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<title>NCBI C++ ToolKit: CHit Class Reference</title>
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<div class="header">
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<a href="#pub-types">Public Types</a> &#124;
<a href="#pub-methods">Public Member Functions</a> &#124;
<a href="#pub-attribs">Public Attributes</a> &#124;
<a href="#pub-static-attribs">Static Public Attributes</a> &#124;
<a href="#pri-types">Private Types</a> &#124;
<a href="#pri-methods">Private Member Functions</a> &#124;
<a href="#pri-attribs">Private Attributes</a> &#124;
<a href="classCHit-members.html">List of all members</a> </div>
<div class="headertitle">
<div class="title">CHit Class Reference<div class="ingroups"><a class="el" href="group__DatatoolGeneratedClasses.html">DatatoolGeneratedClasses</a> &raquo; <a class="el" href="group__dataspec__NCBI__BlastOutput.html">Code generated by DATATOOL from 'blastxml.asn' (module 'NCBI-BlastOutput')</a> &#124; <a class="el" href="group__DatatoolGeneratedClasses.html">DatatoolGeneratedClasses</a> &raquo; <a class="el" href="group__dataspec__NCBI__BlastOutput2.html">Code generated by DATATOOL from 'blastxml2.asn' (module 'NCBI-BlastOutput2')</a></div></div> </div>
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<p>
<a class="el" href = "https://www.ncbi.nlm.nih.gov/toolkitbookgh/?term=CHit">Search Toolkit Book for <i>CHit</i></a>
</p>
<p>A generalized representation of a pairwise alignment.
<a href="classCHit.html#details">More...</a></p>
<p><code>#include &lt;<a class="el" href="algo_2cobalt_2hit_8hpp_source.html">algo/cobalt/hit.hpp</a>&gt;</code></p>
<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
<img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for CHit:</div>
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<area shape="rect" href="classCHit__Base.html" title="CHit_Base –." alt="" coords="27,229,113,256"/>
<area shape="rect" href="classCSerialObject.html" title="Base class for all serializable objects." alt="" coords="19,155,121,181"/>
<area shape="rect" href="classCObject.html" title="CObject –." alt="" coords="35,80,105,107"/>
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<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
<img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for CHit:</div>
<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
</div>
<div id="dynsection-1-content" class="dyncontent" style="display:none;">
<div class="center"><img src="img__coll__graph/classCHit__coll__graph.png" border="0" usemap="#aCHit_coll__map" alt="Collaboration graph"/></div>
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<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
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<tr class="memitem:ae7601ab4889718bc6200637d3d2172e5"><td class="memItemLeft" align="right" valign="top">typedef vector&lt; <a class="el" href="classCHit.html">CHit</a> * &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#ae7601ab4889718bc6200637d3d2172e5">TSubHit</a></td></tr>
<tr class="memdesc:ae7601ab4889718bc6200637d3d2172e5"><td class="mdescLeft">&#160;</td><td class="mdescRight">Hits can be grouped hierarchically. <a href="classCHit.html#ae7601ab4889718bc6200637d3d2172e5">More...</a><br /></td></tr>
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<tr class="inherit_header pub_types_classCHit__Base"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classCHit__Base')"><img src="closed.png" alt="-"/>&#160;Public Types inherited from <a class="el" href="classCHit__Base.html">CHit_Base</a></td></tr>
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&#160;&#160;<a class="el" href="group__dataspec__NCBI__BlastOutput.html#gga5096ae8bca2ea4f301e5c2283ee3aeabac28d312aebdb318059ee0b31d8aec8fa">e_num</a>
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<br />
}</td></tr>
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<tr class="memitem:ga5096ae8bca2ea4f301e5c2283ee3aeab inherit pub_types_classCHit__Base"><td class="memItemLeft" align="right" valign="top">enum class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga5096ae8bca2ea4f301e5c2283ee3aeab">E_memberIndex</a> { <br />
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, <br />
&#160;&#160;<a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gga5096ae8bca2ea4f301e5c2283ee3aeabadd6ac57a46d55e4e9f080b4f7c7a6345">e_accession</a>
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&#160;&#160;<a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gga5096ae8bca2ea4f301e5c2283ee3aeabac28d312aebdb318059ee0b31d8aec8fa">e_num</a>
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, <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gga5096ae8bca2ea4f301e5c2283ee3aeaba97aa59e84d81a37af5b98f8cafe48d24">e_hsps</a>
<br />
}</td></tr>
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<tr class="separator:gae212dee06459e6dc9f8dd07964819118 inherit pub_types_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga0fd986049d94a6d1b5b3edc1d4c1541c inherit pub_types_classCHit__Base"><td class="memItemLeft" align="right" valign="top">typedef list&lt; <a class="el" href="classCRef.html">CRef</a>&lt; <a class="el" href="classCHitDescr.html">CHitDescr</a> &gt; &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga0fd986049d94a6d1b5b3edc1d4c1541c">TDescription</a></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="-"/>&#160;Public Types inherited from <a class="el" href="classCObject.html">CObject</a></td></tr>
<tr class="memitem:ga3cf5f3ac0aef32c4aab1fa66513588cc inherit pub_types_classCObject"><td class="memItemLeft" align="right" valign="top">enum &#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:ga2da943ea997324fcabb60e1a1ed1b71c inherit pub_types_classCObject"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCObjectCounterLocker.html">CObjectCounterLocker</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga2da943ea997324fcabb60e1a1ed1b71c">TLockerType</a></td></tr>
<tr class="memdesc:ga2da943ea997324fcabb60e1a1ed1b71c inherit pub_types_classCObject"><td class="mdescLeft">&#160;</td><td class="mdescRight">Default locker type for <a class="el" href="classCRef.html" title="CRef –.">CRef</a>. <a href="group__Object.html#ga2da943ea997324fcabb60e1a1ed1b71c">More...</a><br /></td></tr>
<tr class="separator:ga2da943ea997324fcabb60e1a1ed1b71c inherit pub_types_classCObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gad6d6ac3cac6272609b70c101aaaeebf9 inherit pub_types_classCObject"><td class="memItemLeft" align="right" valign="top">typedef atomic&lt; <a class="el" href="group__Portability.html#gacb8f7ba15b8bac46f42c33b22099a6de">Uint8</a> &gt;&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:ga2e073b6c5b9c29648510bd99ebe00a5c inherit pub_types_classCObject"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="group__Portability.html#gacb8f7ba15b8bac46f42c33b22099a6de">Uint8</a>&#160;</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">&#160;</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">&#160;</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>
<tr class="memitem:acbaab500b53a39fa14bdbaa4897feb9a"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#acbaab500b53a39fa14bdbaa4897feb9a">CHit</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> seq1_index, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> seq2_index)</td></tr>
<tr class="memdesc:acbaab500b53a39fa14bdbaa4897feb9a"><td class="mdescLeft">&#160;</td><td class="mdescRight">Create an empty alignment. <a href="classCHit.html#acbaab500b53a39fa14bdbaa4897feb9a">More...</a><br /></td></tr>
<tr class="separator:acbaab500b53a39fa14bdbaa4897feb9a"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a61fc61e5f9849478788f15bfb8597b4c"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#a61fc61e5f9849478788f15bfb8597b4c">CHit</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> seq1_index, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> seq2_index, <a class="el" href="structBlastHSP.html">BlastHSP</a> *hsp)</td></tr>
<tr class="memdesc:a61fc61e5f9849478788f15bfb8597b4c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Create an alignment from a BLAST hit. <a href="classCHit.html#a61fc61e5f9849478788f15bfb8597b4c">More...</a><br /></td></tr>
<tr class="separator:a61fc61e5f9849478788f15bfb8597b4c"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a12f6b6bf0386f8f0e6af136b8f8bdf5e"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#a12f6b6bf0386f8f0e6af136b8f8bdf5e">CHit</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> seq1_index, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> seq2_index, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> score, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> objects::CDense_seg &amp;denseg)</td></tr>
<tr class="memdesc:a12f6b6bf0386f8f0e6af136b8f8bdf5e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Create an alignment from a Dense_seg. <a href="classCHit.html#a12f6b6bf0386f8f0e6af136b8f8bdf5e">More...</a><br /></td></tr>
<tr class="separator:a12f6b6bf0386f8f0e6af136b8f8bdf5e"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a8236d50dfeab03ac04d0c1f54f7bb2ef"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#a8236d50dfeab03ac04d0c1f54f7bb2ef">CHit</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> seq1_index, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> seq2_index, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> score, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> objects::CDense_diag &amp;dendiag)</td></tr>
