd9007742abfd8 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga8bf31fa0e483ab3d3495b0750e2a77ce inherit pub_methods_classCSeq__align__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__Seqalign.html#ga8bf31fa0e483ab3d3495b0750e2a77ce">IsSetType</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memdesc:ga8bf31fa0e483ab3d3495b0750e2a77ce inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if a value has been assigned to Type data member. <a href="group__dataspec__NCBI__Seqalign.html#ga8bf31fa0e483ab3d3495b0750e2a77ce">More...</a><br /></td></tr>
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||
<tr class="separator:ga8bf31fa0e483ab3d3495b0750e2a77ce inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga38c75e1e786cf8e8ca770171ac757c49 inherit pub_methods_classCSeq__align__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__Seqalign.html#ga38c75e1e786cf8e8ca770171ac757c49">CanGetType</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memdesc:ga38c75e1e786cf8e8ca770171ac757c49 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetType method. <a href="group__dataspec__NCBI__Seqalign.html#ga38c75e1e786cf8e8ca770171ac757c49">More...</a><br /></td></tr>
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<tr class="separator:ga38c75e1e786cf8e8ca770171ac757c49 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:gaff81f3fd353a7573124c0b0b231ef945 inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#gaff81f3fd353a7573124c0b0b231ef945">ResetType</a> (void)</td></tr>
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<tr class="memdesc:gaff81f3fd353a7573124c0b0b231ef945 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Type data member. <a href="group__dataspec__NCBI__Seqalign.html#gaff81f3fd353a7573124c0b0b231ef945">More...</a><br /></td></tr>
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||
<tr class="separator:gaff81f3fd353a7573124c0b0b231ef945 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:gab5cdbfd165e1a9483f0bc3a3a190c49c inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__Seqalign.html#gac180c46e798d862f504865299b627f3b">TType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#gab5cdbfd165e1a9483f0bc3a3a190c49c">GetType</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memdesc:gab5cdbfd165e1a9483f0bc3a3a190c49c inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Type member data. <a href="group__dataspec__NCBI__Seqalign.html#gab5cdbfd165e1a9483f0bc3a3a190c49c">More...</a><br /></td></tr>
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||
<tr class="separator:gab5cdbfd165e1a9483f0bc3a3a190c49c inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga79bccbf1328946ce5218faa1f698f653 inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga79bccbf1328946ce5218faa1f698f653">SetType</a> (<a class="el" href="group__dataspec__NCBI__Seqalign.html#gac180c46e798d862f504865299b627f3b">TType</a> <a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
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<tr class="memdesc:ga79bccbf1328946ce5218faa1f698f653 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Type data member. <a href="group__dataspec__NCBI__Seqalign.html#ga79bccbf1328946ce5218faa1f698f653">More...</a><br /></td></tr>
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||
<tr class="separator:ga79bccbf1328946ce5218faa1f698f653 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga3010f69bb992aef29dca412dbb1ab06d inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__Seqalign.html#gac180c46e798d862f504865299b627f3b">TType</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga3010f69bb992aef29dca412dbb1ab06d">SetType</a> (void)</td></tr>
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<tr class="memdesc:ga3010f69bb992aef29dca412dbb1ab06d inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Type data member. <a href="group__dataspec__NCBI__Seqalign.html#ga3010f69bb992aef29dca412dbb1ab06d">More...</a><br /></td></tr>
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||
<tr class="separator:ga3010f69bb992aef29dca412dbb1ab06d inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:gaba675f13f15cfa03faf978ac6f837248 inherit pub_methods_classCSeq__align__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__Seqalign.html#gaba675f13f15cfa03faf978ac6f837248">IsSetDim</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memdesc:gaba675f13f15cfa03faf978ac6f837248 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">dimensionality <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Dim data member. <a href="group__dataspec__NCBI__Seqalign.html#gaba675f13f15cfa03faf978ac6f837248">More...</a><br /></td></tr>
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||
<tr class="separator:gaba675f13f15cfa03faf978ac6f837248 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga9f31632ca2ad9efcaa8048efe0162a8f inherit pub_methods_classCSeq__align__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__Seqalign.html#ga9f31632ca2ad9efcaa8048efe0162a8f">CanGetDim</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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||
<tr class="memdesc:ga9f31632ca2ad9efcaa8048efe0162a8f inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetDim method. <a href="group__dataspec__NCBI__Seqalign.html#ga9f31632ca2ad9efcaa8048efe0162a8f">More...</a><br /></td></tr>
|
||
<tr class="separator:ga9f31632ca2ad9efcaa8048efe0162a8f inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga424c61335c15e84eba038aeb916df4a6 inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga424c61335c15e84eba038aeb916df4a6">ResetDim</a> (void)</td></tr>
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||
<tr class="memdesc:ga424c61335c15e84eba038aeb916df4a6 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Dim data member. <a href="group__dataspec__NCBI__Seqalign.html#ga424c61335c15e84eba038aeb916df4a6">More...</a><br /></td></tr>
|
||
<tr class="separator:ga424c61335c15e84eba038aeb916df4a6 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:ga461be965d1ed6dc5ffe6032276c5daca inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga461be965d1ed6dc5ffe6032276c5daca">GetDim</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga461be965d1ed6dc5ffe6032276c5daca inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Dim member data. <a href="group__dataspec__NCBI__Seqalign.html#ga461be965d1ed6dc5ffe6032276c5daca">More...</a><br /></td></tr>
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||
<tr class="separator:ga461be965d1ed6dc5ffe6032276c5daca inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:ga67c7a71b1a62154e77ae6e2fd5edf602 inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga67c7a71b1a62154e77ae6e2fd5edf602">SetDim</a> (<a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> <a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="memdesc:ga67c7a71b1a62154e77ae6e2fd5edf602 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Dim data member. <a href="group__dataspec__NCBI__Seqalign.html#ga67c7a71b1a62154e77ae6e2fd5edf602">More...</a><br /></td></tr>
|
||
<tr class="separator:ga67c7a71b1a62154e77ae6e2fd5edf602 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:gab7777aba07ede2730782274aabee0c8f inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#gab7777aba07ede2730782274aabee0c8f">SetDim</a> (void)</td></tr>
|
||
<tr class="memdesc:gab7777aba07ede2730782274aabee0c8f inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Dim data member. <a href="group__dataspec__NCBI__Seqalign.html#gab7777aba07ede2730782274aabee0c8f">More...</a><br /></td></tr>
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||
<tr class="separator:gab7777aba07ede2730782274aabee0c8f inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:gacf5a34ca1461e6517b19745b0b19c181 inherit pub_methods_classCSeq__align__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__Seqalign.html#gacf5a34ca1461e6517b19745b0b19c181">IsSetScore</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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||
<tr class="memdesc:gacf5a34ca1461e6517b19745b0b19c181 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">for whole alignment <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Score data member. <a href="group__dataspec__NCBI__Seqalign.html#gacf5a34ca1461e6517b19745b0b19c181">More...</a><br /></td></tr>
|
||
<tr class="separator:gacf5a34ca1461e6517b19745b0b19c181 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:ga6450e45da10fb0c6851d96dd141a34ab inherit pub_methods_classCSeq__align__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__Seqalign.html#ga6450e45da10fb0c6851d96dd141a34ab">CanGetScore</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga6450e45da10fb0c6851d96dd141a34ab inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetScore method. <a href="group__dataspec__NCBI__Seqalign.html#ga6450e45da10fb0c6851d96dd141a34ab">More...</a><br /></td></tr>
|
||
<tr class="separator:ga6450e45da10fb0c6851d96dd141a34ab inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga5a6b04dd99993723801205881c51d352 inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga5a6b04dd99993723801205881c51d352">ResetScore</a> (void)</td></tr>
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||
<tr class="memdesc:ga5a6b04dd99993723801205881c51d352 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Score data member. <a href="group__dataspec__NCBI__Seqalign.html#ga5a6b04dd99993723801205881c51d352">More...</a><br /></td></tr>
|
||
<tr class="separator:ga5a6b04dd99993723801205881c51d352 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gae626641a6357ef9b65cc6ed801160c7d inherit pub_methods_classCSeq__align__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__Seqalign.html#ga31490879f6caded03bb483742739611f">TScore</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#gae626641a6357ef9b65cc6ed801160c7d">GetScore</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gae626641a6357ef9b65cc6ed801160c7d inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Score member data. <a href="group__dataspec__NCBI__Seqalign.html#gae626641a6357ef9b65cc6ed801160c7d">More...</a><br /></td></tr>
|
||
<tr class="separator:gae626641a6357ef9b65cc6ed801160c7d inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:ga130fab7afc4087c9117bfffa1edcfef8 inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga31490879f6caded03bb483742739611f">TScore</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga130fab7afc4087c9117bfffa1edcfef8">SetScore</a> (void)</td></tr>
|
||
<tr class="memdesc:ga130fab7afc4087c9117bfffa1edcfef8 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Score data member. <a href="group__dataspec__NCBI__Seqalign.html#ga130fab7afc4087c9117bfffa1edcfef8">More...</a><br /></td></tr>
|
||
<tr class="separator:ga130fab7afc4087c9117bfffa1edcfef8 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:ga55b8df89fe42ba80b3b5f65dd781b87a inherit pub_methods_classCSeq__align__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__Seqalign.html#ga55b8df89fe42ba80b3b5f65dd781b87a">IsSetSegs</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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<tr class="memdesc:ga55b8df89fe42ba80b3b5f65dd781b87a inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if a value has been assigned to Segs data member. <a href="group__dataspec__NCBI__Seqalign.html#ga55b8df89fe42ba80b3b5f65dd781b87a">More...</a><br /></td></tr>
|
||
<tr class="separator:ga55b8df89fe42ba80b3b5f65dd781b87a inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga8662eb8433f504fdeb94c0669a94a999 inherit pub_methods_classCSeq__align__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__Seqalign.html#ga8662eb8433f504fdeb94c0669a94a999">CanGetSegs</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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||
<tr class="memdesc:ga8662eb8433f504fdeb94c0669a94a999 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetSegs method. <a href="group__dataspec__NCBI__Seqalign.html#ga8662eb8433f504fdeb94c0669a94a999">More...</a><br /></td></tr>
|
||
<tr class="separator:ga8662eb8433f504fdeb94c0669a94a999 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga41e4addb9da0677c59e498fb5a8e1eb0 inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga41e4addb9da0677c59e498fb5a8e1eb0">ResetSegs</a> (void)</td></tr>
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<tr class="memdesc:ga41e4addb9da0677c59e498fb5a8e1eb0 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Segs data member. <a href="group__dataspec__NCBI__Seqalign.html#ga41e4addb9da0677c59e498fb5a8e1eb0">More...</a><br /></td></tr>
|
||
<tr class="separator:ga41e4addb9da0677c59e498fb5a8e1eb0 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:gaf462bb35a301f49fffc25fda2baa115f inherit pub_methods_classCSeq__align__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__Seqalign.html#ga8389ef87dff253dde4df333567562e19">TSegs</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#gaf462bb35a301f49fffc25fda2baa115f">GetSegs</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gaf462bb35a301f49fffc25fda2baa115f inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Segs member data. <a href="group__dataspec__NCBI__Seqalign.html#gaf462bb35a301f49fffc25fda2baa115f">More...</a><br /></td></tr>
|
||
<tr class="separator:gaf462bb35a301f49fffc25fda2baa115f inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga52e6df0597d235949052cfbbe3bc78a7 inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga52e6df0597d235949052cfbbe3bc78a7">SetSegs</a> (<a class="el" href="group__dataspec__NCBI__Seqalign.html#ga8389ef87dff253dde4df333567562e19">TSegs</a> &<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="memdesc:ga52e6df0597d235949052cfbbe3bc78a7 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Segs data member. <a href="group__dataspec__NCBI__Seqalign.html#ga52e6df0597d235949052cfbbe3bc78a7">More...</a><br /></td></tr>
|
||
<tr class="separator:ga52e6df0597d235949052cfbbe3bc78a7 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga18495762941f3d365ded6c4974a59ff7 inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga8389ef87dff253dde4df333567562e19">TSegs</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga18495762941f3d365ded6c4974a59ff7">SetSegs</a> (void)</td></tr>
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||
<tr class="memdesc:ga18495762941f3d365ded6c4974a59ff7 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Segs data member. <a href="group__dataspec__NCBI__Seqalign.html#ga18495762941f3d365ded6c4974a59ff7">More...</a><br /></td></tr>
|
||
<tr class="separator:ga18495762941f3d365ded6c4974a59ff7 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga2c26946c5f94868094a1232d1a57a9cb inherit pub_methods_classCSeq__align__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__Seqalign.html#ga2c26946c5f94868094a1232d1a57a9cb">IsSetBounds</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
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||
<tr class="memdesc:ga2c26946c5f94868094a1232d1a57a9cb inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">regions of sequence over which align was computed <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Bounds data member. <a href="group__dataspec__NCBI__Seqalign.html#ga2c26946c5f94868094a1232d1a57a9cb">More...</a><br /></td></tr>
|
||
<tr class="separator:ga2c26946c5f94868094a1232d1a57a9cb inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga3634fcd69dd284276f9a124b324b8f98 inherit pub_methods_classCSeq__align__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__Seqalign.html#ga3634fcd69dd284276f9a124b324b8f98">CanGetBounds</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga3634fcd69dd284276f9a124b324b8f98 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetBounds method. <a href="group__dataspec__NCBI__Seqalign.html#ga3634fcd69dd284276f9a124b324b8f98">More...</a><br /></td></tr>
|
||
<tr class="separator:ga3634fcd69dd284276f9a124b324b8f98 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga943acdb49f38426659a3278464c10757 inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga943acdb49f38426659a3278464c10757">ResetBounds</a> (void)</td></tr>
|
||
<tr class="memdesc:ga943acdb49f38426659a3278464c10757 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Bounds data member. <a href="group__dataspec__NCBI__Seqalign.html#ga943acdb49f38426659a3278464c10757">More...</a><br /></td></tr>
|
||
<tr class="separator:ga943acdb49f38426659a3278464c10757 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gafd74976affc9ac0adf4c3fb2bd07bd69 inherit pub_methods_classCSeq__align__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__Seqalign.html#ga8b1d61f3811d85be053524abb0e963d3">TBounds</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#gafd74976affc9ac0adf4c3fb2bd07bd69">GetBounds</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gafd74976affc9ac0adf4c3fb2bd07bd69 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Bounds member data. <a href="group__dataspec__NCBI__Seqalign.html#gafd74976affc9ac0adf4c3fb2bd07bd69">More...</a><br /></td></tr>
|
||
<tr class="separator:gafd74976affc9ac0adf4c3fb2bd07bd69 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gae662fdebf262a15e86a45890f8f5388a inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga8b1d61f3811d85be053524abb0e963d3">TBounds</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#gae662fdebf262a15e86a45890f8f5388a">SetBounds</a> (void)</td></tr>
|
||
<tr class="memdesc:gae662fdebf262a15e86a45890f8f5388a inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Bounds data member. <a href="group__dataspec__NCBI__Seqalign.html#gae662fdebf262a15e86a45890f8f5388a">More...</a><br /></td></tr>
|
||
<tr class="separator:gae662fdebf262a15e86a45890f8f5388a inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga38241660091b5690801d2116c7d04684 inherit pub_methods_classCSeq__align__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__Seqalign.html#ga38241660091b5690801d2116c7d04684">IsSetId</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga38241660091b5690801d2116c7d04684 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">alignment id <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Id data member. <a href="group__dataspec__NCBI__Seqalign.html#ga38241660091b5690801d2116c7d04684">More...</a><br /></td></tr>
|
||
<tr class="separator:ga38241660091b5690801d2116c7d04684 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gafe6d5df3fa6ef1abbc8864b3d1e32647 inherit pub_methods_classCSeq__align__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__Seqalign.html#gafe6d5df3fa6ef1abbc8864b3d1e32647">CanGetId</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gafe6d5df3fa6ef1abbc8864b3d1e32647 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetId method. <a href="group__dataspec__NCBI__Seqalign.html#gafe6d5df3fa6ef1abbc8864b3d1e32647">More...</a><br /></td></tr>
|
||
<tr class="separator:gafe6d5df3fa6ef1abbc8864b3d1e32647 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga4d87a3ef293a67669c2be1f0eb4837b1 inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga4d87a3ef293a67669c2be1f0eb4837b1">ResetId</a> (void)</td></tr>
|
||
<tr class="memdesc:ga4d87a3ef293a67669c2be1f0eb4837b1 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Id data member. <a href="group__dataspec__NCBI__Seqalign.html#ga4d87a3ef293a67669c2be1f0eb4837b1">More...</a><br /></td></tr>
|
||
<tr class="separator:ga4d87a3ef293a67669c2be1f0eb4837b1 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga0aa01bfeed40f0ee5c6755c0f79230a3 inherit pub_methods_classCSeq__align__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__Seqalign.html#ga72648ee97d4103c54633f45cb6fb9537">TId</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga0aa01bfeed40f0ee5c6755c0f79230a3">GetId</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga0aa01bfeed40f0ee5c6755c0f79230a3 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Id member data. <a href="group__dataspec__NCBI__Seqalign.html#ga0aa01bfeed40f0ee5c6755c0f79230a3">More...</a><br /></td></tr>
|
||
<tr class="separator:ga0aa01bfeed40f0ee5c6755c0f79230a3 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga11cda7c93c62e7c5fc87266e4406d8a7 inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga72648ee97d4103c54633f45cb6fb9537">TId</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga11cda7c93c62e7c5fc87266e4406d8a7">SetId</a> (void)</td></tr>
|
||
<tr class="memdesc:ga11cda7c93c62e7c5fc87266e4406d8a7 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Id data member. <a href="group__dataspec__NCBI__Seqalign.html#ga11cda7c93c62e7c5fc87266e4406d8a7">More...</a><br /></td></tr>
|
||
<tr class="separator:ga11cda7c93c62e7c5fc87266e4406d8a7 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga41663f9f6c1c67740c6f359cd18298cb inherit pub_methods_classCSeq__align__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__Seqalign.html#ga41663f9f6c1c67740c6f359cd18298cb">IsSetExt</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga41663f9f6c1c67740c6f359cd18298cb inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">extra info <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Ext data member. <a href="group__dataspec__NCBI__Seqalign.html#ga41663f9f6c1c67740c6f359cd18298cb">More...</a><br /></td></tr>
|
||
<tr class="separator:ga41663f9f6c1c67740c6f359cd18298cb inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga9c34ce87ea8ec3c2f903597c7a4538e1 inherit pub_methods_classCSeq__align__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__Seqalign.html#ga9c34ce87ea8ec3c2f903597c7a4538e1">CanGetExt</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:ga9c34ce87ea8ec3c2f903597c7a4538e1 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetExt method. <a href="group__dataspec__NCBI__Seqalign.html#ga9c34ce87ea8ec3c2f903597c7a4538e1">More...</a><br /></td></tr>
|
||
<tr class="separator:ga9c34ce87ea8ec3c2f903597c7a4538e1 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:ga333df997f25da6270a1de056706b29bc inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga333df997f25da6270a1de056706b29bc">ResetExt</a> (void)</td></tr>
|
||
<tr class="memdesc:ga333df997f25da6270a1de056706b29bc inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset Ext data member. <a href="group__dataspec__NCBI__Seqalign.html#ga333df997f25da6270a1de056706b29bc">More...</a><br /></td></tr>
|
||
<tr class="separator:ga333df997f25da6270a1de056706b29bc inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:gac61b1407d371db724499483c9b0bebd2 inherit pub_methods_classCSeq__align__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__Seqalign.html#ga73cb7c9e275783e84681fbc2a320b850">TExt</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#gac61b1407d371db724499483c9b0bebd2">GetExt</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:gac61b1407d371db724499483c9b0bebd2 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Get the Ext member data. <a href="group__dataspec__NCBI__Seqalign.html#gac61b1407d371db724499483c9b0bebd2">More...</a><br /></td></tr>
|
||
<tr class="separator:gac61b1407d371db724499483c9b0bebd2 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga929815388a9a85d5ad54057fe35af606 inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga73cb7c9e275783e84681fbc2a320b850">TExt</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga929815388a9a85d5ad54057fe35af606">SetExt</a> (void)</td></tr>
|
||
<tr class="memdesc:ga929815388a9a85d5ad54057fe35af606 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Assign a value to Ext data member. <a href="group__dataspec__NCBI__Seqalign.html#ga929815388a9a85d5ad54057fe35af606">More...</a><br /></td></tr>
|
||
<tr class="separator:ga929815388a9a85d5ad54057fe35af606 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:ga8f2b4d14a8965b73f21d515934dc9e88 inherit pub_methods_classCSeq__align__Base"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga8f2b4d14a8965b73f21d515934dc9e88">Reset</a> (void)</td></tr>
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||
<tr class="memdesc:ga8f2b4d14a8965b73f21d515934dc9e88 inherit pub_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Reset the whole object. <a href="group__dataspec__NCBI__Seqalign.html#ga8f2b4d14a8965b73f21d515934dc9e88">More...</a><br /></td></tr>
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||
<tr class="separator:ga8f2b4d14a8965b73f21d515934dc9e88 inherit pub_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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||
<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>
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||
<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>
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||
<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>
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<tr class="separator:gaf278b96157abad20b5d944fb83d32fb1 inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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||
<tr class="separator:gacb5d8a2e6878e58aeaeaf342081f0b7f inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
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||
<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>
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||
<tr class="separator:ga6c7f903717f7a272091acf5124cfd903 inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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||
<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>
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||
<tr class="separator:ga0daf4906b8f2e6382118c4a018491761 inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
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||
<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>
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||
<tr class="separator:ga7382b4cd30306d9444f85abd912ff61e inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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||
<tr class="separator:gab5506012856f3627d88368a24e1eb254 inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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||
<tr class="separator:ga937551d0a9c61c7ff537ac19ec37904d inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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||
<tr class="separator:gacfc7e87713da36496323f5477db80219 inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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||
<tr class="separator:gae8fa62abf96f3ed3cec903dce6a6a33a inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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||
<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>
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||
<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>
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<tr class="separator:gae38a8715a230c7ed588993c0206d8cb4 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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||
<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>
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<tr class="separator:gae89833a29aad16e7cb252314d2e7f4ab inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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||
<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>
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<tr class="separator:ga5125d96ff932bcd471a734fd174b2022 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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||
<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>
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<tr class="separator:gab2090742c0465c4229f6e0b57c2de566 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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||