<tr class="memdesc:a8236d50dfeab03ac04d0c1f54f7bb2ef"><td class="mdescLeft">&#160;</td><td class="mdescRight">Create an alignment from a Dense_diag. <a href="classCHit.html#a8236d50dfeab03ac04d0c1f54f7bb2ef">More...</a><br /></td></tr>
<tr class="separator:a8236d50dfeab03ac04d0c1f54f7bb2ef"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a16471ebaf022e9e835aa6fcca9876b46"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#a16471ebaf022e9e835aa6fcca9876b46">CHit</a> (<a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> seq1_index, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> seq2_index, <a class="el" href="base_8hpp.html#a82668c1a5428e2d884d0f0c67d97fdf1">TRange</a> seq_range1, <a class="el" href="base_8hpp.html#a82668c1a5428e2d884d0f0c67d97fdf1">TRange</a> seq_range2, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> score, <a class="el" href="classCEditScript.html">CEditScript</a> edit_script)</td></tr>
<tr class="memdesc:a16471ebaf022e9e835aa6fcca9876b46"><td class="mdescLeft">&#160;</td><td class="mdescRight">Create an alignment with all specified parameters. <a href="classCHit.html#a16471ebaf022e9e835aa6fcca9876b46">More...</a><br /></td></tr>
<tr class="separator:a16471ebaf022e9e835aa6fcca9876b46"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ade8d162d4f1bef2580652d39bd7c0f6e"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#ade8d162d4f1bef2580652d39bd7c0f6e">~CHit</a> ()</td></tr>
<tr class="memdesc:ade8d162d4f1bef2580652d39bd7c0f6e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Destructor. <a href="classCHit.html#ade8d162d4f1bef2580652d39bd7c0f6e">More...</a><br /></td></tr>
<tr class="separator:ade8d162d4f1bef2580652d39bd7c0f6e"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a60d366a793bd4c751c1d1a14a7b41dae"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#a60d366a793bd4c751c1d1a14a7b41dae">InsertSubHit</a> (<a class="el" href="classCHit.html">CHit</a> *hit)</td></tr>
<tr class="memdesc:a60d366a793bd4c751c1d1a14a7b41dae"><td class="mdescLeft">&#160;</td><td class="mdescRight">Add a to a <a class="el" href="classCHit.html" title="A generalized representation of a pairwise alignment.">CHit</a>'s list of subhits. <a href="classCHit.html#a60d366a793bd4c751c1d1a14a7b41dae">More...</a><br /></td></tr>
<tr class="separator:a60d366a793bd4c751c1d1a14a7b41dae"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a0ff84da4f65908f9dabcc0f1348798b5"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCHit.html#ae7601ab4889718bc6200637d3d2172e5">TSubHit</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#a0ff84da4f65908f9dabcc0f1348798b5">GetSubHit</a> ()</td></tr>
<tr class="memdesc:a0ff84da4f65908f9dabcc0f1348798b5"><td class="mdescLeft">&#160;</td><td class="mdescRight">Retrieve a list of subhits. <a href="classCHit.html#a0ff84da4f65908f9dabcc0f1348798b5">More...</a><br /></td></tr>
<tr class="separator:a0ff84da4f65908f9dabcc0f1348798b5"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aadb02ad4a88803334256c94d8a02810d"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCEditScript.html">CEditScript</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#aadb02ad4a88803334256c94d8a02810d">GetEditScript</a> ()</td></tr>
<tr class="memdesc:aadb02ad4a88803334256c94d8a02810d"><td class="mdescLeft">&#160;</td><td class="mdescRight">Retrieve the traceback associated with a <a class="el" href="classCHit.html" title="A generalized representation of a pairwise alignment.">CHit</a>. <a href="classCHit.html#aadb02ad4a88803334256c94d8a02810d">More...</a><br /></td></tr>
<tr class="separator:aadb02ad4a88803334256c94d8a02810d"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ae0212e09bf44bac32deedfc7317c01bf"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#ae0212e09bf44bac32deedfc7317c01bf">HasSubHits</a> ()</td></tr>
<tr class="memdesc:ae0212e09bf44bac32deedfc7317c01bf"><td class="mdescLeft">&#160;</td><td class="mdescRight">Query if a <a class="el" href="classCHit.html" title="A generalized representation of a pairwise alignment.">CHit</a> has a hierarchy of subhits available. <a href="classCHit.html#ae0212e09bf44bac32deedfc7317c01bf">More...</a><br /></td></tr>
<tr class="separator:ae0212e09bf44bac32deedfc7317c01bf"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a68f59b3a8136766fda92dfdbdb7c8709"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#a68f59b3a8136766fda92dfdbdb7c8709">AddUpSubHits</a> ()</td></tr>
<tr class="memdesc:a68f59b3a8136766fda92dfdbdb7c8709"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sum the score of all subhits, and make the sequence ranges the union of the ranges of all subhits. <a href="classCHit.html#a68f59b3a8136766fda92dfdbdb7c8709">More...</a><br /></td></tr>
<tr class="separator:a68f59b3a8136766fda92dfdbdb7c8709"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a4fd3a163bfa7ecb665a664dbe0ca618f"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCHit.html">CHit</a> *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#a4fd3a163bfa7ecb665a664dbe0ca618f">Clone</a> ()</td></tr>
<tr class="memdesc:a4fd3a163bfa7ecb665a664dbe0ca618f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Produce an independent copy of a <a class="el" href="classCHit.html" title="A generalized representation of a pairwise alignment.">CHit</a>. <a href="classCHit.html#a4fd3a163bfa7ecb665a664dbe0ca618f">More...</a><br /></td></tr>
<tr class="separator:a4fd3a163bfa7ecb665a664dbe0ca618f"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a61e3b2b920739aa249b9af31d7aab92b"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#a61e3b2b920739aa249b9af31d7aab92b">GetRangeFromSeq2</a> (<a class="el" href="base_8hpp.html#a82668c1a5428e2d884d0f0c67d97fdf1">TRange</a> seq_range2, <a class="el" href="base_8hpp.html#a82668c1a5428e2d884d0f0c67d97fdf1">TRange</a> &amp;seq_range1, <a class="el" href="base_8hpp.html#a82668c1a5428e2d884d0f0c67d97fdf1">TRange</a> &amp;new_seq_range2, <a class="el" href="base_8hpp.html#a82668c1a5428e2d884d0f0c67d97fdf1">TRange</a> &amp;traceback_range)</td></tr>
<tr class="memdesc:a61e3b2b920739aa249b9af31d7aab92b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Retrieve the seq1 range corresponding to a specified seq2 range. <a href="classCHit.html#a61e3b2b920739aa249b9af31d7aab92b">More...</a><br /></td></tr>
<tr class="separator:a61e3b2b920739aa249b9af31d7aab92b"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a000263cc1e4c7f20a7414020b7ec33c9"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#a000263cc1e4c7f20a7414020b7ec33c9">GetRangeFromSeq1</a> (<a class="el" href="base_8hpp.html#a82668c1a5428e2d884d0f0c67d97fdf1">TRange</a> seq_range1, <a class="el" href="base_8hpp.html#a82668c1a5428e2d884d0f0c67d97fdf1">TRange</a> &amp;new_seq_range1, <a class="el" href="base_8hpp.html#a82668c1a5428e2d884d0f0c67d97fdf1">TRange</a> &amp;seq_range2, <a class="el" href="base_8hpp.html#a82668c1a5428e2d884d0f0c67d97fdf1">TRange</a> &amp;traceback_range)</td></tr>
<tr class="memdesc:a000263cc1e4c7f20a7414020b7ec33c9"><td class="mdescLeft">&#160;</td><td class="mdescRight">Retrieve the seq2 range corresponding to a specified seq1 range. <a href="classCHit.html#a000263cc1e4c7f20a7414020b7ec33c9">More...</a><br /></td></tr>
<tr class="separator:a000263cc1e4c7f20a7414020b7ec33c9"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a377dc4366e7dfe8d7ce50e75c0ee268e"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#a377dc4366e7dfe8d7ce50e75c0ee268e">VerifyHit</a> ()</td></tr>
<tr class="memdesc:a377dc4366e7dfe8d7ce50e75c0ee268e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Perform basic integrity checks on a <a class="el" href="classCHit.html" title="A generalized representation of a pairwise alignment.">CHit</a>. <a href="classCHit.html#a377dc4366e7dfe8d7ce50e75c0ee268e">More...</a><br /></td></tr>
<tr class="separator:a377dc4366e7dfe8d7ce50e75c0ee268e"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a45aef14f14da8664ca53393631ce4922"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#a45aef14f14da8664ca53393631ce4922">ResolveSubHitConflicts</a> (<a class="el" href="classCSequence.html">CSequence</a> &amp;seq1, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> **seq2_pssm, <a class="el" href="group__AlgoAlignRoot.html#ga52f93d4188f6edb1940043ae7a67605b">CNWAligner::TScore</a> gap_open, <a class="el" href="group__AlgoAlignRoot.html#ga52f93d4188f6edb1940043ae7a67605b">CNWAligner::TScore</a> gap_extend)</td></tr>
<tr class="memdesc:a45aef14f14da8664ca53393631ce4922"><td class="mdescLeft">&#160;</td><td class="mdescRight">If pairs of subhits have overlapping ranges, either delete one or change one so that the overlap is avoided. <a href="classCHit.html#a45aef14f14da8664ca53393631ce4922">More...</a><br /></td></tr>
<tr class="separator:a45aef14f14da8664ca53393631ce4922"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gae6403c5c4b80c255215910d8c851ec1a"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gae6403c5c4b80c255215910d8c851ec1a">CHit</a> (void)</td></tr>