<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>
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||
<tr class="separator:gaad370ec0ee157f6082b9845338cb2809 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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||
<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>
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||
<tr class="separator:gaf5cddacd7194af14e759f3d89325679b inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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||
<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>
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||
<tr class="separator:ga9f9bbe6d075c90238a43585999d303d9 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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||
<tr class="separator:gaac3600b16f957a209f857aff7f79bf91 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
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||
<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>
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||
<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>
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||
<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>
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||
<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>
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||
<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>
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||
<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>
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||
<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>
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||
<tr class="separator:ae8723856215191ef748f19ff73e8ba4e inherit pub_methods_classCDebugDumpable"><td class="memSeparator" colspan="2"> </td></tr>
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||
<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>
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||
<tr class="separator:acdeaaedfabb4cc4a64108dbb854f4b51 inherit pub_methods_classCDebugDumpable"><td class="memSeparator" colspan="2"> </td></tr>
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||
<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>
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||
<tr class="separator:a4ff9ec248a38f17b7d8deb3f78318a37 inherit pub_methods_classCDebugDumpable"><td class="memSeparator" colspan="2"> </td></tr>
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||
<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>
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||
<tr class="separator:aa0101dfdc0ae0cbd0cb1609c96f96229 inherit pub_methods_classCDebugDumpable"><td class="memSeparator" colspan="2"> </td></tr>
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||
<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>
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||
</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:ac8f0ff6e4f5bac2bd079c1c7725c52e2"><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="classCSeq__align.html#a59b599d4d23745a6ff33afb1bcbf0417">TScoreNameMap</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#ac8f0ff6e4f5bac2bd079c1c7725c52e2">ScoreNameMap</a> ()</td></tr>
|
||
<tr class="separator:ac8f0ff6e4f5bac2bd079c1c7725c52e2"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:a49d2554e931469d7a9f27034aad72591"><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="classCSeq__align.html#a49d2554e931469d7a9f27034aad72591">ScoreName</a> (<a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">EScoreType</a> score)</td></tr>
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||
<tr class="separator:a49d2554e931469d7a9f27034aad72591"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:a4eb373888d6af7611b794ed35df5482b"><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="classCSeq__align.html#a4eb373888d6af7611b794ed35df5482b">HelpText</a> (<a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">EScoreType</a> score)</td></tr>
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||
<tr class="separator:a4eb373888d6af7611b794ed35df5482b"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:ae6401d582f244a2d5ec9eb72bdab8a15"><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="classCSeq__align.html#ae6401d582f244a2d5ec9eb72bdab8a15">IsIntegerScore</a> (<a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">EScoreType</a> score)</td></tr>
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||
<tr class="separator:ae6401d582f244a2d5ec9eb72bdab8a15"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="inherit_header pub_static_methods_classCSeq__align__Base"><td colspan="2" onclick="javascript:toggleInherit('pub_static_methods_classCSeq__align__Base')"><img src="closed.png" alt="-"/> Static Public Member Functions inherited from <a class="el" href="classCSeq__align__Base.html">CSeq_align_Base</a></td></tr>
|
||
<tr class="memitem:ga8b5efb2553ab77361236737cad0e6065 inherit pub_static_methods_classCSeq__align__Base"><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> NCBI_NS_NCBI::CEnumeratedTypeValues *<a class="el" href="group__GenClassSupport.html#gaab9bc228ca2014a5451d4a8d47bee150">ENUM_METHOD_NAME</a>() </td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga8b5efb2553ab77361236737cad0e6065">EType</a> (void)</td></tr>
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||
<tr class="memdesc:ga8b5efb2553ab77361236737cad0e6065 inherit pub_static_methods_classCSeq__align__Base"><td class="mdescLeft"> </td><td class="mdescRight">Access to EType's attributes (values, names) as defined in spec. <a href="group__dataspec__NCBI__Seqalign.html#ga8b5efb2553ab77361236737cad0e6065">More...</a><br /></td></tr>
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<tr class="separator:ga8b5efb2553ab77361236737cad0e6065 inherit pub_static_methods_classCSeq__align__Base"><td class="memSeparator" colspan="2"> </td></tr>
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||
<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>
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||
<tr class="separator:gab2a92c7a5b5900317294b85e854db07e inherit pub_static_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
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||
<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>
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||
<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>
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||
<tr class="separator:gada3dbb83951d0bed9bde06c6c4ede9e2 inherit pub_static_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
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||
<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>
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||
<tr class="separator:ga123d82fb69550b6418ad5d69e752873a inherit pub_static_methods_classCSerialObject"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<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>
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||
<tr class="separator:gae042a181e665dd40945c1c1a7a6bc5d1 inherit pub_static_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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||
<tr class="separator:ga4b6f1beef2a1f37c68f7f3b1aac471d8 inherit pub_static_methods_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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||
<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>
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||
<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>
|
||
</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:a599cbe4e53d7bdd1f3afe232fd69f133"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCConstRef.html">CConstRef</a>< <a class="el" href="classCScore.html">CScore</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a599cbe4e53d7bdd1f3afe232fd69f133">x_GetNamedScore</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> &name) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:a599cbe4e53d7bdd1f3afe232fd69f133"><td class="mdescLeft"> </td><td class="mdescRight">retrieve a named score object <a href="classCSeq__align.html#a599cbe4e53d7bdd1f3afe232fd69f133">More...</a><br /></td></tr>
|
||
<tr class="separator:a599cbe4e53d7bdd1f3afe232fd69f133"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:a17ab1957cd28d6b7d6ce968bcdf72613"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCScore.html">CScore</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a17ab1957cd28d6b7d6ce968bcdf72613">x_SetNamedScore</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> &name)</td></tr>
|
||
<tr class="separator:a17ab1957cd28d6b7d6ce968bcdf72613"><td class="memSeparator" colspan="2"> </td></tr>
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||
<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>
|
||
</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:a90fe4bf50a2424f520efb8d69d3457be"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCSeq__align__Base.html">CSeq_align_Base</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a90fe4bf50a2424f520efb8d69d3457be">Tparent</a></td></tr>
|
||
<tr class="separator:a90fe4bf50a2424f520efb8d69d3457be"><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:ad45c27b777243bb2b56438684f50de0a"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#ad45c27b777243bb2b56438684f50de0a">CSeq_align</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSeq__align.html">CSeq_align</a> &<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="memdesc:ad45c27b777243bb2b56438684f50de0a"><td class="mdescLeft"> </td><td class="mdescRight">Prohibit copy constructor and assignment operator. <a href="classCSeq__align.html#ad45c27b777243bb2b56438684f50de0a">More...</a><br /></td></tr>
|
||
<tr class="separator:ad45c27b777243bb2b56438684f50de0a"><td class="memSeparator" colspan="2"> </td></tr>
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||
<tr class="memitem:a05bda771a42f8e72549a1397b6518794"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCSeq__align.html">CSeq_align</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a05bda771a42f8e72549a1397b6518794">operator=</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSeq__align.html">CSeq_align</a> &<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
|
||
<tr class="separator:a05bda771a42f8e72549a1397b6518794"><td class="memSeparator" colspan="2"> </td></tr>
|
||
<tr class="memitem:a1ec0983af480287bd51eb3f1ed0ebb99"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCSeq__align.html">CSeq_align</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeq__align.html#a1ec0983af480287bd51eb3f1ed0ebb99">x_CreateSubsegAlignment</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> from, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> to) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
|
||
<tr class="memdesc:a1ec0983af480287bd51eb3f1ed0ebb99"><td class="mdescLeft"> </td><td class="mdescRight">Create a partial alignment containing the specified range of segments. <a href="classCSeq__align.html#a1ec0983af480287bd51eb3f1ed0ebb99">More...</a><br /></td></tr>
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||
<tr class="separator:a1ec0983af480287bd51eb3f1ed0ebb99"><td class="memSeparator" colspan="2"> </td></tr>
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</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_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>
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||
<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>
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||
<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>
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||
<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>
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||
<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>
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||
<tr class="separator:gae6d5b68d219dbdb40e88737873a3488c inherit pub_static_attribs_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
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||
<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>
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<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>
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<tr class="separator:ga33e4da9c60adbc3cf2a0ca45ce21a2ba inherit pub_static_attribs_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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||
<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>
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<tr class="separator:ga0a412d4ea79669d73671f89cb3e798a2 inherit pub_static_attribs_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<tr class="separator:gab5880debef7cc7eb2a2891f440cd7569 inherit pub_static_attribs_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<tr class="separator:gaff6eaaf8b9c4040a05fe2325ab75f44e inherit pub_static_attribs_classCObject"><td class="memSeparator" colspan="2"> </td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
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<div class="textblock">
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<p class="definition">Definition at line <a class="el" href="Seq__align_8hpp_source.html#l00054">54</a> of file <a class="el" href="Seq__align_8hpp_source.html">Seq_align.hpp</a>.</p>
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</div><h2 class="groupheader">Member Typedef Documentation</h2>
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<a id="ae8447af5653b27fa09d886821029a4c7"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#ae8447af5653b27fa09d886821029a4c7">◆ </a></span>TLengthRange</h2>
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<td class="memname">typedef pair<<a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a>, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a>> <a class="el" href="classCSeq__align.html#ae8447af5653b27fa09d886821029a4c7">CSeq_align::TLengthRange</a></td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8hpp_source.html#l00192">192</a> of file <a class="el" href="Seq__align_8hpp_source.html">Seq_align.hpp</a>.</p>
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</div>
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<a id="a90fe4bf50a2424f520efb8d69d3457be"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a90fe4bf50a2424f520efb8d69d3457be">◆ </a></span>Tparent</h2>
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<td class="memname">typedef <a class="el" href="classCSeq__align__Base.html">CSeq_align_Base</a> <a class="el" href="classCSeq__align.html#a90fe4bf50a2424f520efb8d69d3457be">CSeq_align::Tparent</a></td>
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<span class="mlabels"><span class="mlabel">private</span></span> </td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8hpp_source.html#l00056">56</a> of file <a class="el" href="Seq__align_8hpp_source.html">Seq_align.hpp</a>.</p>
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</div>
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<a id="a59b599d4d23745a6ff33afb1bcbf0417"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a59b599d4d23745a6ff33afb1bcbf0417">◆ </a></span>TScoreNameMap</h2>
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<td class="memname">typedef <a class="el" href="classmap.html">map</a><<a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a>, <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">EScoreType</a>> <a class="el" href="classCSeq__align.html#a59b599d4d23745a6ff33afb1bcbf0417">CSeq_align::TScoreNameMap</a></td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8hpp_source.html#l00194">194</a> of file <a class="el" href="Seq__align_8hpp_source.html">Seq_align.hpp</a>.</p>
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<h2 class="groupheader">Member Enumeration Documentation</h2>
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<a id="a0a7501fd78111aeea55afdf681847c01"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a0a7501fd78111aeea55afdf681847c01">◆ </a></span>EScoreType</h2>
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<td class="memname">enum <a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">CSeq_align::EScoreType</a></td>
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||
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||
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||
<p>enum controlling known named scores </p>
|
||
<p>A word on scores, since definitions are quite important: Scores here are to be represented as a standard set of computations, comparable across alignment generation algorithms. The class <a class="el" href="classCScoreBuilder.html">CScoreBuilder</a> holds reference implementations for most of the scores below (modulo interpretation difficulties with a score named 'score'). The intended meanings of scores are as follows:</p>
|
||
<p>'score' generic score, definable by any algorithm; not comparable across algorithms.</p>
|
||
<p>'bit_score' BLAST-specific bit score; reference implementation in the BLAST code, which is also exposed in <a class="el" href="classCScoreBuilder.html">CScoreBuilder</a>.</p>
|
||
<p>'e_value' BLAST-specific e-value; reference implementation in the BLAST code, which is also exposed in <a class="el" href="classCScoreBuilder.html">CScoreBuilder</a>.</p>
|
||
<p>alignment length not a score per se, but a useful metric nonetheless. This is the sum of all aligned segments and all gaps; this excludes introns and discontinuities</p>
|
||
<p>percent identity percent identity, computed as *UNGAPPED* percent identity. That is, the computation is strictly (matches) / (matches + mismatches) NOTE: there are, historically, at least four separate methods of computation for this: 1. C++ toolkit (<a class="el" href="classCScoreBuilder.html">CScoreBuilder</a>): ungapped percent identity: (matches) / (matches + mismatches) 2. BLAST: gapped percent identity: (matches) / (alignment length) 3. gbDNA and contig processes: modified alignment length to count each gap as 1 base long always (matches) / (matches + mismatches + gap count) 4. Spidey: compute identity per coverage: (matches) / (stop - start + 1) Several of these are provided directly, as: pct_identity_gap pct_identity_ungap pct_identity_gapopen_only</p>
|
||
<p>alignable bases More a concept than a score. The alignable region of a sequence, as defined by the underlying sequencing technology or biology - that is, the region of a sequence noted as high quality minus a poly-A tail in the case of a cDNA. This quantity can be used in computing more appropriate coverage scores.</p>
|
||
<p>'pct_coverage' Percent of a sequence (query) aligned to another (subject), minus poly-A tail: (matches + mismatches) / (query length - polyA tail)</p>
|
||
<p>alignable percent coverage (<a class="el" href="classNB.html">NB</a>: no named score yet) Percent of the alignable region actually aligned to a subject (matches + mismatches in alignable region) / (length of alignable region)</p>
|
||
<p>exonic coverage (<a class="el" href="classNB.html">NB</a>: no named score yet) Measure of the percent of the query represented in a set of exons (sum of lengths of exon on query) / (query length - polyA)</p>
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||
<dl class="section warning"><dt>Warning</dt><dd>The order of this enumeration and the sc_ScoreNames, sc_ScoreHelpText, and sc_IsInteger arrays must correspond! </dd></dl>
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<table class="fieldtable">
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||
<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01a9cde7240e546570379c51fce0d2fdc07"></a>eScore_Score </td><td class="fielddoc"></td></tr>
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||
<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01a81436b76d980c991533ea073df6595ac"></a>eScore_Blast </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01aa78693920055c96636e6eb8382547bd2"></a>eScore_BitScore </td><td class="fielddoc"></td></tr>
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||
<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01a8e7cb4abab8e31d273ab7ac7cebe904f"></a>eScore_EValue </td><td class="fielddoc"></td></tr>
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||
<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01a8b206034192680e97bec91a259fa2e66"></a>eScore_AlignLength </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01aebeed46a10702323f38954054bf2d75d"></a>eScore_IdentityCount </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01ad014ecd153a9d12cd7d4bcd729ef6f99"></a>eScore_PositiveCount </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01aa82e92f460d31775cbaedf2601241f0a"></a>eScore_NegativeCount </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01afedb2a5a1a642865bc91d97ae7cc115b"></a>eScore_MismatchCount </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01a0e2e5d80919920444278e60f374adf03"></a>eScore_GapCount </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01a1dac2a7e5759c0c4e0f4006794beb216"></a>eScore_PercentIdentity_Gapped </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01aa2d67a9fda6e715efc9880152d362dfe"></a>eScore_PercentIdentity_Ungapped </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01a1c87d321a8d2c8f6f67e63deab8e6cfc"></a>eScore_PercentIdentity_GapOpeningOnly </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01ad4f7605cad81bd97a04504a4c63fbd27"></a>eScore_PercentCoverage </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01a8685247b6667ac4a0eda08c5d6ea24d9"></a>eScore_SumEValue </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01aea89e39c3219df67ffdc6afdd53e657f"></a>eScore_CompAdjMethod </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01adb8117f24d2dfa30ec95a8348b350a57"></a>eScore_HighQualityPercentCoverage </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01afcb9e5d9011e7b58357044c2eb9457c6"></a>eScore_Matches </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01a3db9aec8bf5278e428a88c0908963ad0"></a>eScore_OverallIdentity </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01ae9ca67a00f22300eea1b4711626d3cb7"></a>eScore_Splices </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01a316a91ecb5510dbf7db981d470bb0a18"></a>eScore_ConsensusSplices </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01ae85897f7a9a6dc10da39bc906fb151b5"></a>eScore_ProductCoverage </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01acaa810a22045f0235fc0ec9d9ac76b59"></a>eScore_ExonIdentity </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a0a7501fd78111aeea55afdf681847c01afadc41286b7a24bcb46403235ee3fd0a"></a>eScore_PercentIdentity </td><td class="fielddoc"></td></tr>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8hpp_source.html#l00128">128</a> of file <a class="el" href="Seq__align_8hpp_source.html">Seq_align.hpp</a>.</p>
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<a id="a2e40ec368f73515d029efb850d7aa483"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a2e40ec368f73515d029efb850d7aa483">◆ </a></span>CSeq_align() <span class="overload">[1/2]</span></h2>
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<td class="memname">CSeq_align::CSeq_align </td>
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<td>(</td>
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<td class="paramtype">void </td>
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<p>constructor </p>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8hpp_source.html#l00445">445</a> of file <a class="el" href="Seq__align_8hpp_source.html">Seq_align.hpp</a>.</p>
|
||
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<h2 class="memtitle"><span class="permalink"><a href="#ac873ad1fe8db9ed40f098ca730040e1d">◆ </a></span>~CSeq_align()</h2>
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<td class="memname">CSeq_align::~CSeq_align </td>
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<td>(</td>
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<td class="paramtype">void </td>
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<p>destructor </p>
|
||
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||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00068">68</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
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||
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<h2 class="memtitle"><span class="permalink"><a href="#ad45c27b777243bb2b56438684f50de0a">◆ </a></span>CSeq_align() <span class="overload">[2/2]</span></h2>
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<td class="memname">CSeq_align::CSeq_align </td>
|
||
<td>(</td>
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||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSeq__align.html">CSeq_align</a> & </td>
|
||
<td class="paramname"><em>value</em></td><td>)</td>
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||
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||
<p>Prohibit copy constructor and assignment operator. </p>
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||
<h2 class="groupheader">Member Function Documentation</h2>
|
||
<a id="a8dfa02516df3b7e99f392c053a962ed4"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a8dfa02516df3b7e99f392c053a962ed4">◆ </a></span>AlignLengthRatio()</h2>
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<td class="memname">double CSeq_align::AlignLengthRatio </td>
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<td>(</td>
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<td> const</td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l02017">2017</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="Seq__align_8cpp_source.html#l00153">GetSeqRange()</a>, <a class="el" href="njn__localmaxstatutil_8hpp.html#a528746e9ddcc245107c2546995139b42">r()</a>, <a class="el" href="sljitNativeS390X_8c_source.html#l00069">r0</a>, and <a class="el" href="sljitNativeS390X_8c_source.html#l00070">r1</a>.</p>
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<p class="reference">Referenced by <a class="el" href="score__lookup_8cpp_source.html#l00477">CScore_AlignLengthRatio::Get()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a75181a63597ffedae193a1f9c7d3a2f1">◆ </a></span>CheckNumRows()</h2>
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<td class="memname"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">CSeq_align::TDim</a> CSeq_align::CheckNumRows </td>
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<td>(</td>
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<td class="paramtype">void </td>
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<td class="paramname"></td><td>)</td>
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<td> const</td>
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<p>Validatiors. </p>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00073">73</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="Dense__seg_8cpp_source.html#l00092">CDense_seg::CheckNumRows()</a>, <a class="el" href="Sparse__seg_8cpp_source.html#l00063">CSparse_seg::CheckNumRows()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00133">CSeq_align_Base::C_Segs::e_Dendiag</a>, <a class="el" href="Seq__align___8hpp_source.html#l00134">CSeq_align_Base::C_Segs::e_Denseg</a>, <a class="el" href="Seq__align___8hpp_source.html#l00137">CSeq_align_Base::C_Segs::e_Disc</a>, <a class="el" href="Seq__align___8hpp_source.html#l00139">CSeq_align_Base::C_Segs::e_Sparse</a>, <a class="el" href="Seq__align___8hpp_source.html#l00138">CSeq_align_Base::C_Segs::e_Spliced</a>, <a class="el" href="Seq__align___8hpp_source.html#l00135">CSeq_align_Base::C_Segs::e_Std</a>, <a class="el" href="named__parameters_8hpp_source.html#l00099">Get()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00153">CSeq_align_Base::C_Segs::GetDenseg()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00921">CSeq_align_Base::GetSegs()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00241">CSeq_align_Base::C_Segs::GetSparse()</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00815">ITERATE</a>, and <a class="el" href="ncbiexpt_8hpp_source.html#l00704">NCBI_THROW</a>.</p>