<tr class="separator:gae6403c5c4b80c255215910d8c851ec1a"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaaa015dec762f8a683ca1e6d94d41dd22"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gaaa015dec762f8a683ca1e6d94d41dd22">~CHit</a> (void)</td></tr>
<tr class="separator:gaaa015dec762f8a683ca1e6d94d41dd22"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gae6403c5c4b80c255215910d8c851ec1a"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gae6403c5c4b80c255215910d8c851ec1a">CHit</a> (void)</td></tr>
<tr class="separator:gae6403c5c4b80c255215910d8c851ec1a"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaaa015dec762f8a683ca1e6d94d41dd22"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaaa015dec762f8a683ca1e6d94d41dd22">~CHit</a> (void)</td></tr>
<tr class="separator:gaaa015dec762f8a683ca1e6d94d41dd22"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="inherit_header pub_methods_classCHit__Base"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classCHit__Base')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classCHit__Base.html">CHit_Base</a></td></tr>
<tr class="memitem:ga8afaa6d7e7b0e658e387dfe4e804a4b2 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga8afaa6d7e7b0e658e387dfe4e804a4b2">CHit_Base</a> (void)</td></tr>
<tr class="separator:ga8afaa6d7e7b0e658e387dfe4e804a4b2 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gafe36f15e3c0d28630dbb886fe555e5fc inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gafe36f15e3c0d28630dbb886fe555e5fc">~CHit_Base</a> (void)</td></tr>
<tr class="separator:gafe36f15e3c0d28630dbb886fe555e5fc inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaffa81baec206d6a6ff681e27158e4c64 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gaffa81baec206d6a6ff681e27158e4c64">DECLARE_INTERNAL_TYPE_INFO</a> ()</td></tr>
<tr class="separator:gaffa81baec206d6a6ff681e27158e4c64 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga24705f1cd1e72c8d4ac50a6f76fc4ddb inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga24705f1cd1e72c8d4ac50a6f76fc4ddb">IsSetNum</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:ga24705f1cd1e72c8d4ac50a6f76fc4ddb inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">hit number <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Num data member. <a href="group__dataspec__NCBI__BlastOutput.html#ga24705f1cd1e72c8d4ac50a6f76fc4ddb">More...</a><br /></td></tr>
<tr class="separator:ga24705f1cd1e72c8d4ac50a6f76fc4ddb inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga4ba8a9c12cf14e6560c0c3591d1fa6e0 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga4ba8a9c12cf14e6560c0c3591d1fa6e0">CanGetNum</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:ga4ba8a9c12cf14e6560c0c3591d1fa6e0 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetNum method. <a href="group__dataspec__NCBI__BlastOutput.html#ga4ba8a9c12cf14e6560c0c3591d1fa6e0">More...</a><br /></td></tr>
<tr class="separator:ga4ba8a9c12cf14e6560c0c3591d1fa6e0 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaf9dec320adb0c575b1e30f5f0a91b5c8 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gaf9dec320adb0c575b1e30f5f0a91b5c8">ResetNum</a> (void)</td></tr>
<tr class="memdesc:gaf9dec320adb0c575b1e30f5f0a91b5c8 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Reset Num data member. <a href="group__dataspec__NCBI__BlastOutput.html#gaf9dec320adb0c575b1e30f5f0a91b5c8">More...</a><br /></td></tr>
<tr class="separator:gaf9dec320adb0c575b1e30f5f0a91b5c8 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga972ed0d63a9ac4c8855a7c5ba5c51f8b inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gae212dee06459e6dc9f8dd07964819118">TNum</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga972ed0d63a9ac4c8855a7c5ba5c51f8b">GetNum</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:ga972ed0d63a9ac4c8855a7c5ba5c51f8b inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the Num member data. <a href="group__dataspec__NCBI__BlastOutput.html#ga972ed0d63a9ac4c8855a7c5ba5c51f8b">More...</a><br /></td></tr>
<tr class="separator:ga972ed0d63a9ac4c8855a7c5ba5c51f8b inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gafb81acffaa4bdf1033f2420a4fda6800 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gafb81acffaa4bdf1033f2420a4fda6800">SetNum</a> (<a class="el" href="group__dataspec__NCBI__BlastOutput.html#gae212dee06459e6dc9f8dd07964819118">TNum</a> <a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
<tr class="memdesc:gafb81acffaa4bdf1033f2420a4fda6800 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assign a value to Num data member. <a href="group__dataspec__NCBI__BlastOutput.html#gafb81acffaa4bdf1033f2420a4fda6800">More...</a><br /></td></tr>
<tr class="separator:gafb81acffaa4bdf1033f2420a4fda6800 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga998b0356abb0634c6fa25076de4229d1 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gae212dee06459e6dc9f8dd07964819118">TNum</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga998b0356abb0634c6fa25076de4229d1">SetNum</a> (void)</td></tr>
<tr class="memdesc:ga998b0356abb0634c6fa25076de4229d1 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assign a value to Num data member. <a href="group__dataspec__NCBI__BlastOutput.html#ga998b0356abb0634c6fa25076de4229d1">More...</a><br /></td></tr>
<tr class="separator:ga998b0356abb0634c6fa25076de4229d1 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga80de01dec9dd0ce2d56d53e3a3813fd5 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga80de01dec9dd0ce2d56d53e3a3813fd5">IsSetId</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:ga80de01dec9dd0ce2d56d53e3a3813fd5 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">SeqId of subject <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Id data member. <a href="group__dataspec__NCBI__BlastOutput.html#ga80de01dec9dd0ce2d56d53e3a3813fd5">More...</a><br /></td></tr>
<tr class="separator:ga80de01dec9dd0ce2d56d53e3a3813fd5 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gac5483fb7967487a08a8ede2670f6e072 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gac5483fb7967487a08a8ede2670f6e072">CanGetId</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:gac5483fb7967487a08a8ede2670f6e072 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</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__BlastOutput.html#gac5483fb7967487a08a8ede2670f6e072">More...</a><br /></td></tr>
<tr class="separator:gac5483fb7967487a08a8ede2670f6e072 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga50a747f72b9785ba1ae5eaf600d0453e inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga50a747f72b9785ba1ae5eaf600d0453e">ResetId</a> (void)</td></tr>
<tr class="memdesc:ga50a747f72b9785ba1ae5eaf600d0453e inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Reset Id data member. <a href="group__dataspec__NCBI__BlastOutput.html#ga50a747f72b9785ba1ae5eaf600d0453e">More...</a><br /></td></tr>
<tr class="separator:ga50a747f72b9785ba1ae5eaf600d0453e inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga8d8962043dfc0d068d09efc50771f8b0 inherit pub_methods_classCHit__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__BlastOutput.html#gafd4239db48efc783713e1c48805dd262">TId</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga8d8962043dfc0d068d09efc50771f8b0">GetId</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:ga8d8962043dfc0d068d09efc50771f8b0 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the Id member data. <a href="group__dataspec__NCBI__BlastOutput.html#ga8d8962043dfc0d068d09efc50771f8b0">More...</a><br /></td></tr>
<tr class="separator:ga8d8962043dfc0d068d09efc50771f8b0 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga31c9e2b30a77bfe5d854f83256422235 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga31c9e2b30a77bfe5d854f83256422235">SetId</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput.html#gafd4239db48efc783713e1c48805dd262">TId</a> &amp;<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
<tr class="memdesc:ga31c9e2b30a77bfe5d854f83256422235 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assign a value to Id data member. <a href="group__dataspec__NCBI__BlastOutput.html#ga31c9e2b30a77bfe5d854f83256422235">More...</a><br /></td></tr>
<tr class="separator:ga31c9e2b30a77bfe5d854f83256422235 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga020bfd8446537c17ff7aad7d0217db01 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga020bfd8446537c17ff7aad7d0217db01">SetId</a> (<a class="el" href="group__dataspec__NCBI__BlastOutput.html#gafd4239db48efc783713e1c48805dd262">TId</a> &amp;&amp;<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
<tr class="separator:ga020bfd8446537c17ff7aad7d0217db01 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga2eaec42b07ec2013c387ba94f8eba765 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gafd4239db48efc783713e1c48805dd262">TId</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga2eaec42b07ec2013c387ba94f8eba765">SetId</a> (void)</td></tr>
<tr class="memdesc:ga2eaec42b07ec2013c387ba94f8eba765 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assign a value to Id data member. <a href="group__dataspec__NCBI__BlastOutput.html#ga2eaec42b07ec2013c387ba94f8eba765">More...</a><br /></td></tr>