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<p class="reference">Referenced by <a class="el" href="remove__sequences__from__alignments_8cpp_source.html#l00519">CRemoveSeqFromAlignDlg::ApplyToCSeq_entry()</a>, <a class="el" href="alignment__job_8cpp_source.html#l02252">BuildAlignDataSource()</a>, <a class="el" href="project__view__factory_8cpp_source.html#l00064">IProjectViewFactory::CombineInputObjects()</a>, <a class="el" href="project__view__factory_8cpp_source.html#l00132">IProjectViewFactory::CombineObjects()</a>, <a class="el" href="edit__table__views_8cpp_source.html#l00396">CTableViewWithTextViewNav::CombineObjects()</a>, <a class="el" href="aln__converters_8cpp_source.html#l00064">ConvertSeqAlignToPairwiseAln()</a>, <a class="el" href="aln__converters_8cpp_source.html#l00969">CreatePairwiseAlnFromSeqAlign()</a>, <a class="el" href="multi__align__view_8cpp_source.html#l00868">CMAViewManager::DoTransition()</a>, <a class="el" href="edit__seq__ends__with__align_8cpp_source.html#l00298">CEditSeqEndsWithAlign::FindPosition()</a>, <a class="el" href="edit__seq__ends__with__align_8cpp_source.html#l00283">CEditSeqEndsWithAlign::FindRow()</a>, <a class="el" href="update__seq_8cpp_source.html#l00611">CSequenceUpdater::FindRowInAlignment()</a>, <a class="el" href="Seq__align_8cpp_source.html#l02114">GapLengthRange()</a>, <a class="el" href="alignment__job_8cpp_source.html#l00208">CSGAlignmentJob::GetAlignType()</a>, <a class="el" href="na__utils_8cpp_source.html#l00077">CDataTrackUtils::GetAlignType()</a>, <a class="el" href="alignment__job_8cpp_source.html#l02174">GetAnchors()</a>, <a class="el" href="score__builder_8cpp_source.html#l00182">CScoreBuilder::GetBlastScore()</a>, <a class="el" href="gui_2objutils_2utils_8cpp_source.html#l01161">CSeqUtils::GetLocPlacements()</a>, <a class="el" href="align__group_8cpp_source.html#l00229">CAlignGroup::GroupByStrand()</a>, <a class="el" href="align__filter_8cpp_source.html#l00310">CAlignFilter::Match()</a>, <a class="el" href="multi__align__view_8cpp_source.html#l01045">CMAViewManager::NeedAnchorPanel()</a>, <a class="el" href="patch__sequence_8cpp_source.html#l00204">PatchTargetSequence()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l01176">CTabularFormatter_Defline::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l01294">CTabularFormatter_ProtRef::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l01523">CTabularFormatter_TaxId::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l01573">CTabularFormatter_Comment::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l01664">CTabularFormatter_OrgName::Print()</a>, <a class="el" href="revcomp__sequences_8cpp_source.html#l00283">CRevCompSequencesDlg::RevCompBioSeq()</a>, <a class="el" href="annot__compare__ds_8cpp_source.html#l00536">CFeatCompareJob_Align::Run()</a>, <a class="el" href="score__builder_8cpp_source.html#l00688">s_ComputeTraceback()</a>, <a class="el" href="objcoords_8cpp_source.html#l01017">s_ExtendEntriesFromAlignments()</a>, <a class="el" href="label_8cpp_source.html#l02444">s_GetAlignmentTooltip()</a>, <a class="el" href="gui_2objutils_2utils_8cpp_source.html#l01012">s_GetAlnMapplingLocs()</a>, <a class="el" href="gui_2objutils_2utils_8cpp_source.html#l01771">s_GetRnaMappingLocs()</a>, <a class="el" href="basic__converters_8cpp_source.html#l00350">s_Seq_align_Seq_loc()</a>, <a class="el" href="open__view__manager__impl_8cpp_source.html#l00331">CConversionResultPanel::SetObjects()</a>, <a class="el" href="align__tab__export__job_8cpp_source.html#l00057">sFindAnchorRow()</a>, <a class="el" href="align__tab__export__job_8cpp_source.html#l00165">sGenerateFields()</a>, <a class="el" href="gene__model_8cpp_source.html#l00380">CFeatureGenerator::SImplementation::SMapper::SMapper()</a>, <a class="el" href="convert__raw__to__delta_8cpp_source.html#l00172">UpdateDensegAlignment()</a>, <a class="el" href="Seq__align_8cpp_source.html#l00649">Validate()</a>, <a class="el" href="cleanup__alignments__tool__manager_8cpp_source.html#l00151">CCleanupAlignmentsToolManager::x_AreSelfAlignmentsOnly()</a>, <a class="el" href="edit__table__views_8cpp_source.html#l00342">CTableViewWithTextViewNav::x_EditObject()</a>, <a class="el" href="pkg__sequence__edit_2dll__register_8cpp_source.html#l01170">CSequenceEditingEventHandler::x_FindRelevantAlignRow()</a>, <a class="el" href="validate__panel_8cpp_source.html#l00739">CValidatePanel::x_LaunchEditor()</a>, <a class="el" href="feature__ds_8cpp_source.html#l02855">CBatchFeatJob::x_LoadFeatProducts()</a>, <a class="el" href="split__loader_8cpp_source.html#l00371">CSplitDataLoader::x_SplitAligns()</a>, and <a class="el" href="edit__object__feature__propagate_8cpp_source.html#l00315">CEditObjectFeaturePropagate::xInit()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a0d093ea51ad07028965a50434b7c9fa9">◆ </a></span>CreateDensegFromDisc()</h2>
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<td class="memname"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCSeq__align.html">CSeq_align</a> > CSeq_align::CreateDensegFromDisc </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="structCSeq__align_1_1SSeqIdChooser.html">SSeqIdChooser</a> * </td>
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<td class="paramname"><em>SeqIdChooser</em> = <code>0</code></td><td>)</td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01015">1015</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="test__assert__impl_8h_source.html#l00173">_ASSERT</a>, <a class="el" href="Seq__id_8cpp_source.html#l02266">CSeq_id::AsFastaString()</a>, <a class="el" href="structCSeq__align_1_1SSeqIdChooser.html#af9ecd6ca6c9dd561a089880937e2282b">CSeq_align::SSeqIdChooser::ChooseSeqId()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00100">CSeq_align_Base::eType_not_set</a>, <a class="el" href="named__parameters_8hpp_source.html#l00099">Get()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00421">CDense_seg_Base::GetDim()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00505">CDense_seg_Base::GetIds()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00555">CDense_seg_Base::GetLens()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00465">CDense_seg_Base::GetNumseg()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00896">CSeq_align_Base::GetScore()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00921">CSeq_align_Base::GetSegs()</a>, <a class="el" href="Dense__seg_8cpp_source.html#l00165">CDense_seg::GetSeqStart()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00530">CDense_seg_Base::GetStarts()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00580">CDense_seg_Base::GetStrands()</a>, <a class="el" href="Na__strand_8hpp_source.html#l00075">IsReverse()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00884">CSeq_align_Base::IsSetScore()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00568">CDense_seg_Base::IsSetStrands()</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00815">ITERATE</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l00704">NCBI_THROW</a>, <a class="el" href="string__bind_8c_source.html#l00073">row</a>, <a class="el" href="serialbase_8hpp_source.html#l00482">SerialAssign()</a>, <a class="el" href="serialbase_8hpp_source.html#l00497">SerialEquals()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00427">CDense_seg_Base::SetDim()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00511">CDense_seg_Base::SetIds()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00561">CDense_seg_Base::SetLens()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00474">CDense_seg_Base::SetNumseg()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00902">CSeq_align_Base::SetScore()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00310">CSeq_align_Base::SetSegs()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00536">CDense_seg_Base::SetStarts()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00586">CDense_seg_Base::SetStrands()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00818">CSeq_align_Base::SetType()</a>, <a class="el" href="namespacencbi_1_1grid_1_1netcache_1_1search_1_1fields.html#a0f3896dcec83a75496951b513af45a54">ncbi::grid::netcache::search::fields::size</a>, <a class="el" href="compile__time_8hpp_source.html#l00173">ct::sort()</a>, <a class="el" href="cgiapp_8hpp_source.html#l00690">string</a>, and <a class="el" href="Seq__align_8cpp_source.html#l00649">Validate()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="feature__propagate_8cpp_source.html#l00056">CFeaturePropagator::CFeaturePropagator()</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01596">s_GetIndels()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a1e3f25b2b080d97a62de8ab154c44f4f">◆ </a></span>CreateDensegFromStdseg()</h2>
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<td class="memname"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCSeq__align.html">CSeq_align</a> > CSeq_align::CreateDensegFromStdseg </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="structCSeq__align_1_1SSeqIdChooser.html">SSeqIdChooser</a> * </td>
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<td class="paramname"><em>SeqIdChooser</em> = <code>0</code></td><td>)</td>
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<p>---------------------------------------------------------------------------- PRE : the Seq-align has StdSeg segs POST: Seq_align of type Dense-seg is created with m_Widths if necessary </p>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00728">728</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="Seq__id_8cpp_source.html#l02266">CSeq_id::AsFastaString()</a>, <a class="el" href="Seq__interval___8hpp_source.html#l00464">CSeq_interval_Base::CanGetStrand()</a>, <a class="el" href="structCSeq__align_1_1SSeqIdChooser.html#af9ecd6ca6c9dd561a089880937e2282b">CSeq_align::SSeqIdChooser::ChooseSeqId()</a>, <a class="el" href="Na__strand___8hpp_source.html#l00065">eNa_strand_unknown</a>, <a class="el" href="Seq__align___8hpp_source.html#l00100">CSeq_align_Base::eType_not_set</a>, <a class="el" href="Std__seg___8hpp_source.html#l00295">CStd_seg_Base::GetDim()</a>, <a class="el" href="Seq__interval___8hpp_source.html#l00383">CSeq_interval_Base::GetFrom()</a>, <a class="el" href="Std__seg___8hpp_source.html#l00357">CStd_seg_Base::GetLoc()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00465">CDense_seg_Base::GetNumseg()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00896">CSeq_align_Base::GetScore()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00921">CSeq_align_Base::GetSegs()</a>, <a class="el" href="Seq__interval___8hpp_source.html#l00477">CSeq_interval_Base::GetStrand()</a>, <a class="el" href="Seq__interval___8hpp_source.html#l00430">CSeq_interval_Base::GetTo()</a>, <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>, <a class="el" href="Seq__align___8hpp_source.html#l00884">CSeq_align_Base::IsSetScore()</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00815">ITERATE</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l00704">NCBI_THROW</a>, <a class="el" href="Dense__seg_8hpp_source.html#l00225">CDense_seg::ResetWidths()</a>, <a class="el" href="string__bind_8c_source.html#l00073">row</a>, <a class="el" href="serialbase_8hpp_source.html#l00482">SerialAssign()</a>, <a class="el" href="serialbase_8hpp_source.html#l00497">SerialEquals()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00427">CDense_seg_Base::SetDim()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00511">CDense_seg_Base::SetIds()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00561">CDense_seg_Base::SetLens()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00474">CDense_seg_Base::SetNumseg()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00902">CSeq_align_Base::SetScore()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00310">CSeq_align_Base::SetSegs()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00536">CDense_seg_Base::SetStarts()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00586">CDense_seg_Base::SetStrands()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00818">CSeq_align_Base::SetType()</a>, <a class="el" href="Dense__seg_8hpp_source.html#l00217">CDense_seg::SetWidths()</a>, and <a class="el" href="cgiapp_8hpp_source.html#l00690">string</a>.</p>
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<p class="reference">Referenced by <a class="el" href="alnmix_8cpp_source.html#l00095">CAlnMix::Add()</a>, <a class="el" href="feature__propagate_8cpp_source.html#l00093">CFeaturePropagator::CFeaturePropagator()</a>, <a class="el" href="showalign_8cpp_source.html#l01910">CDisplaySeqalign::DisplaySeqalign()</a>, <a class="el" href="align__format__util_8cpp_source.html#l01336">CAlignFormatUtil::GetAlignmentLength()</a>, <a class="el" href="cigar_8cpp_source.html#l00164">SCigarAlignment::operator()()</a>, <a class="el" href="blastxml2__format_8cpp_source.html#l00096">s_SeqAlignSetToXMLHsps()</a>, <a class="el" href="tabular_8cpp_source.html#l00743">CBlastTabularInfo::SetFields()</a>, <a class="el" href="cigar__formatter_8cpp_source.html#l00084">CCIGAR_Formatter::x_FormatAlignmentRows()</a>, and <a class="el" href="showalign_8cpp_source.html#l01817">CDisplaySeqalign::x_GetAlnVecForSeqalign()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a718ea26ead4d345db111595705e26b04">◆ </a></span>CreateRowSeq_loc()</h2>
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<td class="memname"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCSeq__loc.html">CSeq_loc</a> > CSeq_align::CreateRowSeq_loc </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
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<td class="paramname"><em>row</em></td><td>)</td>
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<td> const</td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l02028">2028</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="Seq__align___8hpp_source.html#l00133">CSeq_align_Base::C_Segs::e_Dendiag</a>, <a class="el" href="Seq__align___8hpp_source.html#l00134">CSeq_align_Base::C_Segs::e_Denseg</a>, <a class="el" href="Seq__align___8hpp_source.html#l00137">CSeq_align_Base::C_Segs::e_Disc</a>, <a class="el" href="Seq__align___8hpp_source.html#l00136">CSeq_align_Base::C_Segs::e_Packed</a>, <a class="el" href="Seq__align___8hpp_source.html#l00139">CSeq_align_Base::C_Segs::e_Sparse</a>, <a class="el" href="Seq__align___8hpp_source.html#l00138">CSeq_align_Base::C_Segs::e_Spliced</a>, <a class="el" href="Seq__align___8hpp_source.html#l00135">CSeq_align_Base::C_Segs::e_Std</a>, <a class="el" href="named__parameters_8hpp_source.html#l00099">Get()</a>, <a class="el" href="Spliced__seg___8hpp_source.html#l00692">CSpliced_seg_Base::GetExons()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00921">CSeq_align_Base::GetSegs()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00219">CSeq_align_Base::C_Segs::GetSpliced()</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00815">ITERATE</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l00704">NCBI_THROW</a>, <a class="el" href="string__bind_8c_source.html#l00073">row</a>, <a class="el" href="Seq__loc_8hpp_source.html#l00983">CSeq_loc::SetInt()</a>, <a class="el" href="Seq__loc_8hpp_source.html#l00987">CSeq_loc::SetMix()</a>, and <a class="el" href="Seq__loc_8hpp_source.html#l00984">CSeq_loc::SetPacked_int()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="variation__util2_8cpp_source.html#l03161">variation::CVariationUtil::FindLocationProperties()</a>, <a class="el" href="internal__stops_8cpp_source.html#l00069">CInternalStopFinder::FindStartStopRanges()</a>, <a class="el" href="desktop__typed__items_8cpp_source.html#l00586">CDesktopAlignItem::s_ContainsFarPointers()</a>, <a class="el" href="pkg__sequence__edit_2dll__register_8cpp_source.html#l01011">CSequenceEditingEventHandler::x_CacheSelectedLocations()</a>, <a class="el" href="alignment__job_8cpp_source.html#l01118">CSGAlignmentJob::x_GetAlignments()</a>, <a class="el" href="gene__model_8cpp_source.html#l02993">CFeatureGenerator::SImplementation::x_HandleCdsExceptions()</a>, and <a class="el" href="id__mapper__app_8cpp_source.html#l00554">CIdMapperTestApp::x_RecurseMapSeqAligns()</a>.</p>
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</div>
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</div>
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<a id="a01fd58c2eeecadeac3fae344bf46dab2"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a01fd58c2eeecadeac3fae344bf46dab2">◆ </a></span>CreateTranslatedDensegFromNADenseg()</h2>
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<td class="memname"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCSeq__align.html">CSeq_align</a> > CSeq_align::CreateTranslatedDensegFromNADenseg </td>
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<td>(</td>
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<td class="paramtype">void </td>
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<td class="paramname"></td><td>)</td>
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<td> const</td>
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<p>Create a Dense-seg with widths from Dense-seg of nucleotides Used by AlnMgr to handle translated nucl2nucl alignments IMPORTANT NOTE: Do *NOT* use for alignments containing proteins; the code will not check for this. </p>
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||
<p>---------------------------------------------------------------------------- PRE : the Seq-align is a Dense-seg of aligned nucleotide sequences POST: Seq_align of type Dense-seg is created with each of the m_Widths equal to 3 and m_Lengths devided by 3.</p>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00953">953</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="serialobject_8cpp_source.html#l00084">CSerialObject::Assign()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00100">CSeq_align_Base::eType_not_set</a>, <a class="el" href="Seq__align___8cpp_source.html#l00153">CSeq_align_Base::C_Segs::GetDenseg()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00421">CDense_seg_Base::GetDim()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00555">CDense_seg_Base::GetLens()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00465">CDense_seg_Base::GetNumseg()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00921">CSeq_align_Base::GetSegs()</a>, <a class="el" href="corelib_2ncbistr_8hpp_source.html#l05078">NStr::IntToString()</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l00704">NCBI_THROW</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00561">CDense_seg_Base::SetLens()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00310">CSeq_align_Base::SetSegs()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00818">CSeq_align_Base::SetType()</a>, <a class="el" href="Dense__seg_8hpp_source.html#l00217">CDense_seg::SetWidths()</a>, <a class="el" href="cgiapp_8hpp_source.html#l00690">string</a>, and <a class="el" href="Dense__seg_8cpp_source.html#l00274">CDense_seg::Validate()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="align__format__util_8cpp_source.html#l01336">CAlignFormatUtil::GetAlignmentLength()</a>, <a class="el" href="blastxml2__format_8cpp_source.html#l00096">s_SeqAlignSetToXMLHsps()</a>, <a class="el" href="tabular_8cpp_source.html#l00743">CBlastTabularInfo::SetFields()</a>, and <a class="el" href="showalign_8cpp_source.html#l01817">CDisplaySeqalign::x_GetAlnVecForSeqalign()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a2816ade4f70cd458a8e7d9916be35518">◆ </a></span>ExonLengthRange()</h2>
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<td class="memname"><a class="el" href="classCSeq__align.html#ae8447af5653b27fa09d886821029a4c7">CSeq_align::TLengthRange</a> CSeq_align::ExonLengthRange </td>
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<td>(</td>
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<td class="paramname"></td><td>)</td>
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<td> const</td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l02214">2214</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="Seq__align_8cpp_source.html#l02092">SLengthRange::AddLength()</a>, <a class="el" href="Spliced__exon___8hpp_source.html#l00814">CSpliced_exon_Base::GetGenomic_end()</a>, <a class="el" href="Spliced__exon___8hpp_source.html#l00767">CSpliced_exon_Base::GetGenomic_start()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00921">CSeq_align_Base::GetSegs()</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00815">ITERATE</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l00704">NCBI_THROW</a>, and <a class="el" href="Seq__align_8cpp_source.html#l02111">SLengthRange::range</a>.</p>
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<p class="reference">Referenced by <a class="el" href="score__lookup_8cpp_source.html#l00619">CScore_MinExonLength::Get()</a>.</p>
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<a id="adf3fc863310039e51c5e63b575104f4f"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#adf3fc863310039e51c5e63b575104f4f">◆ </a></span>FindExt() <span class="overload">[1/2]</span></h2>
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<td class="memname"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCUser__object.html">CUser_object</a> > CSeq_align::FindExt </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> & </td>
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<td class="paramname"><em>ext_type</em></td><td>)</td>
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<td></td>
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<p>Non-const version of <a class="el" href="classCSeq__align.html#ae3d3081b4316011a7ee6b248f2f46f86" title="Find extension by type in ext container.">FindExt()</a>. </p>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l02289">2289</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="Object__id___8hpp_source.html#l00297">CObject_id_Base::GetStr()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00989">CSeq_align_Base::IsSetExt()</a>, <a class="el" href="Object__id___8hpp_source.html#l00291">CObject_id_Base::IsStr()</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00822">NON_CONST_ITERATE</a>, <a class="el" href="ncbiobj_8hpp_source.html#l00773">CRef< C, Locker >::Reset()</a>, and <a class="el" href="Seq__align___8hpp_source.html#l01007">CSeq_align_Base::SetExt()</a>.</p>
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</div>
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<a id="ae3d3081b4316011a7ee6b248f2f46f86"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#ae3d3081b4316011a7ee6b248f2f46f86">◆ </a></span>FindExt() <span class="overload">[2/2]</span></h2>
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<td class="memname"><a class="el" href="classCConstRef.html">CConstRef</a>< <a class="el" href="classCUser__object.html">CUser_object</a> > CSeq_align::FindExt </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> & </td>
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<td class="paramname"><em>ext_type</em></td><td>)</td>
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<td> const</td>
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<p>Find extension by type in ext container. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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||
<table class="params">
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<tr><td class="paramname">ext_type</td><td>String id of the extension to find. </td></tr>
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||
</table>
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</dd>
|
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<dl class="section return"><dt>Returns</dt><dd>User-object of the requested type or NULL. </dd></dl>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l02274">2274</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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||
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<p class="reference">References <a class="el" href="Seq__align___8hpp_source.html#l01001">CSeq_align_Base::GetExt()</a>, <a class="el" href="Object__id___8hpp_source.html#l00297">CObject_id_Base::GetStr()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00989">CSeq_align_Base::IsSetExt()</a>, <a class="el" href="Object__id___8hpp_source.html#l00291">CObject_id_Base::IsStr()</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00815">ITERATE</a>, and <a class="el" href="ncbiobj_8hpp_source.html#l01439">CConstRef< C, Locker >::Reset()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="magicblast__util_8cpp_source.html#l01008">PrintSAM()</a>, and <a class="el" href="magicblast__util_8cpp_source.html#l00441">PrintTabular()</a>.</p>
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<a id="adb3adece65b714acf63aab32a3a1ee56"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#adb3adece65b714acf63aab32a3a1ee56">◆ </a></span>GapLengthRange()</h2>
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<td class="memname"><a class="el" href="classCSeq__align.html#ae8447af5653b27fa09d886821029a4c7">CSeq_align::TLengthRange</a> CSeq_align::GapLengthRange </td>
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||
<td>(</td>
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||
<td class="paramname"></td><td>)</td>
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<td> const</td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l02114">2114</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="Seq__align_8cpp_source.html#l02092">SLengthRange::AddLength()</a>, <a class="el" href="Seq__align_8cpp_source.html#l02101">SLengthRange::AddRange()</a>, <a class="el" href="Seq__align_8cpp_source.html#l00073">CheckNumRows()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00134">CSeq_align_Base::C_Segs::e_Denseg</a>, <a class="el" href="Seq__align___8hpp_source.html#l00137">CSeq_align_Base::C_Segs::e_Disc</a>, <a class="el" href="Seq__align___8hpp_source.html#l00138">CSeq_align_Base::C_Segs::e_Spliced</a>, <a class="el" href="named__parameters_8hpp_source.html#l00099">Get()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00153">CSeq_align_Base::C_Segs::GetDenseg()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00421">CDense_seg_Base::GetDim()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00555">CDense_seg_Base::GetLens()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00465">CDense_seg_Base::GetNumseg()</a>, <a class="el" href="Spliced__exon_8cpp_source.html#l00142">CSpliced_exon::GetRowSeq_insertions()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00921">CSeq_align_Base::GetSegs()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00530">CDense_seg_Base::GetStarts()</a>, <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00815">ITERATE</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l00704">NCBI_THROW</a>, <a class="el" href="njn__localmaxstatutil_8hpp.html#a528746e9ddcc245107c2546995139b42">r()</a>, <a class="el" href="Seq__align_8cpp_source.html#l02111">SLengthRange::range</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01183">s_Distance()</a>.</p>