<tr class="separator:ga2eaec42b07ec2013c387ba94f8eba765 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gae3b4c4b7a71b63a51dea43b710cac8f9 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gae3b4c4b7a71b63a51dea43b710cac8f9">IsSetDef</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:gae3b4c4b7a71b63a51dea43b710cac8f9 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">definition line of subject <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Def data member. <a href="group__dataspec__NCBI__BlastOutput.html#gae3b4c4b7a71b63a51dea43b710cac8f9">More...</a><br /></td></tr>
<tr class="separator:gae3b4c4b7a71b63a51dea43b710cac8f9 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga65dc3b368b8fbbc90ccc663f792f9bc3 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga65dc3b368b8fbbc90ccc663f792f9bc3">CanGetDef</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:ga65dc3b368b8fbbc90ccc663f792f9bc3 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetDef method. <a href="group__dataspec__NCBI__BlastOutput.html#ga65dc3b368b8fbbc90ccc663f792f9bc3">More...</a><br /></td></tr>
<tr class="separator:ga65dc3b368b8fbbc90ccc663f792f9bc3 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga7371035323733c5fe95e5ee594bfeb86 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga7371035323733c5fe95e5ee594bfeb86">ResetDef</a> (void)</td></tr>
<tr class="memdesc:ga7371035323733c5fe95e5ee594bfeb86 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Reset Def data member. <a href="group__dataspec__NCBI__BlastOutput.html#ga7371035323733c5fe95e5ee594bfeb86">More...</a><br /></td></tr>
<tr class="separator:ga7371035323733c5fe95e5ee594bfeb86 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga7a2b696834291e8ae888fe684d3b421e inherit pub_methods_classCHit__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__BlastOutput.html#ga416e0b779a23946bfea487c2cafcd27e">TDef</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga7a2b696834291e8ae888fe684d3b421e">GetDef</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:ga7a2b696834291e8ae888fe684d3b421e inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the Def member data. <a href="group__dataspec__NCBI__BlastOutput.html#ga7a2b696834291e8ae888fe684d3b421e">More...</a><br /></td></tr>
<tr class="separator:ga7a2b696834291e8ae888fe684d3b421e inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga2e1823a1a27a6fa0d389e8919c61db7e inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga2e1823a1a27a6fa0d389e8919c61db7e">SetDef</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga416e0b779a23946bfea487c2cafcd27e">TDef</a> &amp;<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
<tr class="memdesc:ga2e1823a1a27a6fa0d389e8919c61db7e inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assign a value to Def data member. <a href="group__dataspec__NCBI__BlastOutput.html#ga2e1823a1a27a6fa0d389e8919c61db7e">More...</a><br /></td></tr>
<tr class="separator:ga2e1823a1a27a6fa0d389e8919c61db7e inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gae324c94353e2de52687d62c7aa8c0158 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gae324c94353e2de52687d62c7aa8c0158">SetDef</a> (<a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga416e0b779a23946bfea487c2cafcd27e">TDef</a> &amp;&amp;<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
<tr class="separator:gae324c94353e2de52687d62c7aa8c0158 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga2d55ddc7b0947505e563f48cdf242b9a inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga416e0b779a23946bfea487c2cafcd27e">TDef</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga2d55ddc7b0947505e563f48cdf242b9a">SetDef</a> (void)</td></tr>
<tr class="memdesc:ga2d55ddc7b0947505e563f48cdf242b9a inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assign a value to Def data member. <a href="group__dataspec__NCBI__BlastOutput.html#ga2d55ddc7b0947505e563f48cdf242b9a">More...</a><br /></td></tr>
<tr class="separator:ga2d55ddc7b0947505e563f48cdf242b9a inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga1d4cf241604af4ed5062aadb4c30a63c inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga1d4cf241604af4ed5062aadb4c30a63c">IsSetAccession</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:ga1d4cf241604af4ed5062aadb4c30a63c inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">accession <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Accession data member. <a href="group__dataspec__NCBI__BlastOutput.html#ga1d4cf241604af4ed5062aadb4c30a63c">More...</a><br /></td></tr>
<tr class="separator:ga1d4cf241604af4ed5062aadb4c30a63c inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gacf4c319ecc2db8159bf3ef2cffa6a0ec inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gacf4c319ecc2db8159bf3ef2cffa6a0ec">CanGetAccession</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:gacf4c319ecc2db8159bf3ef2cffa6a0ec inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetAccession method. <a href="group__dataspec__NCBI__BlastOutput.html#gacf4c319ecc2db8159bf3ef2cffa6a0ec">More...</a><br /></td></tr>
<tr class="separator:gacf4c319ecc2db8159bf3ef2cffa6a0ec inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga1472c59e703a684c96840e9907d44736 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga1472c59e703a684c96840e9907d44736">ResetAccession</a> (void)</td></tr>
<tr class="memdesc:ga1472c59e703a684c96840e9907d44736 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Reset Accession data member. <a href="group__dataspec__NCBI__BlastOutput.html#ga1472c59e703a684c96840e9907d44736">More...</a><br /></td></tr>
<tr class="separator:ga1472c59e703a684c96840e9907d44736 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gae0cce48af0c1c1d092e13ec1c89bc482 inherit pub_methods_classCHit__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__BlastOutput.html#gab53fc80b90331d68fbe46c0411b6497e">TAccession</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gae0cce48af0c1c1d092e13ec1c89bc482">GetAccession</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:gae0cce48af0c1c1d092e13ec1c89bc482 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the Accession member data. <a href="group__dataspec__NCBI__BlastOutput.html#gae0cce48af0c1c1d092e13ec1c89bc482">More...</a><br /></td></tr>
<tr class="separator:gae0cce48af0c1c1d092e13ec1c89bc482 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga1ae5f6dc75c6cb4f6325e70fed5bbd91 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga1ae5f6dc75c6cb4f6325e70fed5bbd91">SetAccession</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput.html#gab53fc80b90331d68fbe46c0411b6497e">TAccession</a> &amp;<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
<tr class="memdesc:ga1ae5f6dc75c6cb4f6325e70fed5bbd91 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assign a value to Accession data member. <a href="group__dataspec__NCBI__BlastOutput.html#ga1ae5f6dc75c6cb4f6325e70fed5bbd91">More...</a><br /></td></tr>
<tr class="separator:ga1ae5f6dc75c6cb4f6325e70fed5bbd91 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gae33ad81d242b8fad736a5e396b072c57 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gae33ad81d242b8fad736a5e396b072c57">SetAccession</a> (<a class="el" href="group__dataspec__NCBI__BlastOutput.html#gab53fc80b90331d68fbe46c0411b6497e">TAccession</a> &amp;&amp;<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
<tr class="separator:gae33ad81d242b8fad736a5e396b072c57 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga5165bc2ed56fde566633003ba604e8d9 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gab53fc80b90331d68fbe46c0411b6497e">TAccession</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga5165bc2ed56fde566633003ba604e8d9">SetAccession</a> (void)</td></tr>
<tr class="memdesc:ga5165bc2ed56fde566633003ba604e8d9 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assign a value to Accession data member. <a href="group__dataspec__NCBI__BlastOutput.html#ga5165bc2ed56fde566633003ba604e8d9">More...</a><br /></td></tr>
<tr class="separator:ga5165bc2ed56fde566633003ba604e8d9 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga441f25c811d524607aa98a36232d5940 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga441f25c811d524607aa98a36232d5940">IsSetLen</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:ga441f25c811d524607aa98a36232d5940 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">length of subject <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Len data member. <a href="group__dataspec__NCBI__BlastOutput.html#ga441f25c811d524607aa98a36232d5940">More...</a><br /></td></tr>
<tr class="separator:ga441f25c811d524607aa98a36232d5940 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga9b1da8f095e40e1953f5958b1fd9e601 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga9b1da8f095e40e1953f5958b1fd9e601">CanGetLen</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:ga9b1da8f095e40e1953f5958b1fd9e601 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetLen method. <a href="group__dataspec__NCBI__BlastOutput.html#ga9b1da8f095e40e1953f5958b1fd9e601">More...</a><br /></td></tr>
<tr class="separator:ga9b1da8f095e40e1953f5958b1fd9e601 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaad6d92f2fd10f19e600d03e2b444392b inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gaad6d92f2fd10f19e600d03e2b444392b">ResetLen</a> (void)</td></tr>
<tr class="memdesc:gaad6d92f2fd10f19e600d03e2b444392b inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Reset Len data member. <a href="group__dataspec__NCBI__BlastOutput.html#gaad6d92f2fd10f19e600d03e2b444392b">More...</a><br /></td></tr>
<tr class="separator:gaad6d92f2fd10f19e600d03e2b444392b inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gac8561162ac445cf0389e2504ceae9525 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gaaad25207b2fe427f0d6774e2976f85d0">TLen</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gac8561162ac445cf0389e2504ceae9525">GetLen</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:gac8561162ac445cf0389e2504ceae9525 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the Len member data. <a href="group__dataspec__NCBI__BlastOutput.html#gac8561162ac445cf0389e2504ceae9525">More...</a><br /></td></tr>
<tr class="separator:gac8561162ac445cf0389e2504ceae9525 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gace3d47a9abf05aefc768a218a717d65e inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gace3d47a9abf05aefc768a218a717d65e">SetLen</a> (<a class="el" href="group__dataspec__NCBI__BlastOutput.html#gaaad25207b2fe427f0d6774e2976f85d0">TLen</a> <a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
<tr class="memdesc:gace3d47a9abf05aefc768a218a717d65e inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assign a value to Len data member. <a href="group__dataspec__NCBI__BlastOutput.html#gace3d47a9abf05aefc768a218a717d65e">More...</a><br /></td></tr>
<tr class="separator:gace3d47a9abf05aefc768a218a717d65e inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga4e456d6810f81ebb8b05a707196a8088 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gaaad25207b2fe427f0d6774e2976f85d0">TLen</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga4e456d6810f81ebb8b05a707196a8088">SetLen</a> (void)</td></tr>
<tr class="memdesc:ga4e456d6810f81ebb8b05a707196a8088 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assign a value to Len data member. <a href="group__dataspec__NCBI__BlastOutput.html#ga4e456d6810f81ebb8b05a707196a8088">More...</a><br /></td></tr>
<tr class="separator:ga4e456d6810f81ebb8b05a707196a8088 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga0201a947bcb0a40881c275bf0b7489ed inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga0201a947bcb0a40881c275bf0b7489ed">IsSetHsps</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:ga0201a947bcb0a40881c275bf0b7489ed inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">all HSP regions for the given subject <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Hsps data member. <a href="group__dataspec__NCBI__BlastOutput.html#ga0201a947bcb0a40881c275bf0b7489ed">More...</a><br /></td></tr>
<tr class="separator:ga0201a947bcb0a40881c275bf0b7489ed inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaf9055a47fbdcf5f2e44ae8a396b69463 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gaf9055a47fbdcf5f2e44ae8a396b69463">CanGetHsps</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:gaf9055a47fbdcf5f2e44ae8a396b69463 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetHsps method. <a href="group__dataspec__NCBI__BlastOutput.html#gaf9055a47fbdcf5f2e44ae8a396b69463">More...</a><br /></td></tr>
<tr class="separator:gaf9055a47fbdcf5f2e44ae8a396b69463 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaa375b56248543b2a649456af53041adb inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gaa375b56248543b2a649456af53041adb">ResetHsps</a> (void)</td></tr>
<tr class="memdesc:gaa375b56248543b2a649456af53041adb inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Reset Hsps data member. <a href="group__dataspec__NCBI__BlastOutput.html#gaa375b56248543b2a649456af53041adb">More...</a><br /></td></tr>
<tr class="separator:gaa375b56248543b2a649456af53041adb inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga8cb8b5fe742d7a940695cfa37dad46cb inherit pub_methods_classCHit__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__BlastOutput.html#ga74dc5f30b0642a079f673a88be82d634">THsps</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga8cb8b5fe742d7a940695cfa37dad46cb">GetHsps</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:ga8cb8b5fe742d7a940695cfa37dad46cb inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the Hsps member data. <a href="group__dataspec__NCBI__BlastOutput.html#ga8cb8b5fe742d7a940695cfa37dad46cb">More...</a><br /></td></tr>
<tr class="separator:ga8cb8b5fe742d7a940695cfa37dad46cb inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga188b20595a7845ebb8e3d2a3e7de9616 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga74dc5f30b0642a079f673a88be82d634">THsps</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga188b20595a7845ebb8e3d2a3e7de9616">SetHsps</a> (void)</td></tr>
<tr class="memdesc:ga188b20595a7845ebb8e3d2a3e7de9616 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assign a value to Hsps data member. <a href="group__dataspec__NCBI__BlastOutput.html#ga188b20595a7845ebb8e3d2a3e7de9616">More...</a><br /></td></tr>
<tr class="separator:ga188b20595a7845ebb8e3d2a3e7de9616 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga6b264d6c2902d23103b5f60511adf530 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga6b264d6c2902d23103b5f60511adf530">Reset</a> (void)</td></tr>
<tr class="memdesc:ga6b264d6c2902d23103b5f60511adf530 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Reset the whole object. <a href="group__dataspec__NCBI__BlastOutput.html#ga6b264d6c2902d23103b5f60511adf530">More...</a><br /></td></tr>
<tr class="separator:ga6b264d6c2902d23103b5f60511adf530 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga89592cfd3b399b908e7e54cb28a34936 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga89592cfd3b399b908e7e54cb28a34936">CHit_Base</a> (void)</td></tr>
<tr class="separator:ga89592cfd3b399b908e7e54cb28a34936 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga901dc0403241185cf9f0d65c1ea04899 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga901dc0403241185cf9f0d65c1ea04899">~CHit_Base</a> (void)</td></tr>
<tr class="separator:ga901dc0403241185cf9f0d65c1ea04899 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaffa81baec206d6a6ff681e27158e4c64 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaffa81baec206d6a6ff681e27158e4c64">DECLARE_INTERNAL_TYPE_INFO</a> ()</td></tr>
<tr class="separator:gaffa81baec206d6a6ff681e27158e4c64 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga24705f1cd1e72c8d4ac50a6f76fc4ddb inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga24705f1cd1e72c8d4ac50a6f76fc4ddb">IsSetNum</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:ga24705f1cd1e72c8d4ac50a6f76fc4ddb inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">hit number <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Num data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga24705f1cd1e72c8d4ac50a6f76fc4ddb">More...</a><br /></td></tr>
<tr class="separator:ga24705f1cd1e72c8d4ac50a6f76fc4ddb inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga4ba8a9c12cf14e6560c0c3591d1fa6e0 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga4ba8a9c12cf14e6560c0c3591d1fa6e0">CanGetNum</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:ga4ba8a9c12cf14e6560c0c3591d1fa6e0 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetNum method. <a href="group__dataspec__NCBI__BlastOutput2.html#ga4ba8a9c12cf14e6560c0c3591d1fa6e0">More...</a><br /></td></tr>
<tr class="separator:ga4ba8a9c12cf14e6560c0c3591d1fa6e0 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaf9dec320adb0c575b1e30f5f0a91b5c8 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaf9dec320adb0c575b1e30f5f0a91b5c8">ResetNum</a> (void)</td></tr>
<tr class="memdesc:gaf9dec320adb0c575b1e30f5f0a91b5c8 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Reset Num data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gaf9dec320adb0c575b1e30f5f0a91b5c8">More...</a><br /></td></tr>
<tr class="separator:gaf9dec320adb0c575b1e30f5f0a91b5c8 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga3926856cb3283d07047eae0294e53fb3 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gae212dee06459e6dc9f8dd07964819118">TNum</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga3926856cb3283d07047eae0294e53fb3">GetNum</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:ga3926856cb3283d07047eae0294e53fb3 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the Num member data. <a href="group__dataspec__NCBI__BlastOutput2.html#ga3926856cb3283d07047eae0294e53fb3">More...</a><br /></td></tr>
<tr class="separator:ga3926856cb3283d07047eae0294e53fb3 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gafb81acffaa4bdf1033f2420a4fda6800 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gafb81acffaa4bdf1033f2420a4fda6800">SetNum</a> (<a class="el" href="group__dataspec__NCBI__BlastOutput.html#gae212dee06459e6dc9f8dd07964819118">TNum</a> <a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
<tr class="memdesc:gafb81acffaa4bdf1033f2420a4fda6800 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assign a value to Num data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gafb81acffaa4bdf1033f2420a4fda6800">More...</a><br /></td></tr>
<tr class="separator:gafb81acffaa4bdf1033f2420a4fda6800 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gae6450398e0d2358838154017ebba0fd4 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gae212dee06459e6dc9f8dd07964819118">TNum</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gae6450398e0d2358838154017ebba0fd4">SetNum</a> (void)</td></tr>