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||
<p class="reference">Referenced by <a class="el" href="score__lookup_8cpp_source.html#l00245">CScore_LongestGapLength::Get()</a>.</p>
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<a id="a2d99ace5e945d611a25e6150279a7e25"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a2d99ace5e945d611a25e6150279a7e25">◆ </a></span>GetAlignedBases()</h2>
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<td class="memname"><a class="el" href="classCRangeCollection.html">CRangeCollection</a>< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > CSeq_align::GetAlignedBases </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
|
||
<td class="paramname"><em>row</em></td><td>)</td>
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<p>Retrieves the locations of aligned bases in the given row, excluding gaps and incontinuities. </p>
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||
<dl class="exception"><dt>Exceptions</dt><dd>
|
||
<table class="exception">
|
||
<tr><td class="paramname"><a class="el" href="classCSeqalignException.html">CSeqalignException</a></td><td>if alignment type is not supported </td></tr>
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||
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|
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01796">1796</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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||
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<p class="reference">References <a class="el" href="Seq__align___8hpp_source.html#l00134">CSeq_align_Base::C_Segs::e_Denseg</a>, <a class="el" href="Seq__align___8hpp_source.html#l00137">CSeq_align_Base::C_Segs::e_Disc</a>, <a class="el" href="Seq__align___8hpp_source.html#l00138">CSeq_align_Base::C_Segs::e_Spliced</a>, <a class="el" href="named__parameters_8hpp_source.html#l00099">Get()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00153">CSeq_align_Base::C_Segs::GetDenseg()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00421">CDense_seg_Base::GetDim()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00555">CDense_seg_Base::GetLens()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00465">CDense_seg_Base::GetNumseg()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00921">CSeq_align_Base::GetSegs()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00530">CDense_seg_Base::GetStarts()</a>, <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00815">ITERATE</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l00704">NCBI_THROW</a>, and <a class="el" href="string__bind_8c_source.html#l00073">row</a>.</p>
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<p class="reference">Referenced by <a class="el" href="score__lookup_8cpp_source.html#l01368">CScore_Overlap::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l01431">CScore_OverlapBoth::Get()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l00816">CTabularFormatter_GapRanges::Print()</a>, and <a class="el" href="align__filter_8cpp_source.html#l00517">CAlignFilter::x_FuncCall()</a>.</p>
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<a id="ab212b5bf2e03db11215dc938646d484a"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#ab212b5bf2e03db11215dc938646d484a">◆ </a></span>GetAlignLength()</h2>
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<td class="memname"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> CSeq_align::GetAlignLength </td>
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<td>(</td>
|
||
<td class="paramtype"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td>
|
||
<td class="paramname"><em>include_gaps</em> = <code><a class="el" href="ftds14_2freetds_2freetds_2bool_8h.html#a41f9c5fb8b08eb5dc3edce4dcb37fee7">true</a></code></td><td>)</td>
|
||
<td> const</td>
|
||
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|
||
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|
||
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|
||
|
||
<p>Get the length of this alignment. </p>
|
||
<p>This length corresponds to the score 'align_length'. By default, this function computes an alignment length including all gap segments. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01993">1993</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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||
<p class="reference">References <a class="el" href="range_8hpp_source.html#l00272">COpenRange< TSeqPos >::GetWhole()</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01865">s_GetAlignmentLength()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="sam__formatter_8cpp_source.html#l00179">CSAM_CIGAR_Formatter::AddRow()</a>, <a class="el" href="sequpd_8cpp_source.html#l00614">sequpd::CompareAlignments()</a>, <a class="el" href="score__lookup_8cpp_source.html#l00087">CScore_AlignLength::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l00565">CScore_SymmetricOverlap::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l01235">CScore_Coverage::Get()</a>, <a class="el" href="score__builder__base_8cpp_source.html#l00850">CScoreBuilderBase::GetAlignLength()</a>, <a class="el" href="best__placement_8cpp_source.html#l00395">SAlignmentScoringModel::GetIdentOdds()</a>, <a class="el" href="best__placement_8cpp_source.html#l00137">SAlignmentScoringModel::GetScore()</a>, <a class="el" href="asn1_8cpp_source.html#l00935">CAlignModel::MakeSeqAlign()</a>, <a class="el" href="genomic__compart_8cpp_source.html#l00298">SSeqAlignsBySize::operator()()</a>, <a class="el" href="genomic__compart_8cpp_source.html#l00337">SSeqAlignsByPctIdent::operator()()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l02043">CTabularFormatter_AlignLengthRatio::Print()</a>, <a class="el" href="igblast_8cpp_source.html#l00869">s_CompareSeqAlignByEvalue()</a>, <a class="el" href="igblast_8cpp_source.html#l00896">s_CompareSeqAlignByScore()</a>, <a class="el" href="igblast_8cpp_source.html#l00530">s_CompareSeqAlignByScoreAndName()</a>, <a class="el" href="igblast_8hpp_source.html#l00432">ScorePositionSort::s_CompareSeqAlignByScoreAndPosition()</a>, <a class="el" href="score__builder__base_8cpp_source.html#l00285">s_GetCountIdentityMismatch()</a>, <a class="el" href="best__placement_8cpp_source.html#l00321">SAlignmentScoringModel::s_GetIdentOdds_protSS()</a>, <a class="el" href="igblast_8cpp_source.html#l00791">s_IsSeqAlignAsGood()</a>, <a class="el" href="blastxml2__format_8cpp_source.html#l00096">s_SeqAlignSetToXMLHsps()</a>, and <a class="el" href="alignment__scorer_8cpp_source.html#l00213">CWeightedIdentityScorer::ScoreAlignments()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a87c8ad395ebf1b07fbfa4cff17a159f5"></a>
|
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<h2 class="memtitle"><span class="permalink"><a href="#a87c8ad395ebf1b07fbfa4cff17a159f5">◆ </a></span>GetAlignLengthWithinRange()</h2>
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<td class="memname"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> CSeq_align::GetAlignLengthWithinRange </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__RangeSupport.html#gabb457385e479479764dd959a1d182765">TSeqRange</a> & </td>
|
||
<td class="paramname"><em>range</em>, </td>
|
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</tr>
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<tr>
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<td class="paramkey"></td>
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<td></td>
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<td class="paramtype"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td>
|
||
<td class="paramname"><em>include_gaps</em> = <code><a class="el" href="ftds14_2freetds_2freetds_2bool_8h.html#a41f9c5fb8b08eb5dc3edce4dcb37fee7">true</a></code> </td>
|
||
</tr>
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||
<tr>
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<td></td>
|
||
<td>)</td>
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<td></td><td> const</td>
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</tr>
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</table>
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||
</div><div class="memdoc">
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|
||
<p>Get the length of this alignment within a specified range By default, this function computes an alignment length including all gap segments. </p>
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||
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||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l02001">2001</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
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|
||
<p class="reference">References <a class="el" href="namespacecompile__time__bits.html#a440fbf17793b1d9f93090ea6898dac32">compile_time_bits::range()</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01865">s_GetAlignmentLength()</a>.</p>
|
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|
||
<p class="reference">Referenced by <a class="el" href="score__builder__base_8cpp_source.html#l00870">CScoreBuilderBase::GetAlignLength()</a>.</p>
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</div>
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</div>
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<a id="ac5128aef39a4ea6e8c676154beb6c0ed"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#ac5128aef39a4ea6e8c676154beb6c0ed">◆ </a></span>GetAlignLengthWithinRanges()</h2>
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<td class="memname"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> CSeq_align::GetAlignLengthWithinRanges </td>
|
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<td>(</td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCRangeCollection.html">CRangeCollection</a>< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > & </td>
|
||
<td class="paramname"><em>ranges</em>, </td>
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</tr>
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<tr>
|
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<td class="paramkey"></td>
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<td></td>
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||
<td class="paramtype"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td>
|
||
<td class="paramname"><em>include_gaps</em> = <code><a class="el" href="ftds14_2freetds_2freetds_2bool_8h.html#a41f9c5fb8b08eb5dc3edce4dcb37fee7">true</a></code> </td>
|
||
</tr>
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||
<tr>
|
||
<td></td>
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<td>)</td>
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<td></td><td> const</td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Get the length of this alignment within a specified range By default, this function computes an alignment length including all gap segments. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l02010">2010</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="Seq__align_8cpp_source.html#l01865">s_GetAlignmentLength()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="score__builder__base_8cpp_source.html#l01181">CScoreBuilderBase::ComputeScore()</a>, <a class="el" href="score__builder__base_8cpp_source.html#l00893">CScoreBuilderBase::GetAlignLength()</a>, <a class="el" href="score__builder__base_8cpp_source.html#l00537">s_GetPercentCoverage()</a>, and <a class="el" href="score__builder__base_8cpp_source.html#l00453">s_GetPercentIdentity()</a>.</p>
|
||
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</div>
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</div>
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<a id="ab63468109dc5871caa430d34fe7dfba8"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#ab63468109dc5871caa430d34fe7dfba8">◆ </a></span>GetFrameshifts()</h2>
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<tr>
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<td class="memname">vector< <a class="el" href="structCSeq__align_1_1SIndel.html">CSeq_align::SIndel</a> > CSeq_align::GetFrameshifts </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
|
||
<td class="paramname"><em>row</em> = <code>-1</code></td><td>)</td>
|
||
<td> const</td>
|
||
</tr>
|
||
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|
||
</div><div class="memdoc">
|
||
|
||
<p>Retrieves descriptions of all frameshifts on a given row; i.e. </p>
|
||
<p>all gaps with a length that is not a multiple of 3. </p><dl class="exception"><dt>Exceptions</dt><dd>
|
||
<table class="exception">
|
||
<tr><td class="paramname"><a class="el" href="classCSeqalignException.html">CSeqalignException</a></td><td>if alignment type is not supported </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01741">1741</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="range_8hpp_source.html#l00272">COpenRange< TSeqPos >::GetWhole()</a>, <a class="el" href="string__bind_8c_source.html#l00073">row</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01596">s_GetIndels()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a8968c122b97da0f9cd320fc941c8a43d"></a>
|
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<h2 class="memtitle"><span class="permalink"><a href="#a8968c122b97da0f9cd320fc941c8a43d">◆ </a></span>GetFrameshiftsWithinRange()</h2>
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||
<div class="memitem">
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||
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|
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||
<td class="memname">vector< <a class="el" href="structCSeq__align_1_1SIndel.html">CSeq_align::SIndel</a> > CSeq_align::GetFrameshiftsWithinRange </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__RangeSupport.html#gabb457385e479479764dd959a1d182765">TSeqRange</a> & </td>
|
||
<td class="paramname"><em>range</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
|
||
<td class="paramname"><em>row</em> = <code>-1</code> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td> const</td>
|
||
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|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01747">1747</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="namespacecompile__time__bits.html#a440fbf17793b1d9f93090ea6898dac32">compile_time_bits::range()</a>, <a class="el" href="string__bind_8c_source.html#l00073">row</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01596">s_GetIndels()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="tabular__fmt_8cpp_source.html#l02510">CTabularFormatter_Indels::Print()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="ac9542ed1bee82529e62ba6fc4d87e81e"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#ac9542ed1bee82529e62ba6fc4d87e81e">◆ </a></span>GetFrameshiftsWithinRanges()</h2>
|
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|
||
<div class="memitem">
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||
<div class="memproto">
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<table class="memname">
|
||
<tr>
|
||
<td class="memname">vector< <a class="el" href="structCSeq__align_1_1SIndel.html">CSeq_align::SIndel</a> > CSeq_align::GetFrameshiftsWithinRanges </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCRangeCollection.html">CRangeCollection</a>< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > & </td>
|
||
<td class="paramname"><em>ranges</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
|
||
<td class="paramname"><em>row</em> = <code>-1</code> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td> const</td>
|
||
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|
||
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|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01753">1753</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="string__bind_8c_source.html#l00073">row</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01596">s_GetIndels()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="ac01cbd2f42d297bf8129c8bdb40d31bf"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#ac01cbd2f42d297bf8129c8bdb40d31bf">◆ </a></span>GetIndels()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">vector< <a class="el" href="structCSeq__align_1_1SIndel.html">CSeq_align::SIndel</a> > CSeq_align::GetIndels </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
|
||
<td class="paramname"><em>row</em> = <code>-1</code></td><td>)</td>
|
||
<td> const</td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Retrieves descriptions of all indels on a given row. </p>
|
||
<dl class="exception"><dt>Exceptions</dt><dd>
|
||
<table class="exception">
|
||
<tr><td class="paramname"><a class="el" href="classCSeqalignException.html">CSeqalignException</a></td><td>if alignment type is not supported </td></tr>
|
||
</table>
|
||
</dd>
|
||
</dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01777">1777</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="range_8hpp_source.html#l00272">COpenRange< TSeqPos >::GetWhole()</a>, <a class="el" href="string__bind_8c_source.html#l00073">row</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01596">s_GetIndels()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a98b8b94878c00a567c5b45494ceb34d7"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a98b8b94878c00a567c5b45494ceb34d7">◆ </a></span>GetIndelsWithinRange()</h2>
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||
<div class="memitem">
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||
<div class="memproto">
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<table class="memname">
|
||
<tr>
|
||
<td class="memname">vector< <a class="el" href="structCSeq__align_1_1SIndel.html">CSeq_align::SIndel</a> > CSeq_align::GetIndelsWithinRange </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__RangeSupport.html#gabb457385e479479764dd959a1d182765">TSeqRange</a> & </td>
|
||
<td class="paramname"><em>range</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
|
||
<td class="paramname"><em>row</em> = <code>-1</code> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
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<td></td><td> const</td>
|
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|
||
</div><div class="memdoc">
|
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|
||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01783">1783</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="namespacecompile__time__bits.html#a440fbf17793b1d9f93090ea6898dac32">compile_time_bits::range()</a>, <a class="el" href="string__bind_8c_source.html#l00073">row</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01596">s_GetIndels()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="tabular__fmt_8cpp_source.html#l02510">CTabularFormatter_Indels::Print()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a2acb690a377c462a9a9db3c528b2c22b"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a2acb690a377c462a9a9db3c528b2c22b">◆ </a></span>GetIndelsWithinRanges()</h2>
|
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||
<div class="memitem">
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||
<div class="memproto">
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<table class="memname">
|
||
<tr>
|
||
<td class="memname">vector< <a class="el" href="structCSeq__align_1_1SIndel.html">CSeq_align::SIndel</a> > CSeq_align::GetIndelsWithinRanges </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCRangeCollection.html">CRangeCollection</a>< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > & </td>
|
||
<td class="paramname"><em>ranges</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
|
||
<td class="paramname"><em>row</em> = <code>-1</code> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
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<td></td><td> const</td>
|
||
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|
||
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||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01789">1789</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="string__bind_8c_source.html#l00073">row</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01596">s_GetIndels()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a64a1edcedc36bba2e8d554d2a2b2708c"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a64a1edcedc36bba2e8d554d2a2b2708c">◆ </a></span>GetNamedScore() <span class="overload">[1/4]</span></h2>
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<td class="memname"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> CSeq_align::GetNamedScore </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> & </td>
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<p>--------------------------------------------------------------------------- PRE : name of score to return POST: whether or not we found that score; score converted to double </p>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00580">580</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="Seq__align_8cpp_source.html#l00520">x_GetNamedScore()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a80224af23d990db9de01aa7b8a3e9c06">◆ </a></span>GetNamedScore() <span class="overload">[2/4]</span></h2>
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<td class="memname"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> CSeq_align::GetNamedScore </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> & </td>
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<td class="paramname"><em>id</em>, </td>
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<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> & </td>
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<td class="paramname"><em>score</em> </td>
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<p>Get score. </p>
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<p>--------------------------------------------------------------------------- PRE : name of score to return POST: whether or not we found that score; score converted to int </p>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00563">563</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="dbapi_2driver_2types_8hpp_source.html#l01210">int</a>, and <a class="el" href="Seq__align_8cpp_source.html#l00520">x_GetNamedScore()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="score__builder__unit__test_8cpp_source.html#l00087">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="mate__pair__glyph_8cpp_source.html#l00047">CMatePairGlyph::CMatePairGlyph()</a>, <a class="el" href="vecscreen__run_8cpp_source.html#l00322">CVecscreenRun::CFormatter::FormatResults()</a>, <a class="el" href="blast__aligner_8cpp_source.html#l00214">CBlastAligner::GenerateAlignments()</a>, <a class="el" href="blast__aligner_8cpp_source.html#l00367">CRemoteBlastAligner::GenerateAlignments()</a>, <a class="el" href="Seq__align_8cpp_source.html#l00595">GetNamedScore()</a>, <a class="el" href="cuBlast2Seq_8cpp_source.html#l00370">CdBlaster::getPsiBlastEValue()</a>, <a class="el" href="cuBlast2Seq_8cpp_source.html#l00359">CdBlaster::getPsiBlastScore()</a>, <a class="el" href="genomic__compart_8cpp_source.html#l00325">SSeqAlignsByScore::operator()()</a>, <a class="el" href="genomic__compart_8cpp_source.html#l00337">SSeqAlignsByPctIdent::operator()()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l00899">CTabularFormatter_EValue_Mantissa::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l00949">CTabularFormatter_EValue_Exponent::Print()</a>, <a class="el" href="magicblast__util_8cpp_source.html#l01008">PrintSAM()</a>, <a class="el" href="magicblast__util_8cpp_source.html#l00441">PrintTabular()</a>, <a class="el" href="cuBlast2Seq_8cpp_source.html#l00448">CdBlaster::processBlastHits()</a>, <a class="el" href="cuSimpleB2SWrapper_8cpp_source.html#l00338">CSimpleB2SWrapper::processBlastHits()</a>, <a class="el" href="transform__align_8cpp_source.html#l00471">CFeatureGenerator::SImplementation::RecalculateScores()</a>, <a class="el" href="blastp__tests_8cpp_source.html#l00087">CTestBlastp_All::RunTest()</a>, <a class="el" href="gui__object__info__seq__align_8cpp_source.html#l00318">s_AddReciprocityScore()</a>, <a class="el" href="alignment__job_8cpp_source.html#l00348">s_CheckTraceMateAlign()</a>, <a class="el" href="igblast_8cpp_source.html#l00869">s_CompareSeqAlignByEvalue()</a>, <a class="el" href="igblast_8cpp_source.html#l00896">s_CompareSeqAlignByScore()</a>, <a class="el" href="igblast_8cpp_source.html#l00530">s_CompareSeqAlignByScoreAndName()</a>, <a class="el" href="igblast_8hpp_source.html#l00432">ScorePositionSort::s_CompareSeqAlignByScoreAndPosition()</a>, <a class="el" href="label_8cpp_source.html#l02444">s_GetAlignmentTooltip()</a>, <a class="el" href="score__builder__base_8cpp_source.html#l00285">s_GetCountIdentityMismatch()</a>, <a class="el" href="score__builder__base_8cpp_source.html#l00537">s_GetPercentCoverage()</a>, <a class="el" href="alignment__job_8cpp_source.html#l01112">s_IsSecondPassAlignment()</a>, <a class="el" href="igblast_8cpp_source.html#l00791">s_IsSeqAlignAsGood()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00078">s_ScoreAlignments()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00213">CWeightedIdentityScorer::ScoreAlignments()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00400">CClippedScorer::ScoreAlignments()</a>, <a class="el" href="tabular_8cpp_source.html#l01982">CIgBlastTabularInfo::SetAirrFormatData()</a>, <a class="el" href="align__tab__export__job_8cpp_source.html#l00165">sGenerateFields()</a>, <a class="el" href="cuCdUpdater_8cpp_source.html#l00633">CDUpdater::update()</a>, <a class="el" href="table__data__aln__summary_8cpp_source.html#l00294">CTableDataAlnSummary::x_GetAlnSummary()</a>, <a class="el" href="tabular_8cpp_source.html#l00731">CBlastTabularInfo::x_SetQueryCovSeqalign()</a>, <a class="el" href="tabular_8cpp_source.html#l00701">CBlastTabularInfo::x_SetQueryCovSubject()</a>, and <a class="el" href="tabular_8cpp_source.html#l00716">CBlastTabularInfo::x_SetQueryCovUniqSubject()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ac73daf82c97fb571b266a09a9eb81ade">◆ </a></span>GetNamedScore() <span class="overload">[3/4]</span></h2>
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<td class="memname"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> CSeq_align::GetNamedScore </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">EScoreType</a> </td>
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<td class="paramname"><em>type</em>, </td>
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<td class="paramtype">double & </td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00600">600</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="Seq__align_8cpp_source.html#l00563">GetNamedScore()</a>, and <a class="el" href="Seq__align_8cpp_source.html#l00404">sc_ScoreNames</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a179f3a1e25383a6343f481c8221e4a00">◆ </a></span>GetNamedScore() <span class="overload">[4/4]</span></h2>
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<td class="memname"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> CSeq_align::GetNamedScore </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">EScoreType</a> </td>
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<td class="paramname"><em>type</em>, </td>
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<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> & </td>
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<td class="paramname"><em>score</em> </td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00595">595</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="Seq__align_8cpp_source.html#l00563">GetNamedScore()</a>, and <a class="el" href="Seq__align_8cpp_source.html#l00404">sc_ScoreNames</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a5acb629f0eeddc050c5e93de4f14d3ca">◆ </a></span>GetNonFrameshifts()</h2>