<tr class="memdesc:gae6450398e0d2358838154017ebba0fd4 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assign a value to Num data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gae6450398e0d2358838154017ebba0fd4">More...</a><br /></td></tr>
<tr class="separator:gae6450398e0d2358838154017ebba0fd4 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga8309e311e7bb080d021e129f075f4600 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga8309e311e7bb080d021e129f075f4600">IsSetDescription</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:ga8309e311e7bb080d021e129f075f4600 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">ID, title, and taxonomy for each entry in the PIG <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Description data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga8309e311e7bb080d021e129f075f4600">More...</a><br /></td></tr>
<tr class="separator:ga8309e311e7bb080d021e129f075f4600 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaaba1fb22ebe70a12633174ef8e953ce3 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaaba1fb22ebe70a12633174ef8e953ce3">CanGetDescription</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:gaaba1fb22ebe70a12633174ef8e953ce3 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetDescription method. <a href="group__dataspec__NCBI__BlastOutput2.html#gaaba1fb22ebe70a12633174ef8e953ce3">More...</a><br /></td></tr>
<tr class="separator:gaaba1fb22ebe70a12633174ef8e953ce3 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gabcd833acdacc2a2b160cec0507bff73d inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gabcd833acdacc2a2b160cec0507bff73d">ResetDescription</a> (void)</td></tr>
<tr class="memdesc:gabcd833acdacc2a2b160cec0507bff73d inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Reset Description data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gabcd833acdacc2a2b160cec0507bff73d">More...</a><br /></td></tr>
<tr class="separator:gabcd833acdacc2a2b160cec0507bff73d inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga44f2b6742a31bae2101ae88b42dcd5a5 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga0fd986049d94a6d1b5b3edc1d4c1541c">TDescription</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga44f2b6742a31bae2101ae88b42dcd5a5">GetDescription</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:ga44f2b6742a31bae2101ae88b42dcd5a5 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the Description member data. <a href="group__dataspec__NCBI__BlastOutput2.html#ga44f2b6742a31bae2101ae88b42dcd5a5">More...</a><br /></td></tr>
<tr class="separator:ga44f2b6742a31bae2101ae88b42dcd5a5 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaab472519ad82c0d8b0c92389bcded799 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga0fd986049d94a6d1b5b3edc1d4c1541c">TDescription</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaab472519ad82c0d8b0c92389bcded799">SetDescription</a> (void)</td></tr>
<tr class="memdesc:gaab472519ad82c0d8b0c92389bcded799 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assign a value to Description data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gaab472519ad82c0d8b0c92389bcded799">More...</a><br /></td></tr>
<tr class="separator:gaab472519ad82c0d8b0c92389bcded799 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga441f25c811d524607aa98a36232d5940 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga441f25c811d524607aa98a36232d5940">IsSetLen</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:ga441f25c811d524607aa98a36232d5940 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">length of subject <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Len data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga441f25c811d524607aa98a36232d5940">More...</a><br /></td></tr>
<tr class="separator:ga441f25c811d524607aa98a36232d5940 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga9b1da8f095e40e1953f5958b1fd9e601 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga9b1da8f095e40e1953f5958b1fd9e601">CanGetLen</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:ga9b1da8f095e40e1953f5958b1fd9e601 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetLen method. <a href="group__dataspec__NCBI__BlastOutput2.html#ga9b1da8f095e40e1953f5958b1fd9e601">More...</a><br /></td></tr>
<tr class="separator:ga9b1da8f095e40e1953f5958b1fd9e601 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaad6d92f2fd10f19e600d03e2b444392b inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaad6d92f2fd10f19e600d03e2b444392b">ResetLen</a> (void)</td></tr>
<tr class="memdesc:gaad6d92f2fd10f19e600d03e2b444392b inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Reset Len data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gaad6d92f2fd10f19e600d03e2b444392b">More...</a><br /></td></tr>
<tr class="separator:gaad6d92f2fd10f19e600d03e2b444392b inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gad74ef3b07440c52e718d6d5fa7b58145 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gaaad25207b2fe427f0d6774e2976f85d0">TLen</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gad74ef3b07440c52e718d6d5fa7b58145">GetLen</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:gad74ef3b07440c52e718d6d5fa7b58145 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the Len member data. <a href="group__dataspec__NCBI__BlastOutput2.html#gad74ef3b07440c52e718d6d5fa7b58145">More...</a><br /></td></tr>
<tr class="separator:gad74ef3b07440c52e718d6d5fa7b58145 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gace3d47a9abf05aefc768a218a717d65e inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gace3d47a9abf05aefc768a218a717d65e">SetLen</a> (<a class="el" href="group__dataspec__NCBI__BlastOutput.html#gaaad25207b2fe427f0d6774e2976f85d0">TLen</a> <a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
<tr class="memdesc:gace3d47a9abf05aefc768a218a717d65e inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assign a value to Len data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gace3d47a9abf05aefc768a218a717d65e">More...</a><br /></td></tr>
<tr class="separator:gace3d47a9abf05aefc768a218a717d65e inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga9059ad27843a2b9bc83decb111fba00e inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gaaad25207b2fe427f0d6774e2976f85d0">TLen</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga9059ad27843a2b9bc83decb111fba00e">SetLen</a> (void)</td></tr>
<tr class="memdesc:ga9059ad27843a2b9bc83decb111fba00e inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assign a value to Len data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga9059ad27843a2b9bc83decb111fba00e">More...</a><br /></td></tr>
<tr class="separator:ga9059ad27843a2b9bc83decb111fba00e inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga0201a947bcb0a40881c275bf0b7489ed inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga0201a947bcb0a40881c275bf0b7489ed">IsSetHsps</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:ga0201a947bcb0a40881c275bf0b7489ed inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">all HSP regions for the given subject <a class="el" href="structCheck.html">Check</a> if a value has been assigned to Hsps data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga0201a947bcb0a40881c275bf0b7489ed">More...</a><br /></td></tr>
<tr class="separator:ga0201a947bcb0a40881c275bf0b7489ed inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaf9055a47fbdcf5f2e44ae8a396b69463 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaf9055a47fbdcf5f2e44ae8a396b69463">CanGetHsps</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:gaf9055a47fbdcf5f2e44ae8a396b69463 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if it is safe to call GetHsps method. <a href="group__dataspec__NCBI__BlastOutput2.html#gaf9055a47fbdcf5f2e44ae8a396b69463">More...</a><br /></td></tr>
<tr class="separator:gaf9055a47fbdcf5f2e44ae8a396b69463 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaa375b56248543b2a649456af53041adb inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaa375b56248543b2a649456af53041adb">ResetHsps</a> (void)</td></tr>
<tr class="memdesc:gaa375b56248543b2a649456af53041adb inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Reset Hsps data member. <a href="group__dataspec__NCBI__BlastOutput2.html#gaa375b56248543b2a649456af53041adb">More...</a><br /></td></tr>
<tr class="separator:gaa375b56248543b2a649456af53041adb inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gac8ebe010afe66dbf2c4edd30576dd4fb inherit pub_methods_classCHit__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__BlastOutput.html#ga74dc5f30b0642a079f673a88be82d634">THsps</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gac8ebe010afe66dbf2c4edd30576dd4fb">GetHsps</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="memdesc:gac8ebe010afe66dbf2c4edd30576dd4fb inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the Hsps member data. <a href="group__dataspec__NCBI__BlastOutput2.html#gac8ebe010afe66dbf2c4edd30576dd4fb">More...</a><br /></td></tr>
<tr class="separator:gac8ebe010afe66dbf2c4edd30576dd4fb inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga9fd41008b70a6a5782ca758e0bf30f3e inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga74dc5f30b0642a079f673a88be82d634">THsps</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga9fd41008b70a6a5782ca758e0bf30f3e">SetHsps</a> (void)</td></tr>