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<td class="memname">vector< <a class="el" href="structCSeq__align_1_1SIndel.html">CSeq_align::SIndel</a> > CSeq_align::GetNonFrameshifts </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
|
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<td class="paramname"><em>row</em> = <code>-1</code></td><td>)</td>
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<p>Retrieves descriptions of all non-frameshift indels on a given row; i.e. </p>
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<p>all gaps with a length that is a multiple of 3. </p><dl class="exception"><dt>Exceptions</dt><dd>
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<table class="exception">
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<tr><td class="paramname"><a class="el" href="classCSeqalignException.html">CSeqalignException</a></td><td>if alignment type is not supported </td></tr>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01759">1759</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="range_8hpp_source.html#l00272">COpenRange< TSeqPos >::GetWhole()</a>, <a class="el" href="string__bind_8c_source.html#l00073">row</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01596">s_GetIndels()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a2fd557f3bb33caa1612ad80f130fb8b4">◆ </a></span>GetNonFrameshiftsWithinRange()</h2>
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<td class="memname">vector< <a class="el" href="structCSeq__align_1_1SIndel.html">CSeq_align::SIndel</a> > CSeq_align::GetNonFrameshiftsWithinRange </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__RangeSupport.html#gabb457385e479479764dd959a1d182765">TSeqRange</a> & </td>
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<td class="paramname"><em>range</em>, </td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
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<td class="paramname"><em>row</em> = <code>-1</code> </td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01765">1765</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="namespacecompile__time__bits.html#a440fbf17793b1d9f93090ea6898dac32">compile_time_bits::range()</a>, <a class="el" href="string__bind_8c_source.html#l00073">row</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01596">s_GetIndels()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="tabular__fmt_8cpp_source.html#l02510">CTabularFormatter_Indels::Print()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#abba500351271d04d8e09f393049f21e3">◆ </a></span>GetNonFrameshiftsWithinRanges()</h2>
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<td class="memname">vector< <a class="el" href="structCSeq__align_1_1SIndel.html">CSeq_align::SIndel</a> > CSeq_align::GetNonFrameshiftsWithinRanges </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCRangeCollection.html">CRangeCollection</a>< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > & </td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01771">1771</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="string__bind_8c_source.html#l00073">row</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01596">s_GetIndels()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ac4dcd004970024f04f0aede4cb678fd4">◆ </a></span>GetNumFrameshifts()</h2>
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<td class="memname"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> CSeq_align::GetNumFrameshifts </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
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<p>Retrieves the number of times a given row shifts frames; i.e. </p>
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<p>the number of gaps with a length that is not a multiple of 3. </p><dl class="exception"><dt>Exceptions</dt><dd>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01716">1716</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="range_8hpp_source.html#l00272">COpenRange< TSeqPos >::GetWhole()</a>, <a class="el" href="string__bind_8c_source.html#l00073">row</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01596">s_GetIndels()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="score__lookup_8cpp_source.html#l00176">CScore_FrameShifts::Get()</a>, and <a class="el" href="best__placement_8cpp_source.html#l00137">SAlignmentScoringModel::GetScore()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#abc9277371560e91505524972298d1e95">◆ </a></span>GetNumFrameshiftsWithinRange()</h2>
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<td class="memname"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> CSeq_align::GetNumFrameshiftsWithinRange </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__RangeSupport.html#gabb457385e479479764dd959a1d182765">TSeqRange</a> & </td>
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<td class="paramname"><em>range</em>, </td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
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<td class="paramname"><em>row</em> = <code>-1</code> </td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01725">1725</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="namespacecompile__time__bits.html#a440fbf17793b1d9f93090ea6898dac32">compile_time_bits::range()</a>, <a class="el" href="string__bind_8c_source.html#l00073">row</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01596">s_GetIndels()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="score__lookup_8cpp_source.html#l00176">CScore_FrameShifts::Get()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a69513924865028222e35f58234a95106">◆ </a></span>GetNumFrameshiftsWithinRanges()</h2>
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<td class="memname"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> CSeq_align::GetNumFrameshiftsWithinRanges </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCRangeCollection.html">CRangeCollection</a>< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > & </td>
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<td class="paramname"><em>ranges</em>, </td>
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<td class="paramkey"></td>
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<td></td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
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<td class="paramname"><em>row</em> = <code>-1</code> </td>
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<td>)</td>
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<td></td><td> const</td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01733">1733</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="string__bind_8c_source.html#l00073">row</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01596">s_GetIndels()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#af7a953721b2c699a28cd5ae12f7fd49c">◆ </a></span>GetNumGapOpenings()</h2>
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<td class="memname"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> CSeq_align::GetNumGapOpenings </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
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<td class="paramname"><em>row</em> = <code>-1</code></td><td>)</td>
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<td> const</td>
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<p>Retrieves the number of gap openings in a given row in an alignment (ignoring how many gaps are in the gapped region); all gaps by default. </p>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<table class="exception">
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<tr><td class="paramname"><a class="el" href="classCSeqalignException.html">CSeqalignException</a></td><td>if alignment type is not supported </td></tr>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01557">1557</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="range_8hpp_source.html#l00272">COpenRange< TSeqPos >::GetWhole()</a>, <a class="el" href="string__bind_8c_source.html#l00073">row</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01455">s_GetGapCount()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="score__lookup_8cpp_source.html#l00121">CScore_GapCount::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l00176">CScore_FrameShifts::Get()</a>, <a class="el" href="score__builder__base_8cpp_source.html#l00844">CScoreBuilderBase::GetGapCount()</a>, <a class="el" href="best__placement_8cpp_source.html#l00137">SAlignmentScoringModel::GetScore()</a>, and <a class="el" href="tabular__fmt_8cpp_source.html#l00538">CTabularFormatter_GapCount::Print()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a40feccb2adfcbdf6ee99dbe290b1e2d0">◆ </a></span>GetNumGapOpeningsWithinRange()</h2>
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<td class="memname"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> CSeq_align::GetNumGapOpeningsWithinRange </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__RangeSupport.html#gabb457385e479479764dd959a1d182765">TSeqRange</a> & </td>
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<td class="paramname"><em>range</em>, </td>
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<td class="paramkey"></td>
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<td></td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
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<td class="paramname"><em>row</em> = <code>-1</code> </td>
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<td></td>
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<td>)</td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01570">1570</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="namespacecompile__time__bits.html#a440fbf17793b1d9f93090ea6898dac32">compile_time_bits::range()</a>, <a class="el" href="string__bind_8c_source.html#l00073">row</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01455">s_GetGapCount()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="score__lookup_8cpp_source.html#l00176">CScore_FrameShifts::Get()</a>, and <a class="el" href="score__builder__base_8cpp_source.html#l00863">CScoreBuilderBase::GetGapCount()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a1dd42a36ca228931b0f4db55caa0e802">◆ </a></span>GetNumGapOpeningsWithinRanges()</h2>
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<td class="memname"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> CSeq_align::GetNumGapOpeningsWithinRanges </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCRangeCollection.html">CRangeCollection</a>< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > & </td>
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<td class="paramname"><em>ranges</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
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<td class="paramname"><em>row</em> = <code>-1</code> </td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01582">1582</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="string__bind_8c_source.html#l00073">row</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01455">s_GetGapCount()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="score__builder__base_8cpp_source.html#l00886">CScoreBuilderBase::GetGapCount()</a>, and <a class="el" href="score__builder__base_8cpp_source.html#l00453">s_GetPercentIdentity()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a801ec9a68d0cb752aea142758dc1532d">◆ </a></span>GetSeq_id()</h2>
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<td class="memname"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSeq__id.html">CSeq_id</a> & CSeq_align::GetSeq_id </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
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<td class="paramname"><em>row</em></td><td>)</td>
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<td> const</td>
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<p>Get seq-id (the first one if segments have different ids). </p>
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<p>Throw exception if row is invalid. </p>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00317">317</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="Seq__align___8hpp_source.html#l00133">CSeq_align_Base::C_Segs::e_Dendiag</a>, <a class="el" href="Seq__align___8hpp_source.html#l00134">CSeq_align_Base::C_Segs::e_Denseg</a>, <a class="el" href="Seq__align___8hpp_source.html#l00137">CSeq_align_Base::C_Segs::e_Disc</a>, <a class="el" href="Seq__align___8hpp_source.html#l00139">CSeq_align_Base::C_Segs::e_Sparse</a>, <a class="el" href="Seq__align___8hpp_source.html#l00138">CSeq_align_Base::C_Segs::e_Spliced</a>, <a class="el" href="Seq__align___8hpp_source.html#l00135">CSeq_align_Base::C_Segs::e_Std</a>, <a class="el" href="named__parameters_8hpp_source.html#l00099">Get()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00153">CSeq_align_Base::C_Segs::GetDenseg()</a>, <a class="el" href="Seq__loc_8hpp_source.html#l00941">CSeq_loc::GetId()</a>, <a class="el" href="Spliced__seg___8hpp_source.html#l00509">CSpliced_seg_Base::GetProduct_id()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00921">CSeq_align_Base::GetSegs()</a>, <a class="el" href="Dense__seg_8cpp_source.html#l00154">CDense_seg::GetSeq_id()</a>, <a class="el" href="Sparse__seg_8cpp_source.html#l00072">CSparse_seg::GetSeq_id()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00241">CSeq_align_Base::C_Segs::GetSparse()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00219">CSeq_align_Base::C_Segs::GetSpliced()</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00815">ITERATE</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l00704">NCBI_THROW</a>, and <a class="el" href="string__bind_8c_source.html#l00073">row</a>.</p>
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<p class="reference">Referenced by <a class="el" href="prj__helper_8cpp_source.html#l00105">CGBProjectHelper::AddProjectItemsFromRID()</a>, <a class="el" href="vdb2blast__util_8cpp_source.html#l00623">CVDBBlastUtil::AddSubjectsToScope()</a>, <a class="el" href="bl2seq__unit__test_8cpp_source.html#l03333">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="variation__util_8cpp_source.html#l00157">variation_ref::CVariationUtil::CheckExonBoundary()</a>, <a class="el" href="variation__util2_8cpp_source.html#l00262">variation::CVariationUtil::CheckExonBoundary()</a>, <a class="el" href="project__view__factory_8cpp_source.html#l00064">IProjectViewFactory::CombineInputObjects()</a>, <a class="el" href="project__view__factory_8cpp_source.html#l00132">IProjectViewFactory::CombineObjects()</a>, <a class="el" href="edit__table__views_8cpp_source.html#l00396">CTableViewWithTextViewNav::CombineObjects()</a>, <a class="el" href="named__collection__score__impl_8cpp_source.html#l00265">Compare()</a>, <a class="el" href="score__builder__base_8cpp_source.html#l01181">CScoreBuilderBase::ComputeScore()</a>, <a class="el" href="aln__converters_8cpp_source.html#l00969">CreatePairwiseAlnFromSeqAlign()</a>, <a class="el" href="multi__align__view_8cpp_source.html#l00868">CMAViewManager::DoTransition()</a>, <a class="el" href="seqalignfilter_8cpp_source.html#l00848">CSeqAlignFilter::FilterByAccessionType()</a>, <a class="el" href="seqalignfilter_8cpp_source.html#l00752">CSeqAlignFilter::FilterByTaxonomy()</a>, <a class="el" href="variation__util2_8cpp_source.html#l03161">variation::CVariationUtil::FindLocationProperties()</a>, <a class="el" href="edit__seq__ends__with__align_8cpp_source.html#l00283">CEditSeqEndsWithAlign::FindRow()</a>, <a class="el" href="update__seq_8cpp_source.html#l00611">CSequenceUpdater::FindRowInAlignment()</a>, <a class="el" href="internal__stops_8cpp_source.html#l00069">CInternalStopFinder::FindStartStopRanges()</a>, <a class="el" href="score__lookup_8cpp_source.html#l01368">CScore_Overlap::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l01431">CScore_OverlapBoth::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l01497">CScore_OrdinalPos::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l00176">CScore_FrameShifts::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l00266">CScore_3PrimeUnaligned::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l00304">CScore_Polya::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l00507">CScore_SequenceLength::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l00565">CScore_SymmetricOverlap::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l00821">CScore_StartStopCodon::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l01169">CScore_CdsScore::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l01235">CScore_Coverage::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l01277">CScore_Taxid::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l01596">CScore_BlastRatio::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l01756">CScore_GeneID::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l01845">CScore_RibosomalSlippage::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l01882">CScore_SegPct::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l01970">CScore_Entropy::Get()</a>, <a class="el" href="micro__introns_8cpp_source.html#l00076">GetAlignmentForRna()</a>, <a class="el" href="alignment__job_8cpp_source.html#l00208">CSGAlignmentJob::GetAlignType()</a>, <a class="el" href="na__utils_8cpp_source.html#l00077">CDataTrackUtils::GetAlignType()</a>, <a class="el" href="alignment__job_8cpp_source.html#l02174">GetAnchors()</a>, <a class="el" href="score__builder_8cpp_source.html#l00404">CScoreBuilder::GetBlastScoreProtToNucl()</a>, <a class="el" href="score__builder_8cpp_source.html#l00334">CScoreBuilder::GetBlastScoreStd()</a>, <a class="el" href="align__format__util_8cpp_source.html#l04010">CAlignFormatUtil::GetDbType()</a>, <a class="el" href="desktop__typed__items_8cpp_source.html#l00605">CDesktopAlignItem::GetDescription()</a>, <a class="el" href="variation__util2_8cpp_source.html#l03516">variation::GetFocusLocusIDs()</a>, <a class="el" href="gui_2objutils_2utils_8cpp_source.html#l01161">CSeqUtils::GetLocPlacements()</a>, <a class="el" href="seq__align__util_8cpp_source.html#l00113">CProductStringBuilder::GetProductString()</a>, <a class="el" href="objtools_2validator_2utilities_8cpp_source.html#l00399">GetReportableSeqIdForAlignment()</a>, <a class="el" href="align__format__util_8cpp_source.html#l04037">CAlignFormatUtil::GetSeqAlignCalcParams()</a>, <a class="el" href="align__format__util_8cpp_source.html#l04290">CAlignFormatUtil::GetSeqAlignSetCalcParamsFromASN()</a>, <a class="el" href="comment__item_8cpp_source.html#l00293">CCommentItem::GetStringForTPA()</a>, <a class="el" href="hgvs__parser2_8cpp_source.html#l00793">variation::GetUniquePrimaryTranscriptId()</a>, <a class="el" href="merge__tree__app_8cpp_source.html#l00123">CMergeTreeThread::Main()</a>, <a class="el" href="collection__scores__unit__test_8cpp_source.html#l00214">MakeKey()</a>, <a class="el" href="align__filter_8cpp_source.html#l00310">CAlignFilter::Match()</a>, <a class="el" href="merge__tree_8cpp_source.html#l00306">CTreeAlignMerger::Merge_AllAtOnce()</a>, <a class="el" href="merge__tree_8cpp_source.html#l00552">CTreeAlignMerger::Merge_Pairwise()</a>, <a class="el" href="multi__align__view_8cpp_source.html#l01045">CMAViewManager::NeedAnchorPanel()</a>, <a class="el" href="advanced__cleanup_8cpp_source.html#l00803">SAlignSortByQueryId::operator()()</a>, <a class="el" href="align__sort_8cpp_source.html#l00244">CAlignSort::SAlignExtractor::operator()()</a>, <a class="el" href="gff3__writer_8cpp_source.html#l01159">SCompareAlignments::operator()()</a>, <a class="el" href="gff3flybase__writer_8cpp_source.html#l00540">SFlybaseCompareAlignments::operator()()</a>, <a class="el" href="patch__sequence_8cpp_source.html#l00204">PatchTargetSequence()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l00098">CTabularFormatter_AllSeqIds::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l00169">CTabularFormatter_SeqId::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l00639">CTabularFormatter_MismatchPositions::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l01176">CTabularFormatter_Defline::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l01294">CTabularFormatter_ProtRef::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l01573">CTabularFormatter_Comment::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l01806">CTabularFormatter_SeqChrom::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l01863">CTabularFormatter_SeqClone::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l01923">CTabularFormatter_Tech::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l02175">CTabularFormatter_AssemblyInfo::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l02313">CTabularFormatter_PatchType::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l02397">CTabularFormatter_NearestGap::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l02510">CTabularFormatter_Indels::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l02576">CTabularFormatter_GeneSymbol::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l02675">CTabularFormatter_StartCodonChanges::Print()</a>, <a class="el" href="magicblast__util_8cpp_source.html#l01008">PrintSAM()</a>, <a class="el" href="magicblast__util_8cpp_source.html#l00441">PrintTabular()</a>, <a class="el" href="project__exons_8cpp_source.html#l01515">ProjectExons()</a>, <a class="el" href="variation__util_8cpp_source.html#l00458">variation_ref::CVariationUtil::Remap()</a>, <a class="el" href="variation__util2_8cpp_source.html#l00492">variation::CVariationUtil::Remap()</a>, <a class="el" href="variation__util2_8cpp_source.html#l00633">variation::CVariationUtil::RemapToAnnotatedTarget()</a>, <a class="el" href="revcomp__sequences_8cpp_source.html#l00283">CRevCompSequencesDlg::RevCompBioSeq()</a>, <a class="el" href="merge__tree__app_8cpp_source.html#l00244">CMergeyApp::Run()</a>, <a class="el" href="annot__compare__ds_8cpp_source.html#l00536">CFeatCompareJob_Align::Run()</a>, <a class="el" href="demo__genomic__compart_8cpp_source.html#l00111">CTestCompartApplication::Run()</a>, <a class="el" href="cobalt__app_8cpp_source.html#l00368">CMultiApplication::Run()</a>, <a class="el" href="single__aln__tests_8cpp_source.html#l00173">CTestSingleAln_All::RunTest()</a>, <a class="el" href="alignment__job_8cpp_source.html#l00348">s_CheckTraceMateAlign()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l02596">s_CodonVariation()</a>, <a class="el" href="igblast_8cpp_source.html#l00869">s_CompareSeqAlignByEvalue()</a>, <a class="el" href="igblast_8cpp_source.html#l00530">s_CompareSeqAlignByScoreAndName()</a>, <a class="el" href="igblast_8hpp_source.html#l00432">ScorePositionSort::s_CompareSeqAlignByScoreAndPosition()</a>, <a class="el" href="objcoords_8cpp_source.html#l01017">s_ExtendEntriesFromAlignments()</a>, <a class="el" href="blast__results_8cpp_source.html#l00453">s_ExtractSeqId()</a>, <a class="el" href="seqalignfilter__unit__test_8cpp_source.html#l00116">s_GetAlignedSeqGi()</a>, <a class="el" href="align__compare_8cpp_source.html#l00081">s_GetAlignmentSpans_Interval()</a>, <a class="el" href="label_8cpp_source.html#l02444">s_GetAlignmentTooltip()</a>, <a class="el" href="gbproject__tool_8cpp_source.html#l00255">s_GetAlignTitle()</a>, <a class="el" href="gui_2objutils_2utils_8cpp_source.html#l01012">s_GetAlnMapplingLocs()</a>, <a class="el" href="tabular_8cpp_source.html#l01528">s_GetCigarString()</a>, <a class="el" href="score__builder__base_8cpp_source.html#l00285">s_GetCountIdentityMismatch()</a>, <a class="el" href="score__builder__base_8cpp_source.html#l00537">s_GetPercentCoverage()</a>, <a class="el" href="single__aln__tests_8cpp_source.html#l00103">s_GetPolyA_genomic_priming()</a>, <a class="el" href="gui_2objutils_2utils_8cpp_source.html#l01771">s_GetRnaMappingLocs()</a>, <a class="el" href="score__builder__base_8cpp_source.html#l00127">s_GetSplicedSegIdentityMismatch()</a>, <a class="el" href="score__builder__base_8cpp_source.html#l00506">s_IsProteinToGenomic()</a>, <a class="el" href="seqalignfilter_8cpp_source.html#l00793">s_ModifySeqAlnWithFilteredSeqIDs()</a>, <a class="el" href="basic__converters_8cpp_source.html#l00350">s_Seq_align_Seq_loc()</a>, <a class="el" href="igblast_8cpp_source.html#l00858">s_SeqAlignInSet()</a>, <a class="el" href="blastxml2__format_8cpp_source.html#l00096">s_SeqAlignSetToXMLHsps()</a>, <a class="el" href="cobalt__unit__test_8cpp_source.html#l00776">s_TestResultAlignment()</a>, <a class="el" href="seqalignfilter_8cpp_source.html#l00575">s_UpdateSeqAlnWithFilteredSeqIDs()</a>, <a class="el" href="seqalignfilter_8cpp_source.html#l00553">s_UpdateSubjectInSeqalign()</a>, <a class="el" href="align__compare_8cpp_source.html#l00711">CAlignCompare::SAlignment::SAlignment()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00213">CWeightedIdentityScorer::ScoreAlignments()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00324">COverlapScorer::ScoreAlignments()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00400">CClippedScorer::ScoreAlignments()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00558">CCommonComponentScorer::ScoreAlignments()</a>, <a class="el" href="tabular_8cpp_source.html#l01982">CIgBlastTabularInfo::SetAirrFormatData()</a>, <a class="el" href="objcoords_8cpp_source.html#l00722">CReportEntry::SetAlignment()</a>, <a class="el" href="tabular_8cpp_source.html#l00743">CBlastTabularInfo::SetFields()</a>, <a class="el" href="tabular_8cpp_source.html#l02500">CIgBlastTabularInfo::SetIgAnnotation()</a>, <a class="el" href="open__view__manager__impl_8cpp_source.html#l00331">CConversionResultPanel::SetObjects()</a>, <a class="el" href="align__tab__export__job_8cpp_source.html#l00057">sFindAnchorRow()</a>, <a class="el" href="align__tab__export__job_8cpp_source.html#l00165">sGenerateFields()</a>, <a class="el" href="lds2_8cpp_source.html#l00247">CLDS2_AnnotType_Hook::SkipObject()</a>, <a class="el" href="gene__model_8cpp_source.html#l00380">CFeatureGenerator::SImplementation::SMapper::SMapper()</a>, <a class="el" href="transform__align_8cpp_source.html#l00137">CFeatureGenerator::SImplementation::StitchSmallHoles()</a>, <a class="el" href="bl2seq__unit__test_8cpp_source.html#l00346">testResultAlignments()</a>, <a class="el" href="gene__model_8cpp_source.html#l00609">CFeatureGenerator::SImplementation::TransformProteinAlignToTranscript()</a>, <a class="el" href="convert__raw__to__delta_8cpp_source.html#l00172">UpdateDensegAlignment()</a>, <a class="el" href="igblast_8cpp_source.html#l01500">CIgBlast::x_AnnotateC()</a>, <a class="el" href="igblast_8cpp_source.html#l01473">CIgBlast::x_AnnotateD()</a>, <a class="el" href="igblast_8cpp_source.html#l01595">CIgBlast::x_AnnotateDJ()</a>, <a class="el" href="igblast_8cpp_source.html#l01645">CIgBlast::x_AnnotateDomain()</a>, <a class="el" href="igblast_8cpp_source.html#l01561">CIgBlast::x_AnnotateJ()</a>, <a class="el" href="cleanup__alignments__tool__manager_8cpp_source.html#l00151">CCleanupAlignmentsToolManager::x_AreSelfAlignmentsOnly()</a>, <a class="el" href="update__seq_8cpp_source.html#l01345">CSequenceUpdater::x_ChangeIDInFeature()</a>, <a class="el" href="gene__model_8cpp_source.html#l01917">CFeatureGenerator::SImplementation::x_CreateCdsFeature()</a>, <a class="el" href="inversion__merge__aligner_8cpp_source.html#l00264">CInversionMergeAligner::x_CreateDiscAlignment()</a>, <a class="el" href="gene__model_8cpp_source.html#l01455">CFeatureGenerator::SImplementation::x_CreateProteinBioseq()</a>, <a class="el" href="edit__table__views_8cpp_source.html#l00342">CTableViewWithTextViewNav::x_EditObject()</a>, <a class="el" href="psi__pssm__input_8cpp_source.html#l00144">CPsiBlastInputData::x_ExtractQueryForPssm()</a>, <a class="el" href="cdd__pssm__input_8cpp_source.html#l00441">CCddInputData::x_ExtractQueryForPssm()</a>, <a class="el" href="igblast_8cpp_source.html#l01238">CIgBlast::x_FillJDomain()</a>, <a class="el" href="pkg__sequence__edit_2dll__register_8cpp_source.html#l01170">CSequenceEditingEventHandler::x_FindRelevantAlignRow()</a>, <a class="el" href="unordered__spliter_8cpp_source.html#l00471">CUnorderedSplitter::x_FixAlignment()</a>, <a class="el" href="align__filter_8cpp_source.html#l00517">CAlignFilter::x_FuncCall()</a>, <a class="el" href="table__data__aln__summary_8cpp_source.html#l00294">CTableDataAlnSummary::x_GetAlnSummary()</a>, <a class="el" href="vecscreen__run_8cpp_source.html#l00286">CVecscreenRun::CFormatter::x_GetIdsAndTitlesForSeqAlign()</a>, <a class="el" href="gene__model_8cpp_source.html#l00473">CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons()</a>, <a class="el" href="showdefline_8cpp_source.html#l01480">CShowBlastDefline::x_GetScoreInfo()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00729">CCommonComponentScorer::x_GetSeqHistCompList()</a>, <a class="el" href="primary__item_8cpp_source.html#l00277">CPrimaryItem::x_GetStrForPrimary()</a>, <a class="el" href="gene__model_8cpp_source.html#l02993">CFeatureGenerator::SImplementation::x_HandleCdsExceptions()</a>, <a class="el" href="gene__model_8cpp_source.html#l02706">CFeatureGenerator::SImplementation::x_HandleRnaExceptions()</a>, <a class="el" href="validate__panel_8cpp_source.html#l00739">CValidatePanel::x_LaunchEditor()</a>, <a class="el" href="feature__ds_8cpp_source.html#l02855">CBatchFeatJob::x_LoadFeatProducts()</a>, <a class="el" href="merge__tree_8cpp_source.html#l00852">CTreeAlignMerger::x_MakeMergeableGroups()</a>, <a class="el" href="primercheck_8cpp_source.html#l00455">COligoSpecificityCheck::x_NW_alignment()</a>, <a class="el" href="gff__reader_8cpp_source.html#l01205">CGFFReader::x_PlaceAlignment()</a>, <a class="el" href="xcompareannotsdemo_8cpp_source.html#l01048">CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile()</a>, <a class="el" href="align__filter_8cpp_source.html#l00966">CAlignFilter::x_Query_Op()</a>, <a class="el" href="alignment__quality__score_8cpp_source.html#l00194">CSGAlnQualityScore::x_RetrieveQualityMap()</a>, <a class="el" href="primercheck_8cpp_source.html#l00952">COligoSpecificityCheck::x_SavePrimerInfo()</a>, <a class="el" href="primercheck_8cpp_source.html#l00848">COligoSpecificityCheck::x_SequencesMappedToSameTarget()</a>, <a class="el" href="rps_8cpp_source.html#l00664">CMultiAligner::x_SetDomainHits()</a>, <a class="el" href="tabular_8cpp_source.html#l00701">CBlastTabularInfo::x_SetQueryCovSubject()</a>, <a class="el" href="tabular_8cpp_source.html#l00716">CBlastTabularInfo::x_SetQueryCovUniqSubject()</a>, <a class="el" href="split__loader_8cpp_source.html#l00371">CSplitDataLoader::x_SplitAligns()</a>, and <a class="el" href="edit__object__feature__propagate_8cpp_source.html#l00315">CEditObjectFeaturePropagate::xInit()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a4a8a8b945db67efbe59e74fe8c03593d">◆ </a></span>GetSeqRange()</h2>