<tr class="memdesc:ga9fd41008b70a6a5782ca758e0bf30f3e inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assign a value to Hsps data member. <a href="group__dataspec__NCBI__BlastOutput2.html#ga9fd41008b70a6a5782ca758e0bf30f3e">More...</a><br /></td></tr>
<tr class="separator:ga9fd41008b70a6a5782ca758e0bf30f3e inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga2cc38498eb5f0cbc3b5f99b2d41fff92 inherit pub_methods_classCHit__Base"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga2cc38498eb5f0cbc3b5f99b2d41fff92">Reset</a> (void)</td></tr>
<tr class="memdesc:ga2cc38498eb5f0cbc3b5f99b2d41fff92 inherit pub_methods_classCHit__Base"><td class="mdescLeft">&#160;</td><td class="mdescRight">Reset the whole object. <a href="group__dataspec__NCBI__BlastOutput2.html#ga2cc38498eb5f0cbc3b5f99b2d41fff92">More...</a><br /></td></tr>
<tr class="separator:ga2cc38498eb5f0cbc3b5f99b2d41fff92 inherit pub_methods_classCHit__Base"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="inherit_header pub_methods_classCSerialObject"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classCSerialObject')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classCSerialObject.html">CSerialObject</a></td></tr>
<tr class="memitem:ga8575b1015c4a4f3336b6e1c0a4324b71 inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top">&#160;</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">&#160;</td></tr>
<tr class="memitem:gaf278b96157abad20b5d944fb83d32fb1 inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#gaf278b96157abad20b5d944fb83d32fb1">~CSerialObject</a> (void)</td></tr>
<tr class="separator:gaf278b96157abad20b5d944fb83d32fb1 inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gacb5d8a2e6878e58aeaeaf342081f0b7f inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCTypeInfo.html">CTypeInfo</a> *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#gacb5d8a2e6878e58aeaeaf342081f0b7f">GetThisTypeInfo</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> =0</td></tr>
<tr class="separator:gacb5d8a2e6878e58aeaeaf342081f0b7f inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga6c7f903717f7a272091acf5124cfd903 inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</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> &amp;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">&#160;</td><td class="mdescRight">Set object to copy of another one. <a href="group__GenClassSupport.html#ga6c7f903717f7a272091acf5124cfd903">More...</a><br /></td></tr>
<tr class="separator:ga6c7f903717f7a272091acf5124cfd903 inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gae694abd95a4753598c398540f3467d99 inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</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> &amp;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">&#160;</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">&#160;</td></tr>
<tr class="memitem:ga0daf4906b8f2e6382118c4a018491761 inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</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">&#160;</td><td class="mdescRight">Define method for dumping debug information. <a href="group__GenClassSupport.html#ga0daf4906b8f2e6382118c4a018491761">More...</a><br /></td></tr>
<tr class="separator:ga0daf4906b8f2e6382118c4a018491761 inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga7382b4cd30306d9444f85abd912ff61e inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#ga7382b4cd30306d9444f85abd912ff61e">ThrowUnassigned</a> (<a class="el" href="group__GenClassSupport.html#ga4045c609bd35431331d0055309404111">TMemberIndex</a> index) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="separator:ga7382b4cd30306d9444f85abd912ff61e inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gab5506012856f3627d88368a24e1eb254 inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#gab5506012856f3627d88368a24e1eb254">ThrowUnassigned</a> (<a class="el" href="group__GenClassSupport.html#ga4045c609bd35431331d0055309404111">TMemberIndex</a> index, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> char *<a class="el" href="dbapi__sample__base_8hpp.html#a8334353b550f5c3b6d2ea57d716ab2e2">file_name</a>, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> file_line) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="separator:gab5506012856f3627d88368a24e1eb254 inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga937551d0a9c61c7ff537ac19ec37904d inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</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">&#160;</td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if object data type has namespace name. <a href="group__GenClassSupport.html#ga937551d0a9c61c7ff537ac19ec37904d">More...</a><br /></td></tr>
<tr class="separator:ga937551d0a9c61c7ff537ac19ec37904d inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga901688404844d3c9be43320e1d51c485 inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> &amp;&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:gacfc7e87713da36496323f5477db80219 inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</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">&#160;</td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if data type has namespace prefix. <a href="group__GenClassSupport.html#gacfc7e87713da36496323f5477db80219">More...</a><br /></td></tr>
<tr class="separator:gacfc7e87713da36496323f5477db80219 inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gae8fa62abf96f3ed3cec903dce6a6a33a inherit pub_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> &amp;&#160;</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">&#160;</td><td class="mdescRight">Get namespace prefix. <a href="group__GenClassSupport.html#gae8fa62abf96f3ed3cec903dce6a6a33a">More...</a><br /></td></tr>
<tr class="separator:gae8fa62abf96f3ed3cec903dce6a6a33a inherit pub_methods_classCSerialObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="inherit_header pub_methods_classCObject"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classCObject')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classCObject.html">CObject</a></td></tr>
<tr class="memitem:gae38a8715a230c7ed588993c0206d8cb4 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#gae38a8715a230c7ed588993c0206d8cb4">CObject</a> (void)</td></tr>
<tr class="memdesc:gae38a8715a230c7ed588993c0206d8cb4 inherit pub_methods_classCObject"><td class="mdescLeft">&#160;</td><td class="mdescRight">Constructor. <a href="group__Object.html#gae38a8715a230c7ed588993c0206d8cb4">More...</a><br /></td></tr>
<tr class="separator:gae38a8715a230c7ed588993c0206d8cb4 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gae89833a29aad16e7cb252314d2e7f4ab inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">&#160;</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> &amp;src)</td></tr>
<tr class="memdesc:gae89833a29aad16e7cb252314d2e7f4ab inherit pub_methods_classCObject"><td class="mdescLeft">&#160;</td><td class="mdescRight">Copy constructor. <a href="group__Object.html#gae89833a29aad16e7cb252314d2e7f4ab">More...</a><br /></td></tr>
<tr class="separator:gae89833a29aad16e7cb252314d2e7f4ab inherit pub_methods_classCObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga5125d96ff932bcd471a734fd174b2022 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga5125d96ff932bcd471a734fd174b2022">~CObject</a> (void)</td></tr>
<tr class="memdesc:ga5125d96ff932bcd471a734fd174b2022 inherit pub_methods_classCObject"><td class="mdescLeft">&#160;</td><td class="mdescRight">Destructor. <a href="group__Object.html#ga5125d96ff932bcd471a734fd174b2022">More...</a><br /></td></tr>
<tr class="separator:ga5125d96ff932bcd471a734fd174b2022 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gab2090742c0465c4229f6e0b57c2de566 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCObject.html">CObject</a> &amp;&#160;</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> &amp;src) <a class="el" href="group__Exception.html#ga8b97bb3687e603604470b18da8e56e91">THROWS_NONE</a></td></tr>
<tr class="memdesc:gab2090742c0465c4229f6e0b57c2de566 inherit pub_methods_classCObject"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assignment operator. <a href="group__Object.html#gab2090742c0465c4229f6e0b57c2de566">More...</a><br /></td></tr>
<tr class="separator:gab2090742c0465c4229f6e0b57c2de566 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaad370ec0ee157f6082b9845338cb2809 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#gaad370ec0ee157f6082b9845338cb2809">CanBeDeleted</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__Exception.html#ga8b97bb3687e603604470b18da8e56e91">THROWS_NONE</a></td></tr>
<tr class="memdesc:gaad370ec0ee157f6082b9845338cb2809 inherit pub_methods_classCObject"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if object can be deleted. <a href="group__Object.html#gaad370ec0ee157f6082b9845338cb2809">More...</a><br /></td></tr>
<tr class="separator:gaad370ec0ee157f6082b9845338cb2809 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaf5cddacd7194af14e759f3d89325679b inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#gaf5cddacd7194af14e759f3d89325679b">IsAllocatedInPool</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__Exception.html#ga8b97bb3687e603604470b18da8e56e91">THROWS_NONE</a></td></tr>