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<td class="memname"><a class="el" href="classCRange.html">CRange</a>< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > CSeq_align::GetSeqRange </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
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<td class="paramname"><em>row</em></td><td>)</td>
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<td> const</td>
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<p>GetSeqRange <a class="el" href="classNB.html">NB</a>: On a Spliced-seg, in case the product-type is protein, these only return the amin part of Prot-pos. </p>
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<p>The frame is ignored. </p>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00153">153</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="Seq__id_8cpp_source.html#l00318">CSeq_id::Assign()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00843">CSeq_align_Base::CanGetDim()</a>, <a class="el" href="range_8hpp_source.html#l00345">COpenRange< Position >::CombineWith()</a>, <a class="el" href="Seq__id_8cpp_source.html#l00411">CSeq_id::Compare()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00133">CSeq_align_Base::C_Segs::e_Dendiag</a>, <a class="el" href="Seq__align___8hpp_source.html#l00134">CSeq_align_Base::C_Segs::e_Denseg</a>, <a class="el" href="Seq__align___8hpp_source.html#l00137">CSeq_align_Base::C_Segs::e_Disc</a>, <a class="el" href="Seq__align___8hpp_source.html#l00139">CSeq_align_Base::C_Segs::e_Sparse</a>, <a class="el" href="Seq__align___8hpp_source.html#l00138">CSeq_align_Base::C_Segs::e_Spliced</a>, <a class="el" href="Seq__align___8hpp_source.html#l00135">CSeq_align_Base::C_Segs::e_Std</a>, <a class="el" href="Seq__id_8hpp_source.html#l00583">CSeq_id::e_YES</a>, <a class="el" href="range_8hpp_source.html#l00148">COpenRange< Position >::Empty()</a>, <a class="el" href="named__parameters_8hpp_source.html#l00099">Get()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00153">CSeq_align_Base::C_Segs::GetDenseg()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00856">CSeq_align_Base::GetDim()</a>, <a class="el" href="Seq__interval___8hpp_source.html#l00383">CSeq_interval_Base::GetFrom()</a>, <a class="el" href="Seq__interval___8hpp_source.html#l00517">CSeq_interval_Base::GetId()</a>, <a class="el" href="Seq__point___8hpp_source.html#l00390">CSeq_point_Base::GetId()</a>, <a class="el" href="Seq__loc___8cpp_source.html#l00194">CSeq_loc_Base::GetInt()</a>, <a class="el" href="Seq__loc___8cpp_source.html#l00238">CSeq_loc_Base::GetPnt()</a>, <a class="el" href="Seq__point___8hpp_source.html#l00303">CSeq_point_Base::GetPoint()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00921">CSeq_align_Base::GetSegs()</a>, <a class="el" href="Dense__seg_8hpp_source.html#l00234">CDense_seg::GetSeqRange()</a>, <a class="el" href="Sparse__seg_8cpp_source.html#l00201">CSparse_seg::GetSeqRange()</a>, <a class="el" href="Spliced__seg_8cpp_source.html#l00299">CSpliced_seg::GetSeqRange()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00241">CSeq_align_Base::C_Segs::GetSparse()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00219">CSeq_align_Base::C_Segs::GetSpliced()</a>, <a class="el" href="Seq__interval___8hpp_source.html#l00430">CSeq_interval_Base::GetTo()</a>, <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>, <a class="el" href="Seq__loc___8hpp_source.html#l00528">CSeq_loc_Base::IsInt()</a>, <a class="el" href="Seq__loc___8hpp_source.html#l00540">CSeq_loc_Base::IsPnt()</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00815">ITERATE</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l00704">NCBI_THROW</a>, and <a class="el" href="string__bind_8c_source.html#l00073">row</a>.</p>
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<p class="reference">Referenced by <a class="el" href="Seq__align_8cpp_source.html#l02017">AlignLengthRatio()</a>, <a class="el" href="objtools_2align__format_2vectorscreen_8cpp_source.html#l00128">AlnFromRangeAscendingSort()</a>, <a class="el" href="alignment__job_8cpp_source.html#l02252">BuildAlignDataSource()</a>, <a class="el" href="score__lookup_8cpp_source.html#l01368">CScore_Overlap::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l01431">CScore_OverlapBoth::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l01882">CScore_SegPct::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l01970">CScore_Entropy::Get()</a>, <a class="el" href="alignment__job_8cpp_source.html#l00208">CSGAlignmentJob::GetAlignType()</a>, <a class="el" href="Seq__align_8cpp_source.html#l00252">GetSeqStart()</a>, <a class="el" href="Seq__align_8cpp_source.html#l00273">GetSeqStop()</a>, <a class="el" href="align__filter_8cpp_source.html#l00310">CAlignFilter::Match()</a>, <a class="el" href="genomic__compart_8cpp_source.html#l00298">SSeqAlignsBySize::operator()()</a>, <a class="el" href="align__sort_8cpp_source.html#l00244">CAlignSort::SAlignExtractor::operator()()</a>, <a class="el" href="patch__sequence_8cpp_source.html#l00204">PatchTargetSequence()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l00237">CTabularFormatter_AlignStart::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l00301">CTabularFormatter_AlignEnd::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l00639">CTabularFormatter_MismatchPositions::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l00816">CTabularFormatter_GapRanges::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l01385">CTabularFormatter_ExonIntrons::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l02043">CTabularFormatter_AlignLengthRatio::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l02397">CTabularFormatter_NearestGap::Print()</a>, <a class="el" href="magicblast__util_8cpp_source.html#l01008">PrintSAM()</a>, <a class="el" href="magicblast__util_8cpp_source.html#l00441">PrintTabular()</a>, <a class="el" href="annot__compare__ds_8cpp_source.html#l00536">CFeatCompareJob_Align::Run()</a>, <a class="el" href="demo__genomic__compart_8cpp_source.html#l00111">CTestCompartApplication::Run()</a>, <a class="el" href="single__aln__tests_8cpp_source.html#l00173">CTestSingleAln_All::RunTest()</a>, <a class="el" href="align__compare_8cpp_source.html#l00277">s_GetAlignmentSpans_Exon()</a>, <a class="el" href="align__compare_8cpp_source.html#l00361">s_GetAlignmentSpans_Span()</a>, <a class="el" href="label_8cpp_source.html#l02444">s_GetAlignmentTooltip()</a>, <a class="el" href="tabular_8cpp_source.html#l01528">s_GetCigarString()</a>, <a class="el" href="basic__converters_8cpp_source.html#l00350">s_Seq_align_Seq_loc()</a>, <a class="el" href="align__compare_8cpp_source.html#l00711">CAlignCompare::SAlignment::SAlignment()</a>, <a class="el" href="genomic__compart__unit__test_8cpp_source.html#l00055">SCompartmentData::SCompartmentData()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00187">CExpansionScorer::ScoreAlignments()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00246">CHangScorer::ScoreAlignments()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00400">CClippedScorer::ScoreAlignments()</a>, <a class="el" href="align__tab__export__job_8cpp_source.html#l00165">sGenerateFields()</a>, <a class="el" href="lds2_8cpp_source.html#l00247">CLDS2_AnnotType_Hook::SkipObject()</a>, <a class="el" href="align__compare_8cpp_source.html#l00902">CAlignCompare::SAlignment::Slice()</a>, <a class="el" href="gene__model_8cpp_source.html#l03974">CFeatureGenerator::SImplementation::x_CheckMatch()</a>, <a class="el" href="result__set_8cpp_source.html#l00395">CQuerySet::x_ContainsAlignment()</a>, <a class="el" href="objtools_2align__format_2vectorscreen_8cpp_source.html#l00210">CVecscreen::x_GetMatchType()</a>, <a class="el" href="gene__model_8cpp_source.html#l02706">CFeatureGenerator::SImplementation::x_HandleRnaExceptions()</a>, <a class="el" href="primercheck_8cpp_source.html#l01456">COligoSpecificityCheck::x_IsPcrLengthInRange()</a>, <a class="el" href="unordered__spliter_8cpp_source.html#l00547">CUnorderedSplitter::x_MakeAlignmentPairUnique()</a>, <a class="el" href="xcompareannotsdemo_8cpp_source.html#l01048">CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile()</a>, <a class="el" href="alignment__quality__score_8cpp_source.html#l00194">CSGAlnQualityScore::x_RetrieveQualityMap()</a>, <a class="el" href="primercheck_8cpp_source.html#l00952">COligoSpecificityCheck::x_SavePrimerInfo()</a>, <a class="el" href="primercheck_8cpp_source.html#l00848">COligoSpecificityCheck::x_SequencesMappedToSameTarget()</a>, and <a class="el" href="primercheck_8cpp_source.html#l01994">COligoSpecificityTemplate::x_SortHit()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a9d9970a4214c3b03f879e5d439f1b74d">◆ </a></span>GetSeqStart()</h2>
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<td class="memname"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> CSeq_align::GetSeqStart </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
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<td class="paramname"><em>row</em></td><td>)</td>
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<td> const</td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00252">252</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="Seq__align___8hpp_source.html#l00133">CSeq_align_Base::C_Segs::e_Dendiag</a>, <a class="el" href="Seq__align___8hpp_source.html#l00134">CSeq_align_Base::C_Segs::e_Denseg</a>, <a class="el" href="Seq__align___8hpp_source.html#l00137">CSeq_align_Base::C_Segs::e_Disc</a>, <a class="el" href="Seq__align___8hpp_source.html#l00139">CSeq_align_Base::C_Segs::e_Sparse</a>, <a class="el" href="Seq__align___8hpp_source.html#l00138">CSeq_align_Base::C_Segs::e_Spliced</a>, <a class="el" href="Seq__align___8hpp_source.html#l00135">CSeq_align_Base::C_Segs::e_Std</a>, <a class="el" href="Seq__align___8cpp_source.html#l00153">CSeq_align_Base::C_Segs::GetDenseg()</a>, <a class="el" href="Range___8hpp_source.html#l00222">CRange_Base::GetFrom()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00921">CSeq_align_Base::GetSegs()</a>, <a class="el" href="Seq__align_8cpp_source.html#l00153">GetSeqRange()</a>, <a class="el" href="Dense__seg_8cpp_source.html#l00165">CDense_seg::GetSeqStart()</a>, <a class="el" href="Sparse__seg_8cpp_source.html#l00118">CSparse_seg::GetSeqStart()</a>, <a class="el" href="Spliced__seg_8cpp_source.html#l00348">CSpliced_seg::GetSeqStart()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00241">CSeq_align_Base::C_Segs::GetSparse()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00219">CSeq_align_Base::C_Segs::GetSpliced()</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l00704">NCBI_THROW</a>, and <a class="el" href="string__bind_8c_source.html#l00073">row</a>.</p>
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<p class="reference">Referenced by <a class="el" href="prj__helper_8cpp_source.html#l00105">CGBProjectHelper::AddProjectItemsFromRID()</a>, <a class="el" href="bl2seq__unit__test_8cpp_source.html#l00094">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="named__collection__score__impl_8cpp_source.html#l00265">Compare()</a>, <a class="el" href="vecscreen__run_8cpp_source.html#l00322">CVecscreenRun::CFormatter::FormatResults()</a>, <a class="el" href="banded__aligner_8cpp_source.html#l00569">CInstance::GapDistance()</a>, <a class="el" href="score__lookup_8cpp_source.html#l00449">CScore_AlignStartStop::Get()</a>, <a class="el" href="project__exons_8cpp_source.html#l00171">GetUnalignedLength_3p()</a>, <a class="el" href="project__exons_8cpp_source.html#l00186">GetUnalignedLength_5p()</a>, <a class="el" href="banded__aligner_8cpp_source.html#l00551">CInstance::IsAlignmentContained()</a>, <a class="el" href="banded__aligner_8cpp_source.html#l00593">CInstance::MergeIn()</a>, <a class="el" href="magicblast_8cpp_source.html#l00586">compare_alignments_fwrev_first::operator()()</a>, <a class="el" href="magicblast_8cpp_source.html#l00615">compare_alignments_revfw_first::operator()()</a>, <a class="el" href="advanced__cleanup_8cpp_source.html#l00803">SAlignSortByQueryId::operator()()</a>, <a class="el" href="align__sort_8cpp_source.html#l00244">CAlignSort::SAlignExtractor::operator()()</a>, <a class="el" href="gff3__writer_8cpp_source.html#l01159">SCompareAlignments::operator()()</a>, <a class="el" href="gff3flybase__writer_8cpp_source.html#l00540">SFlybaseCompareAlignments::operator()()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l00237">CTabularFormatter_AlignStart::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l00301">CTabularFormatter_AlignEnd::Print()</a>, <a class="el" href="magicblast__util_8cpp_source.html#l01008">PrintSAM()</a>, <a class="el" href="magicblast__util_8cpp_source.html#l00441">PrintTabular()</a>, <a class="el" href="variation__util2_8cpp_source.html#l00492">variation::CVariationUtil::Remap()</a>, <a class="el" href="single__aln__tests_8cpp_source.html#l00173">CTestSingleAln_All::RunTest()</a>, <a class="el" href="igblast_8hpp_source.html#l00432">ScorePositionSort::s_CompareSeqAlignByScoreAndPosition()</a>, <a class="el" href="igblast_8cpp_source.html#l00911">s_DJNotCompatible()</a>, <a class="el" href="align__compare_8cpp_source.html#l00148">s_GetAlignmentMismatches()</a>, <a class="el" href="Seq__align_8cpp_source.html#l01596">s_GetIndels()</a>, <a class="el" href="single__aln__tests_8cpp_source.html#l00103">s_GetPolyA_genomic_priming()</a>, <a class="el" href="igblast_8cpp_source.html#l00858">s_SeqAlignInSet()</a>, <a class="el" href="blastxml2__format_8cpp_source.html#l00096">s_SeqAlignSetToXMLHsps()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00324">COverlapScorer::ScoreAlignments()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00558">CCommonComponentScorer::ScoreAlignments()</a>, <a class="el" href="tabular_8cpp_source.html#l01982">CIgBlastTabularInfo::SetAirrFormatData()</a>, <a class="el" href="align__format__util_8cpp_source.html#l01277">CAlignFormatUtil::SortHspByMasterStartAscending()</a>, <a class="el" href="align__format__util_8cpp_source.html#l01307">CAlignFormatUtil::SortHspBySubjectStartAscending()</a>, <a class="el" href="result__set_8cpp_source.html#l00333">CQuerySet::x_AlreadyContains()</a>, <a class="el" href="igblast_8cpp_source.html#l01500">CIgBlast::x_AnnotateC()</a>, <a class="el" href="igblast_8cpp_source.html#l01473">CIgBlast::x_AnnotateD()</a>, <a class="el" href="igblast_8cpp_source.html#l01595">CIgBlast::x_AnnotateDJ()</a>, <a class="el" href="igblast_8cpp_source.html#l01645">CIgBlast::x_AnnotateDomain()</a>, <a class="el" href="igblast_8cpp_source.html#l01561">CIgBlast::x_AnnotateJ()</a>, <a class="el" href="igblast_8cpp_source.html#l00839">CIgBlast::x_AnnotateV()</a>, <a class="el" href="inversion__merge__aligner_8cpp_source.html#l00264">CInversionMergeAligner::x_CreateDiscAlignment()</a>, <a class="el" href="igblast_8cpp_source.html#l01238">CIgBlast::x_FillJDomain()</a>, <a class="el" href="table__data__aln__summary_8cpp_source.html#l00294">CTableDataAlnSummary::x_GetAlnSummary()</a>, <a class="el" href="primary__item_8cpp_source.html#l00277">CPrimaryItem::x_GetStrForPrimary()</a>, <a class="el" href="primercheck_8cpp_source.html#l01456">COligoSpecificityCheck::x_IsPcrLengthInRange()</a>, <a class="el" href="xcompareannotsdemo_8cpp_source.html#l01048">CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile()</a>, <a class="el" href="alignment__quality__score_8cpp_source.html#l00194">CSGAlnQualityScore::x_RetrieveQualityMap()</a>, <a class="el" href="magicblast_8cpp_source.html#l00651">CMagicBlastResults::x_SetInfo()</a>, <a class="el" href="tabular_8cpp_source.html#l00731">CBlastTabularInfo::x_SetQueryCovSeqalign()</a>, and <a class="el" href="update__seq__panel_8cpp_source.html#l00783">CUpdateSeqPanel::x_SetUpdateTypes()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a6e0fe43fbf04caafc3f808e5ce35c75f">◆ </a></span>GetSeqStop()</h2>
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<td class="memname"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> CSeq_align::GetSeqStop </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
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<td class="paramname"><em>row</em></td><td>)</td>
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<td> const</td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00273">273</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="Seq__align___8hpp_source.html#l00133">CSeq_align_Base::C_Segs::e_Dendiag</a>, <a class="el" href="Seq__align___8hpp_source.html#l00134">CSeq_align_Base::C_Segs::e_Denseg</a>, <a class="el" href="Seq__align___8hpp_source.html#l00137">CSeq_align_Base::C_Segs::e_Disc</a>, <a class="el" href="Seq__align___8hpp_source.html#l00139">CSeq_align_Base::C_Segs::e_Sparse</a>, <a class="el" href="Seq__align___8hpp_source.html#l00138">CSeq_align_Base::C_Segs::e_Spliced</a>, <a class="el" href="Seq__align___8hpp_source.html#l00135">CSeq_align_Base::C_Segs::e_Std</a>, <a class="el" href="Seq__align___8cpp_source.html#l00153">CSeq_align_Base::C_Segs::GetDenseg()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00921">CSeq_align_Base::GetSegs()</a>, <a class="el" href="Seq__align_8cpp_source.html#l00153">GetSeqRange()</a>, <a class="el" href="Dense__seg_8cpp_source.html#l00203">CDense_seg::GetSeqStop()</a>, <a class="el" href="Sparse__seg_8cpp_source.html#l00157">CSparse_seg::GetSeqStop()</a>, <a class="el" href="Spliced__seg_8cpp_source.html#l00357">CSpliced_seg::GetSeqStop()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00241">CSeq_align_Base::C_Segs::GetSparse()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00219">CSeq_align_Base::C_Segs::GetSpliced()</a>, <a class="el" href="Range___8hpp_source.html#l00269">CRange_Base::GetTo()</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l00704">NCBI_THROW</a>, and <a class="el" href="string__bind_8c_source.html#l00073">row</a>.</p>
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<p class="reference">Referenced by <a class="el" href="prj__helper_8cpp_source.html#l00105">CGBProjectHelper::AddProjectItemsFromRID()</a>, <a class="el" href="vecscreen__run_8cpp_source.html#l00322">CVecscreenRun::CFormatter::FormatResults()</a>, <a class="el" href="banded__aligner_8cpp_source.html#l00569">CInstance::GapDistance()</a>, <a class="el" href="score__lookup_8cpp_source.html#l00449">CScore_AlignStartStop::Get()</a>, <a class="el" href="score__lookup_8cpp_source.html#l00266">CScore_3PrimeUnaligned::Get()</a>, <a class="el" href="project__exons_8cpp_source.html#l00171">GetUnalignedLength_3p()</a>, <a class="el" href="project__exons_8cpp_source.html#l00186">GetUnalignedLength_5p()</a>, <a class="el" href="banded__aligner_8cpp_source.html#l00551">CInstance::IsAlignmentContained()</a>, <a class="el" href="banded__aligner_8cpp_source.html#l00593">CInstance::MergeIn()</a>, <a class="el" href="advanced__cleanup_8cpp_source.html#l00803">SAlignSortByQueryId::operator()()</a>, <a class="el" href="align__sort_8cpp_source.html#l00244">CAlignSort::SAlignExtractor::operator()()</a>, <a class="el" href="gff3__writer_8cpp_source.html#l01159">SCompareAlignments::operator()()</a>, <a class="el" href="gff3flybase__writer_8cpp_source.html#l00540">SFlybaseCompareAlignments::operator()()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l00237">CTabularFormatter_AlignStart::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l00301">CTabularFormatter_AlignEnd::Print()</a>, <a class="el" href="variation__util2_8cpp_source.html#l00492">variation::CVariationUtil::Remap()</a>, <a class="el" href="single__aln__tests_8cpp_source.html#l00173">CTestSingleAln_All::RunTest()</a>, <a class="el" href="igblast_8cpp_source.html#l00911">s_DJNotCompatible()</a>, <a class="el" href="align__compare_8cpp_source.html#l00148">s_GetAlignmentMismatches()</a>, <a class="el" href="Seq__align_8cpp_source.html#l01596">s_GetIndels()</a>, <a class="el" href="single__aln__tests_8cpp_source.html#l00103">s_GetPolyA_genomic_priming()</a>, <a class="el" href="igblast_8cpp_source.html#l00858">s_SeqAlignInSet()</a>, <a class="el" href="blastxml2__format_8cpp_source.html#l00096">s_SeqAlignSetToXMLHsps()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00324">COverlapScorer::ScoreAlignments()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00558">CCommonComponentScorer::ScoreAlignments()</a>, <a class="el" href="tabular_8cpp_source.html#l01982">CIgBlastTabularInfo::SetAirrFormatData()</a>, <a class="el" href="align__format__util_8cpp_source.html#l01277">CAlignFormatUtil::SortHspByMasterStartAscending()</a>, <a class="el" href="align__format__util_8cpp_source.html#l01307">CAlignFormatUtil::SortHspBySubjectStartAscending()</a>, <a class="el" href="result__set_8cpp_source.html#l00333">CQuerySet::x_AlreadyContains()</a>, <a class="el" href="igblast_8cpp_source.html#l01500">CIgBlast::x_AnnotateC()</a>, <a class="el" href="igblast_8cpp_source.html#l01473">CIgBlast::x_AnnotateD()</a>, <a class="el" href="igblast_8cpp_source.html#l01595">CIgBlast::x_AnnotateDJ()</a>, <a class="el" href="igblast_8cpp_source.html#l01645">CIgBlast::x_AnnotateDomain()</a>, <a class="el" href="igblast_8cpp_source.html#l01561">CIgBlast::x_AnnotateJ()</a>, <a class="el" href="igblast_8cpp_source.html#l00839">CIgBlast::x_AnnotateV()</a>, <a class="el" href="inversion__merge__aligner_8cpp_source.html#l00264">CInversionMergeAligner::x_CreateDiscAlignment()</a>, <a class="el" href="igblast_8cpp_source.html#l01238">CIgBlast::x_FillJDomain()</a>, <a class="el" href="table__data__aln__summary_8cpp_source.html#l00294">CTableDataAlnSummary::x_GetAlnSummary()</a>, <a class="el" href="primary__item_8cpp_source.html#l00277">CPrimaryItem::x_GetStrForPrimary()</a>, <a class="el" href="primercheck_8cpp_source.html#l01456">COligoSpecificityCheck::x_IsPcrLengthInRange()</a>, <a class="el" href="xcompareannotsdemo_8cpp_source.html#l01048">CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile()</a>, <a class="el" href="alignment__quality__score_8cpp_source.html#l00194">CSGAlnQualityScore::x_RetrieveQualityMap()</a>, <a class="el" href="tabular_8cpp_source.html#l00731">CBlastTabularInfo::x_SetQueryCovSeqalign()</a>, and <a class="el" href="update__seq__panel_8cpp_source.html#l00783">CUpdateSeqPanel::x_SetUpdateTypes()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#aaf45eabbfe89cfc16dced0bceb9b0cea">◆ </a></span>GetSeqStrand()</h2>
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<td class="memname"><a class="el" href="group__dataspec__NCBI__Seqloc.html#ga2d4d48fde1d3f62563eac193a3b5afae">ENa_strand</a> CSeq_align::GetSeqStrand </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
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<td class="paramname"><em>row</em></td><td>)</td>
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<td> const</td>
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<p>Get strand (the first one if segments have different strands). </p>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00294">294</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="Seq__align___8hpp_source.html#l00133">CSeq_align_Base::C_Segs::e_Dendiag</a>, <a class="el" href="Seq__align___8hpp_source.html#l00134">CSeq_align_Base::C_Segs::e_Denseg</a>, <a class="el" href="Seq__align___8hpp_source.html#l00137">CSeq_align_Base::C_Segs::e_Disc</a>, <a class="el" href="Seq__align___8hpp_source.html#l00139">CSeq_align_Base::C_Segs::e_Sparse</a>, <a class="el" href="Seq__align___8hpp_source.html#l00138">CSeq_align_Base::C_Segs::e_Spliced</a>, <a class="el" href="Seq__align___8hpp_source.html#l00135">CSeq_align_Base::C_Segs::e_Std</a>, <a class="el" href="Seq__align__set___8hpp_source.html#l00166">CSeq_align_set_Base::Get()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00726">CSeq_align_Base::C_Segs::GetDendiag()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00153">CSeq_align_Base::C_Segs::GetDenseg()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00197">CSeq_align_Base::C_Segs::GetDisc()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00921">CSeq_align_Base::GetSegs()</a>, <a class="el" href="Dense__seg_8cpp_source.html#l00241">CDense_seg::GetSeqStrand()</a>, <a class="el" href="Sparse__seg_8cpp_source.html#l00093">CSparse_seg::GetSeqStrand()</a>, <a class="el" href="Spliced__seg_8cpp_source.html#l00056">CSpliced_seg::GetSeqStrand()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00241">CSeq_align_Base::C_Segs::GetSparse()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00219">CSeq_align_Base::C_Segs::GetSpliced()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00752">CSeq_align_Base::C_Segs::GetStd()</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l00704">NCBI_THROW</a>, and <a class="el" href="string__bind_8c_source.html#l00073">row</a>.</p>
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||
<p class="reference">Referenced by <a class="el" href="vecscreen__run_8cpp_source.html#l00322">CVecscreenRun::CFormatter::FormatResults()</a>, <a class="el" href="score__builder_8cpp_source.html#l00404">CScoreBuilder::GetBlastScoreProtToNucl()</a>, <a class="el" href="best__placement_8cpp_source.html#l00542">SAlignmentScoringModel::GetPolyA_length()</a>, <a class="el" href="seq__align__util_8cpp_source.html#l00113">CProductStringBuilder::GetProductString()</a>, <a class="el" href="project__exons_8cpp_source.html#l00201">GetTerminalPartialness()</a>, <a class="el" href="project__exons_8cpp_source.html#l00171">GetUnalignedLength_3p()</a>, <a class="el" href="project__exons_8cpp_source.html#l00186">GetUnalignedLength_5p()</a>, <a class="el" href="align__group_8cpp_source.html#l00229">CAlignGroup::GroupByStrand()</a>, <a class="el" href="Seq__align_8cpp_source.html#l02186">IntronLengthRange()</a>, <a class="el" href="banded__aligner_8cpp_source.html#l00551">CInstance::IsAlignmentContained()</a>, <a class="el" href="merge__tree__app_8cpp_source.html#l00123">CMergeTreeThread::Main()</a>, <a class="el" href="merge__tree_8cpp_source.html#l00306">CTreeAlignMerger::Merge_AllAtOnce()</a>, <a class="el" href="merge__tree_8cpp_source.html#l00552">CTreeAlignMerger::Merge_Pairwise()</a>, <a class="el" href="magicblast_8cpp_source.html#l00586">compare_alignments_fwrev_first::operator()()</a>, <a class="el" href="magicblast_8cpp_source.html#l00615">compare_alignments_revfw_first::operator()()</a>, <a class="el" href="align__sort_8cpp_source.html#l00244">CAlignSort::SAlignExtractor::operator()()</a>, <a class="el" href="gff3__writer_8cpp_source.html#l01159">SCompareAlignments::operator()()</a>, <a class="el" href="gff3flybase__writer_8cpp_source.html#l00540">SFlybaseCompareAlignments::operator()()</a>, <a class="el" href="patch__sequence_8cpp_source.html#l00204">PatchTargetSequence()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l00237">CTabularFormatter_AlignStart::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l00301">CTabularFormatter_AlignEnd::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l00362">CTabularFormatter_AlignStrand::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l00639">CTabularFormatter_MismatchPositions::Print()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l01385">CTabularFormatter_ExonIntrons::Print()</a>, <a class="el" href="magicblast__util_8cpp_source.html#l01008">PrintSAM()</a>, <a class="el" href="magicblast__util_8cpp_source.html#l00441">PrintTabular()</a>, <a class="el" href="project__exons_8cpp_source.html#l01515">ProjectExons()</a>, <a class="el" href="merge__tree__app_8cpp_source.html#l00244">CMergeyApp::Run()</a>, <a class="el" href="annot__compare__ds_8cpp_source.html#l00536">CFeatCompareJob_Align::Run()</a>, <a class="el" href="igblast_8hpp_source.html#l00432">ScorePositionSort::s_CompareSeqAlignByScoreAndPosition()</a>, <a class="el" href="score__builder_8cpp_source.html#l00688">s_ComputeTraceback()</a>, <a class="el" href="align__compare_8cpp_source.html#l00148">s_GetAlignmentMismatches()</a>, <a class="el" href="label_8cpp_source.html#l02444">s_GetAlignmentTooltip()</a>, <a class="el" href="tabular_8cpp_source.html#l01528">s_GetCigarString()</a>, <a class="el" href="single__aln__tests_8cpp_source.html#l00089">s_GetSeqStrand()</a>, <a class="el" href="blastxml2__format_8cpp_source.html#l00096">s_SeqAlignSetToXMLHsps()</a>, <a class="el" href="align__compare_8cpp_source.html#l00711">CAlignCompare::SAlignment::SAlignment()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00324">COverlapScorer::ScoreAlignments()</a>, <a class="el" href="tabular_8cpp_source.html#l01982">CIgBlastTabularInfo::SetAirrFormatData()</a>, <a class="el" href="align__tab__export__job_8cpp_source.html#l00165">sGenerateFields()</a>, <a class="el" href="alignment__assistant_8cpp_source.html#l01546">CAlignmentAssistant::TranslateLocations()</a>, <a class="el" href="igblast_8cpp_source.html#l01500">CIgBlast::x_AnnotateC()</a>, <a class="el" href="igblast_8cpp_source.html#l01645">CIgBlast::x_AnnotateDomain()</a>, <a class="el" href="gene__model_8cpp_source.html#l03974">CFeatureGenerator::SImplementation::x_CheckMatch()</a>, <a class="el" href="inversion__merge__aligner_8cpp_source.html#l00264">CInversionMergeAligner::x_CreateDiscAlignment()</a>, <a class="el" href="igblast_8cpp_source.html#l01238">CIgBlast::x_FillJDomain()</a>, <a class="el" href="table__data__aln__summary_8cpp_source.html#l00294">CTableDataAlnSummary::x_GetAlnSummary()</a>, <a class="el" href="primary__item_8cpp_source.html#l00277">CPrimaryItem::x_GetStrForPrimary()</a>, <a class="el" href="merge__tree_8cpp_source.html#l00852">CTreeAlignMerger::x_MakeMergeableGroups()</a>, <a class="el" href="objtools_2align__format_2vectorscreen_8cpp_source.html#l00377">CVecscreen::x_MergeSeqalign()</a>, <a class="el" href="align__filter_8cpp_source.html#l00966">CAlignFilter::x_Query_Op()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l01988">CTabularFormatter_DiscStrand::x_RecurseStrands()</a>, <a class="el" href="alignment__quality__score_8cpp_source.html#l00194">CSGAlnQualityScore::x_RetrieveQualityMap()</a>, and <a class="el" href="magicblast_8cpp_source.html#l00651">CMagicBlastResults::x_SetInfo()</a>.</p>
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</div>
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</div>
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<a id="a2511741b3a06c6e995e135d134f48083"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a2511741b3a06c6e995e135d134f48083">◆ </a></span>GetTotalGapCount()</h2>
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<td class="memname"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> CSeq_align::GetTotalGapCount </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
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<td class="paramname"><em>row</em> = <code>-1</code></td><td>)</td>
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<td> const</td>
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</tr>
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</div><div class="memdoc">
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<p>Retrieves the total number of gaps in the given row an alignment; all gaps by default. </p>
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<dl class="exception"><dt>Exceptions</dt><dd>
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||
<table class="exception">
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||
<tr><td class="paramname"><a class="el" href="classCSeqalignException.html">CSeqalignException</a></td><td>if alignment type is not supported </td></tr>
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</table>
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</dd>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01550">1550</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="range_8hpp_source.html#l00272">COpenRange< TSeqPos >::GetWhole()</a>, <a class="el" href="string__bind_8c_source.html#l00073">row</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01455">s_GetGapCount()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="score__lookup_8cpp_source.html#l00121">CScore_GapCount::Get()</a>, <a class="el" href="score__builder__base_8cpp_source.html#l00838">CScoreBuilderBase::GetGapBaseCount()</a>, <a class="el" href="tabular__fmt_8cpp_source.html#l00844">CTabularFormatter_GapBaseCount::Print()</a>, and <a class="el" href="blastxml2__format_8cpp_source.html#l00096">s_SeqAlignSetToXMLHsps()</a>.</p>
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</div>
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</div>
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<a id="a9aa843619a79e4bbd532d9920f0aef8d"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a9aa843619a79e4bbd532d9920f0aef8d">◆ </a></span>GetTotalGapCountWithinRange()</h2>
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<tr>
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<td class="memname"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> CSeq_align::GetTotalGapCountWithinRange </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__RangeSupport.html#gabb457385e479479764dd959a1d182765">TSeqRange</a> & </td>
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<td class="paramname"><em>range</em>, </td>
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</tr>
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<tr>
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<td class="paramkey"></td>
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<td></td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
|
||
<td class="paramname"><em>row</em> = <code>-1</code> </td>
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</tr>
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<tr>
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<td></td>
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<td>)</td>
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<td></td><td> const</td>
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</div><div class="memdoc">
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01564">1564</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="namespacecompile__time__bits.html#a440fbf17793b1d9f93090ea6898dac32">compile_time_bits::range()</a>, <a class="el" href="string__bind_8c_source.html#l00073">row</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01455">s_GetGapCount()</a>.</p>
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||
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<p class="reference">Referenced by <a class="el" href="score__builder__base_8cpp_source.html#l00856">CScoreBuilderBase::GetGapBaseCount()</a>.</p>
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</div>
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</div>
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<a id="a8315dc19cc8a8386d64a96ea0709353f"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a8315dc19cc8a8386d64a96ea0709353f">◆ </a></span>GetTotalGapCountWithinRanges()</h2>
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<div class="memitem">
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<tr>
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<td class="memname"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> CSeq_align::GetTotalGapCountWithinRanges </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCRangeCollection.html">CRangeCollection</a>< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > & </td>
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<td class="paramname"><em>ranges</em>, </td>
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</tr>
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<tr>
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<td class="paramkey"></td>
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<td></td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
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||
<td class="paramname"><em>row</em> = <code>-1</code> </td>
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</tr>
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<tr>
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<td></td>
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<td>)</td>
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<td></td><td> const</td>
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</div><div class="memdoc">
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01576">1576</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="string__bind_8c_source.html#l00073">row</a>, and <a class="el" href="Seq__align_8cpp_source.html#l01455">s_GetGapCount()</a>.</p>
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||
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<p class="reference">Referenced by <a class="el" href="score__builder__base_8cpp_source.html#l00879">CScoreBuilderBase::GetGapBaseCount()</a>.</p>
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</div>
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</div>
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<a id="a4eb373888d6af7611b794ed35df5482b"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a4eb373888d6af7611b794ed35df5482b">◆ </a></span>HelpText()</h2>
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<table class="memname">
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<tr>
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<td class="memname"><a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> CSeq_align::HelpText </td>
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||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">EScoreType</a> </td>
|
||
<td class="paramname"><em>score</em></td><td>)</td>
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<td></td>
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</tr>
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</td>
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<td class="mlabels-right">
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<span class="mlabels"><span class="mlabel">static</span></span> </td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00508">508</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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||
<p class="reference">References <a class="el" href="Seq__align_8cpp_source.html#l00430">sc_ScoreHelpText</a>.</p>
|
||
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||
<p class="reference">Referenced by <a class="el" href="score__lookup_8cpp_source.html#l02370">CScoreLookup::HelpText()</a>.</p>
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</div>
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</div>
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<a id="a49565489afe3881528c9017803c9f68b"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a49565489afe3881528c9017803c9f68b">◆ </a></span>IntronLengthRange()</h2>
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<div class="memitem">
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<div class="memproto">
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<table class="memname">
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<tr>
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<td class="memname"><a class="el" href="classCSeq__align.html#ae8447af5653b27fa09d886821029a4c7">CSeq_align::TLengthRange</a> CSeq_align::IntronLengthRange </td>
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||
<td>(</td>
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<td class="paramname"></td><td>)</td>
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<td> const</td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l02186">2186</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="Seq__align_8cpp_source.html#l02092">SLengthRange::AddLength()</a>, <a class="el" href="Na__strand___8hpp_source.html#l00067">eNa_strand_minus</a>, <a class="el" href="Spliced__exon___8hpp_source.html#l00814">CSpliced_exon_Base::GetGenomic_end()</a>, <a class="el" href="Spliced__exon___8hpp_source.html#l00767">CSpliced_exon_Base::GetGenomic_start()</a>, <a class="el" href="range_8hpp_source.html#l00158">COpenRange< Position >::GetLength()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00921">CSeq_align_Base::GetSegs()</a>, <a class="el" href="Seq__align_8cpp_source.html#l00294">GetSeqStrand()</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00815">ITERATE</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l00704">NCBI_THROW</a>, <a class="el" href="ctools_2ctransition_2ncbistd_8hpp_source.html#l00225">NULL</a>, and <a class="el" href="Seq__align_8cpp_source.html#l02111">SLengthRange::range</a>.</p>
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||
<p class="reference">Referenced by <a class="el" href="score__lookup_8cpp_source.html#l00642">CScore_MaxIntronLength::Get()</a>.</p>
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<a id="ae6401d582f244a2d5ec9eb72bdab8a15"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#ae6401d582f244a2d5ec9eb72bdab8a15">◆ </a></span>IsIntegerScore()</h2>
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<td class="memname"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> CSeq_align::IsIntegerScore </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">EScoreType</a> </td>
|
||
<td class="paramname"><em>score</em></td><td>)</td>
|
||
<td></td>
|
||
</tr>
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||
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||
</td>
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||
<td class="mlabels-right">
|
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<span class="mlabels"><span class="mlabel">static</span></span> </td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00513">513</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="Seq__align_8cpp_source.html#l00456">sc_IsInteger</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="score__builder__base_8cpp_source.html#l00912">CScoreBuilderBase::AddScore()</a>, and <a class="el" href="score__lookup_8cpp_source.html#l02406">CScoreLookup::IsIntegerScore()</a>.</p>
|
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<a id="a2ccc4265d1325463617fde3a586319da"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a2ccc4265d1325463617fde3a586319da">◆ </a></span>OffsetRow()</h2>
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<table class="memname">
|
||
<tr>
|
||
<td class="memname">void CSeq_align::OffsetRow </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
|
||
<td class="paramname"><em>row</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__AppFramework.html#ga92c3033316f74e84da312174e871d85c">TSignedSeqPos</a> </td>
|
||
<td class="paramname"><em>offset</em> </td>
|
||
</tr>
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||
<tr>
|
||
<td></td>
|
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<td>)</td>
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||
<td></td><td></td>
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||
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||
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||
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|
||
|
||
<p>Offset row's coords. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01332">1332</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="Seq__align___8hpp_source.html#l00133">CSeq_align_Base::C_Segs::e_Dendiag</a>, <a class="el" href="Seq__align___8hpp_source.html#l00134">CSeq_align_Base::C_Segs::e_Denseg</a>, <a class="el" href="Seq__align___8hpp_source.html#l00137">CSeq_align_Base::C_Segs::e_Disc</a>, <a class="el" href="Seq__align___8hpp_source.html#l00135">CSeq_align_Base::C_Segs::e_Std</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l00704">NCBI_THROW</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00822">NON_CONST_ITERATE</a>, <a class="el" href="ftds100_2freetds_2replacements_8h_source.html#l00160">offset</a>, <a class="el" href="Dense__seg_8cpp_source.html#l00890">CDense_seg::OffsetRow()</a>, <a class="el" href="string__bind_8c_source.html#l00073">row</a>, <a class="el" href="Seq__align___8cpp_source.html#l00159">CSeq_align_Base::C_Segs::SetDenseg()</a>, and <a class="el" href="Seq__align___8hpp_source.html#l00930">CSeq_align_Base::SetSegs()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="far__pointer__seq_8cpp_source.html#l00270">CFarPointerSeq::GetCommand()</a>, and <a class="el" href="blast__seqalign_8cpp_source.html#l01515">RemapToQueryLoc()</a>.</p>
|
||
|
||
</div>
|
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</div>
|
||
<a id="a05bda771a42f8e72549a1397b6518794"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a05bda771a42f8e72549a1397b6518794">◆ </a></span>operator=()</h2>
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||
<div class="memitem">
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<div class="memproto">
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<tr>
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<td class="mlabels-left">
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||
<table class="memname">
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<td class="memname"><a class="el" href="classCSeq__align.html">CSeq_align</a>& CSeq_align::operator= </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSeq__align.html">CSeq_align</a> & </td>
|
||
<td class="paramname"><em>value</em></td><td>)</td>
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||
<td></td>
|
||
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</td>
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<td class="mlabels-right">
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<span class="mlabels"><span class="mlabel">private</span></span> </td>
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||
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</div><div class="memdoc">
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||
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<a id="a83652f375f028ffd6deffc15ca945d4b"></a>
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||
<h2 class="memtitle"><span class="permalink"><a href="#a83652f375f028ffd6deffc15ca945d4b">◆ </a></span>RemapToLoc()</h2>
|
||
|
||
<div class="memitem">
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||
<div class="memproto">
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||
<table class="memname">
|
||
<tr>
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||
<td class="memname">void CSeq_align::RemapToLoc </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
|
||
<td class="paramname"><em>row</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="classCSeq__loc.html">CSeq_loc</a> & </td>
|
||
<td class="paramname"><em>dst_loc</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>ignore_strand</em> = <code><a class="el" href="ftds14_2freetds_2freetds_2bool_8h.html#a65e9886d74aaee76545e83dd09011727">false</a></code> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
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||
<td></td><td></td>
|
||
</tr>
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||
</table>
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||
</div><div class="memdoc">
|
||
<dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000189">Deprecated:</a></b></dt><dd>(use sequence::RemapAlignToLoc()) </dd></dl>
|
||
<dl class="section see"><dt>See also</dt><dd><a class="el" href="group__ObjUtilSeqAlign.html#ga55046566c695f79417a64f12924a583a" title="Remap seq-align row to the seq-loc.">RemapAlignToLoc</a></dd></dl>
|
||
<dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000249">Deprecated:</a></b></dt><dd></dd></dl>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01365">1365</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="Seq__align___8hpp_source.html#l00134">CSeq_align_Base::C_Segs::e_Denseg</a>, <a class="el" href="Seq__align___8hpp_source.html#l00137">CSeq_align_Base::C_Segs::e_Disc</a>, <a class="el" href="Seq__loc___8hpp_source.html#l00101">CSeq_loc_Base::e_Int</a>, <a class="el" href="Seq__align___8hpp_source.html#l00135">CSeq_align_Base::C_Segs::e_Std</a>, <a class="el" href="Seq__loc___8hpp_source.html#l00100">CSeq_loc_Base::e_Whole</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l00704">NCBI_THROW</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00822">NON_CONST_ITERATE</a>, <a class="el" href="Dense__seg_8cpp_source.html#l00922">CDense_seg::RemapToLoc()</a>, <a class="el" href="string__bind_8c_source.html#l00073">row</a>, <a class="el" href="Seq__align___8cpp_source.html#l00159">CSeq_align_Base::C_Segs::SetDenseg()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00930">CSeq_align_Base::SetSegs()</a>, and <a class="el" href="Seq__loc___8hpp_source.html#l00475">CSeq_loc_Base::Which()</a>.</p>
|
||
|
||
</div>
|
||
</div>
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||
<a id="a8345d5f956b4ddc58976e8f4115f8db8"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a8345d5f956b4ddc58976e8f4115f8db8">◆ </a></span>ResetNamedScore() <span class="overload">[1/2]</span></h2>
|
||
|
||
<div class="memitem">
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||
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||
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||
<td class="memname">void CSeq_align::ResetNamedScore </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> & </td>
|
||
<td class="paramname"><em>name</em></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00606">606</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="Seq__align___8hpp_source.html#l00884">CSeq_align_Base::IsSetScore()</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00822">NON_CONST_ITERATE</a>, and <a class="el" href="Seq__align___8hpp_source.html#l00902">CSeq_align_Base::SetScore()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="score__builder__base_8cpp_source.html#l00912">CScoreBuilderBase::AddScore()</a>, <a class="el" href="transform__align_8cpp_source.html#l00447">CFeatureGenerator::SImplementation::ClearScores()</a>, <a class="el" href="transform__align_8cpp_source.html#l00471">CFeatureGenerator::SImplementation::RecalculateScores()</a>, and <a class="el" href="Seq__align_8cpp_source.html#l00619">ResetNamedScore()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a67b6cc4b7e39f1e59ba3e51d1f6dca5e"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a67b6cc4b7e39f1e59ba3e51d1f6dca5e">◆ </a></span>ResetNamedScore() <span class="overload">[2/2]</span></h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void CSeq_align::ResetNamedScore </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">EScoreType</a> </td>
|
||
<td class="paramname"><em>type</em></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00619">619</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="Seq__align_8cpp_source.html#l00606">ResetNamedScore()</a>, and <a class="el" href="Seq__align_8cpp_source.html#l00404">sc_ScoreNames</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a302e1860f81ea4eed8f968111801e8a7"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a302e1860f81ea4eed8f968111801e8a7">◆ </a></span>Reverse()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void CSeq_align::Reverse </td>
|
||
<td>(</td>
|
||
<td class="paramtype">void </td>
|
||
<td class="paramname"></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Reverse the segments' orientation NOTE: currently *only* works for dense-seg. </p>
|
||
<p>--------------------------------------------------------------------------- PRE : currently only implemented for dense-seg segments POST: same alignment, opposite orientation </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00685">685</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="Seq__align___8hpp_source.html#l00134">CSeq_align_Base::C_Segs::e_Denseg</a>, <a class="el" href="Seq__align___8hpp_source.html#l00921">CSeq_align_Base::GetSegs()</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l00704">NCBI_THROW</a>, <a class="el" href="Dense__seg_8cpp_source.html#l00644">CDense_seg::Reverse()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00159">CSeq_align_Base::C_Segs::SetDenseg()</a>, and <a class="el" href="Seq__align___8hpp_source.html#l00930">CSeq_align_Base::SetSegs()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="tabular_8cpp_source.html#l01982">CIgBlastTabularInfo::SetAirrFormatData()</a>, <a class="el" href="primercheck_8cpp_source.html#l01495">COligoSpecificityCheck::x_AnalyzeOnePrimer()</a>, and <a class="el" href="objtools_2align__format_2vectorscreen_8cpp_source.html#l00377">CVecscreen::x_MergeSeqalign()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a49d2554e931469d7a9f27034aad72591"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a49d2554e931469d7a9f27034aad72591">◆ </a></span>ScoreName()</h2>
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||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<table class="mlabels">
|
||
<tr>
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<td class="mlabels-left">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname"><a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> CSeq_align::ScoreName </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">EScoreType</a> </td>
|
||
<td class="paramname"><em>score</em></td><td>)</td>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">static</span></span> </td>
|
||
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|
||
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|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00503">503</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="Seq__align_8cpp_source.html#l00404">sc_ScoreNames</a>, and <a class="el" href="static__set_8hpp_source.html#l00065">SStaticPair< FirstType, SecondType >::second</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="score__builder__base_8cpp_source.html#l01013">CScoreBuilderBase::AddSplignScores()</a>, and <a class="el" href="score__builder__base_8cpp_source.html#l01181">CScoreBuilderBase::ComputeScore()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="ac8f0ff6e4f5bac2bd079c1c7725c52e2"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#ac8f0ff6e4f5bac2bd079c1c7725c52e2">◆ </a></span>ScoreNameMap()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<table class="mlabels">
|
||
<tr>
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||
<td class="mlabels-left">
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||
<table class="memname">
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||
<tr>
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||
<td class="memname"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSeq__align.html#a59b599d4d23745a6ff33afb1bcbf0417">CSeq_align::TScoreNameMap</a> & CSeq_align::ScoreNameMap </td>
|
||
<td>(</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>
|
||
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|
||
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||
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|
||
|
||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00483">483</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="ncbimtx_8hpp_source.html#l00496">DEFINE_STATIC_FAST_MUTEX</a>, <a class="el" href="map_8hpp_source.html#l00149">map_checker< Container >::empty()</a>, <a class="el" href="Seq__align_8hpp_source.html#l00133">eScore_Blast</a>, <a class="el" href="Seq__align_8hpp_source.html#l00185">eScore_ExonIdentity</a>, <a class="el" href="static__set_8hpp_source.html#l00064">SStaticPair< FirstType, SecondType >::first</a>, <a class="el" href="Seq__align_8cpp_source.html#l00404">sc_ScoreNames</a>, and <a class="el" href="static__set_8hpp_source.html#l00065">SStaticPair< FirstType, SecondType >::second</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="score__builder__base_8cpp_source.html#l01013">CScoreBuilderBase::AddSplignScores()</a>, <a class="el" href="score__lookup_8cpp_source.html#l02390">CScoreLookup::Complexity()</a>, <a class="el" href="score__lookup_8cpp_source.html#l02432">CScoreLookup::GetScore()</a>, <a class="el" href="score__lookup_8cpp_source.html#l02370">CScoreLookup::HelpText()</a>, <a class="el" href="score__lookup_8cpp_source.html#l02406">CScoreLookup::IsIntegerScore()</a>, and <a class="el" href="score__lookup_8cpp_source.html#l02356">CScoreLookup::PrintDictionary()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="ab341f680226edd9c4d6c60520b80f6a8"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#ab341f680226edd9c4d6c60520b80f6a8">◆ </a></span>SetNamedScore() <span class="overload">[1/4]</span></h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void CSeq_align::SetNamedScore </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> & </td>
|
||
<td class="paramname"><em>id</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype">double </td>
|
||
<td class="paramname"><em>score</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
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||
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||
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|
||
|
||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00642">642</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="Seq__align_8cpp_source.html#l00537">x_SetNamedScore()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a731dda257ee388ccb949ef71c394916f"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a731dda257ee388ccb949ef71c394916f">◆ </a></span>SetNamedScore() <span class="overload">[2/4]</span></h2>
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||
|
||
<div class="memitem">
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||
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|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void CSeq_align::SetNamedScore </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> & </td>
|
||
<td class="paramname"><em>id</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>score</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
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||
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||
</div><div class="memdoc">
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||
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00636">636</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="Seq__align_8cpp_source.html#l00537">x_SetNamedScore()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="score__builder__base_8cpp_source.html#l00912">CScoreBuilderBase::AddScore()</a>, <a class="el" href="ngalign__job_8cpp_source.html#l00099">AddStandardAlignmentScores()</a>, <a class="el" href="score__builder_8cpp_source.html#l00888">CScoreBuilder::AddTieBreaker()</a>, <a class="el" href="pssmcreate__cdd__unit__test_8cpp_source.html#l00870">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="blast__aligner_8cpp_source.html#l00214">CBlastAligner::GenerateAlignments()</a>, <a class="el" href="blast__aligner_8cpp_source.html#l00367">CRemoteBlastAligner::GenerateAlignments()</a>, <a class="el" href="asn1_8cpp_source.html#l00935">CAlignModel::MakeSeqAlign()</a>, <a class="el" href="named__collection__score__impl_8cpp_source.html#l00331">MakeSubjectScores()</a>, <a class="el" href="demo__seqtest_8cpp_source.html#l00085">CDemoSeqQaApp::Run()</a>, <a class="el" href="magicblast_8cpp_source.html#l00334">s_CreateSeqAlign()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00187">CExpansionScorer::ScoreAlignments()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00213">CWeightedIdentityScorer::ScoreAlignments()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00246">CHangScorer::ScoreAlignments()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00324">COverlapScorer::ScoreAlignments()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00400">CClippedScorer::ScoreAlignments()</a>, <a class="el" href="alignment__scorer_8cpp_source.html#l00558">CCommonComponentScorer::ScoreAlignments()</a>, <a class="el" href="advanced__cleanup_8cpp_source.html#l00783">CAdvancedAlignCleanup::x_AddStandardAlignmentScores()</a>, <a class="el" href="pssmcreate__cdd__unit__test_8cpp_source.html#l01073">CPssmCddInputTest::x_CreateAlignment()</a>, <a class="el" href="inversion__merge__aligner_8cpp_source.html#l00264">CInversionMergeAligner::x_CreateDiscAlignment()</a>, <a class="el" href="objtools_2align__format_2vectorscreen_8cpp_source.html#l00377">CVecscreen::x_MergeSeqalign()</a>, <a class="el" href="merge__aligner_8cpp_source.html#l00167">CMergeAligner::x_MergeSeqAlignSet()</a>, <a class="el" href="banded__aligner_8cpp_source.html#l00166">CInstancedAligner::x_RunAligner()</a>, and <a class="el" href="gff2__reader_8cpp_source.html#l01110">CGff2Reader::xAlignmentSetScore()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="ac83f06633e6c67f200244622627617f9"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#ac83f06633e6c67f200244622627617f9">◆ </a></span>SetNamedScore() <span class="overload">[3/4]</span></h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void CSeq_align::SetNamedScore </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">EScoreType</a> </td>
|
||
<td class="paramname"><em>type</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype">double </td>
|
||
<td class="paramname"><em>score</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
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||
</table>
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||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00630">630</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="Seq__align_8cpp_source.html#l00404">sc_ScoreNames</a>, and <a class="el" href="Seq__align_8cpp_source.html#l00537">x_SetNamedScore()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a6171d9165ae21c54d89e2144f7cb99b5"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a6171d9165ae21c54d89e2144f7cb99b5">◆ </a></span>SetNamedScore() <span class="overload">[4/4]</span></h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<table class="memname">
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||
<tr>
|
||
<td class="memname">void CSeq_align::SetNamedScore </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01">EScoreType</a> </td>
|
||
<td class="paramname"><em>type</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>score</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
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||
</table>
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</div><div class="memdoc">
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||
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||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00624">624</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="Seq__align_8cpp_source.html#l00404">sc_ScoreNames</a>, and <a class="el" href="Seq__align_8cpp_source.html#l00537">x_SetNamedScore()</a>.</p>
|
||
|
||
</div>
|
||
</div>
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||
<a id="a87ed9d4eac3797922458bf943b5b8112"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a87ed9d4eac3797922458bf943b5b8112">◆ </a></span>SplitOnLongDiscontinuity()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
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||
<table class="memname">
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||
<tr>
|
||
<td class="memname">void CSeq_align::SplitOnLongDiscontinuity </td>
|
||
<td>(</td>
|
||
<td class="paramtype">list< <a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCSeq__align.html">CSeq_align</a> > > & </td>
|
||
<td class="paramname"><em>aligns</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td>
|
||
<td class="paramname"><em>discontinuity_threshold</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td> const</td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Split the alignment at any discontinuity greater than threshold; populate aligns list with new alignments. </p>
|
||
<p>If alignment contains no long discontinuities, populate aligns list with a singleton reference to self. Splitting works only for Denseg and Disc; for all other segment types, this function simply populates aligns with a singleton reference to self. This function is only implemented for pairwise alignments; it throws an exception if Dim is more than 2. </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l01217">1217</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="Seq__align___8hpp_source.html#l00134">CSeq_align_Base::C_Segs::e_Denseg</a>, <a class="el" href="Seq__align___8hpp_source.html#l00137">CSeq_align_Base::C_Segs::e_Disc</a>, <a class="el" href="range_8hpp_source.html#l00148">COpenRange< Position >::Empty()</a>, <a class="el" href="group__GenClassSupport.html#ggae820720c5bbb78691337c9dfa21adf60a64c3acc11ffdb1be30ea339290bd1508">eUnknown</a>, <a class="el" href="Seq__align__set___8hpp_source.html#l00166">CSeq_align_set_Base::Get()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00153">CSeq_align_Base::C_Segs::GetDenseg()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00856">CSeq_align_Base::GetDim()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00197">CSeq_align_Base::C_Segs::GetDisc()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00555">CDense_seg_Base::GetLens()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00465">CDense_seg_Base::GetNumseg()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00921">CSeq_align_Base::GetSegs()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00530">CDense_seg_Base::GetStarts()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00837">CSeq_align_Base::IsSetDim()</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00815">ITERATE</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l00704">NCBI_THROW</a>, <a class="el" href="range_8hpp_source.html#l00152">COpenRange< Position >::NotEmpty()</a>, <a class="el" href="Seq__align_8cpp_source.html#l01183">s_Distance()</a>, <a class="el" href="Seq__align_8cpp_source.html#l01193">s_GetJoinedAlignment()</a>, <a class="el" href="Seq__align__set___8hpp_source.html#l00172">CSeq_align_set_Base::Set()</a>, and <a class="el" href="Seq__align_8cpp_source.html#l02230">x_CreateSubsegAlignment()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a7c073ec76fa340c940566afd99f7ba00"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a7c073ec76fa340c940566afd99f7ba00">◆ </a></span>SwapRows()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
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||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void CSeq_align::SwapRows </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
|
||
<td class="paramname"><em>row1</em>, </td>
|
||
</tr>
|
||
<tr>
|
||
<td class="paramkey"></td>
|
||
<td></td>
|
||
<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Seqalign.html#ga54ad0aeb1e6312f218c88b223d3b7890">TDim</a> </td>
|
||
<td class="paramname"><em>row2</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td></td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p>Swap the position of two rows in the alignment NOTE: currently *only* works for dense-seg & disc. </p>
|
||
<p>--------------------------------------------------------------------------- PRE : currently only implemented for dense-seg segments; two row numbers POST: same alignment, position of the two rows has been swapped </p>
|
||
|
||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00701">701</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="Seq__align___8hpp_source.html#l00134">CSeq_align_Base::C_Segs::e_Denseg</a>, <a class="el" href="Seq__align___8hpp_source.html#l00137">CSeq_align_Base::C_Segs::e_Disc</a>, <a class="el" href="Seq__align___8hpp_source.html#l00135">CSeq_align_Base::C_Segs::e_Std</a>, <a class="el" href="Seq__align___8hpp_source.html#l00921">CSeq_align_Base::GetSegs()</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l00704">NCBI_THROW</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00822">NON_CONST_ITERATE</a>, <a class="el" href="Seq__align___8cpp_source.html#l00159">CSeq_align_Base::C_Segs::SetDenseg()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00203">CSeq_align_Base::C_Segs::SetDisc()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00930">CSeq_align_Base::SetSegs()</a>, <a class="el" href="Dense__seg_8cpp_source.html#l00686">CDense_seg::SwapRows()</a>, and <a class="el" href="Seq__align__set_8cpp_source.html#l00058">CSeq_align_set::SwapRows()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="ad6c982af80b7728ad3777a1d0a26f89d"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#ad6c982af80b7728ad3777a1d0a26f89d">◆ </a></span>Validate()</h2>
|
||
|
||
<div class="memitem">
|
||
<div class="memproto">
|
||
<table class="memname">
|
||
<tr>
|
||
<td class="memname">void CSeq_align::Validate </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td>
|
||
<td class="paramname"><em>full_test</em> = <code><a class="el" href="ftds14_2freetds_2freetds_2bool_8h.html#a65e9886d74aaee76545e83dd09011727">false</a></code></td><td>)</td>
|
||
<td> const</td>
|
||
</tr>
|
||
</table>
|
||
</div><div class="memdoc">
|
||
|
||
<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00649">649</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
|
||
|
||
<p class="reference">References <a class="el" href="Seq__align_8cpp_source.html#l00073">CheckNumRows()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00133">CSeq_align_Base::C_Segs::e_Dendiag</a>, <a class="el" href="Seq__align___8hpp_source.html#l00134">CSeq_align_Base::C_Segs::e_Denseg</a>, <a class="el" href="Seq__align___8hpp_source.html#l00137">CSeq_align_Base::C_Segs::e_Disc</a>, <a class="el" href="Seq__align___8hpp_source.html#l00139">CSeq_align_Base::C_Segs::e_Sparse</a>, <a class="el" href="Seq__align___8hpp_source.html#l00138">CSeq_align_Base::C_Segs::e_Spliced</a>, <a class="el" href="Seq__align___8hpp_source.html#l00135">CSeq_align_Base::C_Segs::e_Std</a>, <a class="el" href="named__parameters_8hpp_source.html#l00099">Get()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00153">CSeq_align_Base::C_Segs::GetDenseg()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00921">CSeq_align_Base::GetSegs()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00241">CSeq_align_Base::C_Segs::GetSparse()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00219">CSeq_align_Base::C_Segs::GetSpliced()</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00815">ITERATE</a>, <a class="el" href="ncbiexpt_8hpp_source.html#l00704">NCBI_THROW</a>, <a class="el" href="Dense__seg_8cpp_source.html#l00274">CDense_seg::Validate()</a>, <a class="el" href="Sparse__seg_8cpp_source.html#l00055">CSparse_seg::Validate()</a>, and <a class="el" href="Spliced__seg_8cpp_source.html#l00159">CSpliced_seg::Validate()</a>.</p>
|
||
|
||
<p class="reference">Referenced by <a class="el" href="unit__test__gene__model_8cpp_source.html#l00278">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="Seq__align_8cpp_source.html#l01015">CreateDensegFromDisc()</a>, <a class="el" href="align__cleanup_8cpp_source.html#l00057">CAlignCleanup::CreatePairwiseFromMultiple()</a>, <a class="el" href="aln__container_8cpp_source.html#l00054">CAlnContainer::insert()</a>, <a class="el" href="aln__build__app_8cpp_source.html#l00077">CAlnBuildApp::InsertAln()</a>, <a class="el" href="aln__test__app_8cpp_source.html#l00082">CAlnTestApp::InsertAln()</a>, <a class="el" href="pairwise__aln__app_8cpp_source.html#l00083">CPairwiseAlnApp::InsertAln()</a>, <a class="el" href="unit__test__alnmgr_8cpp_source.html#l00104">LoadAligns()</a>, <a class="el" href="asn1_8cpp_source.html#l00985">CAnnotationASN1::CImplementationData::model2spliced_seq_align()</a>, <a class="el" href="seqids__extractor_8hpp_source.html#l00112">CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator()()</a>, <a class="el" href="aln__tests_8hpp_source.html#l00087">CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::push_back()</a>, <a class="el" href="Seq__align_8cpp_source.html#l01193">s_GetJoinedAlignment()</a>, <a class="el" href="gff3__writer_8cpp_source.html#l00293">CGff3Writer::WriteAlign()</a>, <a class="el" href="align__cleanup_8cpp_source.html#l00260">CAlignCleanup::x_Cleanup_AnchoredAln()</a>, <a class="el" href="alignment__job_8cpp_source.html#l01359">CSGAlignmentJob::x_CreateAlignGlyphsForCrossOriginAlign()</a>, <a class="el" href="merge__alignments__tool__manager_8cpp_source.html#l00186">CMergeAlignmentsJob::x_CreateProjectItems()</a>, <a class="el" href="Seq__align_8cpp_source.html#l02230">x_CreateSubsegAlignment()</a>, and <a class="el" href="merge__tree_8cpp_source.html#l00795">CTreeAlignMerger::x_MakeSeqAlign()</a>.</p>
|
||
|
||
</div>
|
||
</div>
|
||
<a id="a1ec0983af480287bd51eb3f1ed0ebb99"></a>
|
||
<h2 class="memtitle"><span class="permalink"><a href="#a1ec0983af480287bd51eb3f1ed0ebb99">◆ </a></span>x_CreateSubsegAlignment()</h2>
|
||
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||
<div class="memitem">
|
||
<div class="memproto">
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||
<table class="mlabels">
|
||
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||
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<td class="memname"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCSeq__align.html">CSeq_align</a> > CSeq_align::x_CreateSubsegAlignment </td>
|
||
<td>(</td>
|
||
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
|
||
<td class="paramname"><em>from</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>to</em> </td>
|
||
</tr>
|
||
<tr>
|
||
<td></td>
|
||
<td>)</td>
|
||
<td></td><td> const</td>
|
||
</tr>
|
||
</table>
|
||
</td>
|
||
<td class="mlabels-right">
|
||
<span class="mlabels"><span class="mlabel">private</span></span> </td>
|
||
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|
||
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||
</div><div class="memdoc">
|
||
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<p>Create a partial alignment containing the specified range of segments. </p>
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<p>Can only be called for Denseg alignments. </p>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l02230">2230</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <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="Seq__align___8hpp_source.html#l00103">CSeq_align_Base::eType_partial</a>, <a class="el" href="Seq__align___8cpp_source.html#l00153">CSeq_align_Base::C_Segs::GetDenseg()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00505">CDense_seg_Base::GetIds()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00555">CDense_seg_Base::GetLens()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00465">CDense_seg_Base::GetNumseg()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00921">CSeq_align_Base::GetSegs()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00530">CDense_seg_Base::GetStarts()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00580">CDense_seg_Base::GetStrands()</a>, <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00568">CDense_seg_Base::IsSetStrands()</a>, <a class="el" href="serialbase_8hpp_source.html#l00696">MSerial_AsnText</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00427">CDense_seg_Base::SetDim()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00865">CSeq_align_Base::SetDim()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00511">CDense_seg_Base::SetIds()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00561">CDense_seg_Base::SetLens()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00474">CDense_seg_Base::SetNumseg()</a>, <a class="el" href="Seq__align___8cpp_source.html#l00310">CSeq_align_Base::SetSegs()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00536">CDense_seg_Base::SetStarts()</a>, <a class="el" href="Dense__seg___8hpp_source.html#l00586">CDense_seg_Base::SetStrands()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00818">CSeq_align_Base::SetType()</a>, <a class="el" href="Dense__seg_8cpp_source.html#l00344">CDense_seg::TrimEndGaps()</a>, and <a class="el" href="Seq__align_8cpp_source.html#l00649">Validate()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="Seq__align_8cpp_source.html#l01217">SplitOnLongDiscontinuity()</a>.</p>
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</div>
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</div>
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<a id="a599cbe4e53d7bdd1f3afe232fd69f133"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a599cbe4e53d7bdd1f3afe232fd69f133">◆ </a></span>x_GetNamedScore()</h2>
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<div class="memproto">
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<td class="memname"><a class="el" href="classCConstRef.html">CConstRef</a>< <a class="el" href="classCScore.html">CScore</a> > CSeq_align::x_GetNamedScore </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> & </td>
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<td class="paramname"><em>name</em></td><td>)</td>
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<td> const</td>
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</td>
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<td class="mlabels-right">
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<span class="mlabels"><span class="mlabel">protected</span></span> </td>
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<p>retrieve a named score object </p>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00520">520</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="Seq__align___8hpp_source.html#l00896">CSeq_align_Base::GetScore()</a>, <a class="el" href="Seq__align___8hpp_source.html#l00884">CSeq_align_Base::IsSetScore()</a>, and <a class="el" href="ncbimisc_8hpp_source.html#l00815">ITERATE</a>.</p>
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<p class="reference">Referenced by <a class="el" href="Seq__align_8cpp_source.html#l00563">GetNamedScore()</a>.</p>
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</div>
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<a id="a17ab1957cd28d6b7d6ce968bcdf72613"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a17ab1957cd28d6b7d6ce968bcdf72613">◆ </a></span>x_SetNamedScore()</h2>
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<div class="memproto">
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<td class="memname"><a class="el" href="classCRef.html">CRef</a>< <a class="el" href="classCScore.html">CScore</a> > CSeq_align::x_SetNamedScore </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> & </td>
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<td class="paramname"><em>name</em></td><td>)</td>
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<td></td>
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<span class="mlabels"><span class="mlabel">protected</span></span> </td>
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<p class="definition">Definition at line <a class="el" href="Seq__align_8cpp_source.html#l00537">537</a> of file <a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a>.</p>
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<p class="reference">References <a class="el" href="Seq__align___8hpp_source.html#l00884">CSeq_align_Base::IsSetScore()</a>, <a class="el" href="ncbimisc_8hpp_source.html#l00822">NON_CONST_ITERATE</a>, <a class="el" href="ncbiobj_8hpp_source.html#l00773">CRef< C, Locker >::Reset()</a>, and <a class="el" href="Seq__align___8hpp_source.html#l00902">CSeq_align_Base::SetScore()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="Seq__align_8cpp_source.html#l00624">SetNamedScore()</a>.</p>
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</div>
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</div>
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<hr/>The documentation for this class was generated from the following files:<ul>
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<li>include/objects/seqalign/<a class="el" href="Seq__align_8hpp_source.html">Seq_align.hpp</a></li>
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<li>src/objects/seqalign/<a class="el" href="Seq__align_8cpp_source.html">Seq_align.cpp</a></li>
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</ul>
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<address style="align: right;"><small>Modified on Fri Sep 20 14:58:29 2024 by modify_doxy.py rev. 669887</small></address>
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