<tr class="memdesc:gaf5cddacd7194af14e759f3d89325679b inherit pub_methods_classCObject"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if object is allocated in memory pool (not system heap) <a href="group__Object.html#gaf5cddacd7194af14e759f3d89325679b">More...</a><br /></td></tr>
<tr class="separator:gaf5cddacd7194af14e759f3d89325679b inherit pub_methods_classCObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga9f9bbe6d075c90238a43585999d303d9 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga9f9bbe6d075c90238a43585999d303d9">Referenced</a> (void) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__Exception.html#ga8b97bb3687e603604470b18da8e56e91">THROWS_NONE</a></td></tr>
<tr class="memdesc:ga9f9bbe6d075c90238a43585999d303d9 inherit pub_methods_classCObject"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if object is referenced. <a href="group__Object.html#ga9f9bbe6d075c90238a43585999d303d9">More...</a><br /></td></tr>
<tr class="separator:ga9f9bbe6d075c90238a43585999d303d9 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaac3600b16f957a209f857aff7f79bf91 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a>&#160;</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">&#160;</td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> if object is referenced only once. <a href="group__Object.html#gaac3600b16f957a209f857aff7f79bf91">More...</a><br /></td></tr>
<tr class="separator:gaac3600b16f957a209f857aff7f79bf91 inherit pub_methods_classCObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga7161c8a13b08e627baa2ea0d75d679dc inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:ga827e9544b3a20642fcb736160f203bab inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:ga5f08a74874b48c0e4a3d8e54343d4c90 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:ga52d3bc7d4f90411a190da81d7fd8d931 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</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">&#160;</td><td class="mdescRight">Mark this object as not allocated in heap &ndash; 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">&#160;</td></tr>
<tr class="memitem:ga35fd00918a29221f823c8e8d5d67fee2 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</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">&#160;</td><td class="mdescRight">Mark this object as allocated in heap &ndash; 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">&#160;</td></tr>
<tr class="memitem:ga9a8f931b70ac3730f364ad6078580424 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void *&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:gabb964e1c3096b1efe242a3c63bbb8120 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void *&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:gafde2770a20ee356b8a60cc81cca42366 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:ga5ea75357098dc7fea6cca8fb81620856 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:ga37f436bf6f5a3d46b7363e104fccedf3 inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void *&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:ga54499c2fd0381ad8505bc120d5da84ff inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:ga981e7384172734070f47a3a9b53d0c3c inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void *&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:ga5c29219485b863e8a846c3076d321c7e inherit pub_methods_classCObject"><td class="memItemLeft" align="right" valign="top">void&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="inherit_header pub_methods_classCDebugDumpable"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classCDebugDumpable')"><img src="closed.png" alt="-"/>&#160;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">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCDebugDumpable.html#ae8723856215191ef748f19ff73e8ba4e">CDebugDumpable</a> (void)</td></tr>
<tr class="separator:ae8723856215191ef748f19ff73e8ba4e inherit pub_methods_classCDebugDumpable"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:acdeaaedfabb4cc4a64108dbb854f4b51 inherit pub_methods_classCDebugDumpable"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCDebugDumpable.html#acdeaaedfabb4cc4a64108dbb854f4b51">~CDebugDumpable</a> (void)</td></tr>
<tr class="separator:acdeaaedfabb4cc4a64108dbb854f4b51 inherit pub_methods_classCDebugDumpable"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a4ff9ec248a38f17b7d8deb3f78318a37 inherit pub_methods_classCDebugDumpable"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCDebugDumpable.html#a4ff9ec248a38f17b7d8deb3f78318a37">DebugDumpText</a> (ostream &amp;<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> &amp;bundle, unsigned <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> <a class="el" href="ct__nlmzip__trees_8cpp.html#a431c74c4b26732a3a7de689109eb6b65">depth</a>) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="separator:a4ff9ec248a38f17b7d8deb3f78318a37 inherit pub_methods_classCDebugDumpable"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aa0101dfdc0ae0cbd0cb1609c96f96229 inherit pub_methods_classCDebugDumpable"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCDebugDumpable.html#aa0101dfdc0ae0cbd0cb1609c96f96229">DebugDumpFormat</a> (<a class="el" href="classCDebugDumpFormatter.html">CDebugDumpFormatter</a> &amp;ddf, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> &amp;bundle, unsigned <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> <a class="el" href="ct__nlmzip__trees_8cpp.html#a431c74c4b26732a3a7de689109eb6b65">depth</a>) <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a></td></tr>
<tr class="separator:aa0101dfdc0ae0cbd0cb1609c96f96229 inherit pub_methods_classCDebugDumpable"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a19047c92521e5f3ad2a14bab26a49b51 inherit pub_methods_classCDebugDumpable"><td class="memItemLeft" align="right" valign="top">void&#160;</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">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-attribs"></a>
Public Attributes</h2></td></tr>
<tr class="memitem:aae6d0920a29f57838fb2b4a115dee6ba"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#aae6d0920a29f57838fb2b4a115dee6ba">m_SeqIndex1</a></td></tr>
<tr class="memdesc:aae6d0920a29f57838fb2b4a115dee6ba"><td class="mdescLeft">&#160;</td><td class="mdescRight">Numerical identifier for first sequence in alignment. <a href="classCHit.html#aae6d0920a29f57838fb2b4a115dee6ba">More...</a><br /></td></tr>
<tr class="separator:aae6d0920a29f57838fb2b4a115dee6ba"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ab0ea5f8851a79f17da18404a9f7c00af"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#ab0ea5f8851a79f17da18404a9f7c00af">m_SeqIndex2</a></td></tr>
<tr class="memdesc:ab0ea5f8851a79f17da18404a9f7c00af"><td class="mdescLeft">&#160;</td><td class="mdescRight">Numerical identifier for second sequence in alignment. <a href="classCHit.html#ab0ea5f8851a79f17da18404a9f7c00af">More...</a><br /></td></tr>
<tr class="separator:ab0ea5f8851a79f17da18404a9f7c00af"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a84670daf0a817644571023bbf6311147"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#a84670daf0a817644571023bbf6311147">m_Score</a></td></tr>
<tr class="memdesc:a84670daf0a817644571023bbf6311147"><td class="mdescLeft">&#160;</td><td class="mdescRight">Score of alignment. <a href="classCHit.html#a84670daf0a817644571023bbf6311147">More...</a><br /></td></tr>
<tr class="separator:a84670daf0a817644571023bbf6311147"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ab47f81d0ca3eaaa1891c7770ae0af530"><td class="memItemLeft" align="right" valign="top"><a class="el" href="base_8hpp.html#a82668c1a5428e2d884d0f0c67d97fdf1">TRange</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#ab47f81d0ca3eaaa1891c7770ae0af530">m_SeqRange1</a></td></tr>
<tr class="memdesc:ab47f81d0ca3eaaa1891c7770ae0af530"><td class="mdescLeft">&#160;</td><td class="mdescRight">The range of offsets on the first sequence. <a href="classCHit.html#ab47f81d0ca3eaaa1891c7770ae0af530">More...</a><br /></td></tr>
<tr class="separator:ab47f81d0ca3eaaa1891c7770ae0af530"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ad3dfe32864b86dde081aa629561b9fc6"><td class="memItemLeft" align="right" valign="top"><a class="el" href="base_8hpp.html#a82668c1a5428e2d884d0f0c67d97fdf1">TRange</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#ad3dfe32864b86dde081aa629561b9fc6">m_SeqRange2</a></td></tr>
<tr class="memdesc:ad3dfe32864b86dde081aa629561b9fc6"><td class="mdescLeft">&#160;</td><td class="mdescRight">The range of offsets on the second sequence. <a href="classCHit.html#ad3dfe32864b86dde081aa629561b9fc6">More...</a><br /></td></tr>
<tr class="separator:ad3dfe32864b86dde081aa629561b9fc6"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-attribs"></a>
Static Public Attributes</h2></td></tr>
<tr class="memitem:ab9b21171a449e2e88599b398aa46f3ff"><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>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#ab9b21171a449e2e88599b398aa46f3ff">kMinHitSize</a> = 2</td></tr>
<tr class="memdesc:ab9b21171a449e2e88599b398aa46f3ff"><td class="mdescLeft">&#160;</td><td class="mdescRight">Not always used, but useful to avoid extremely small hits. <a href="classCHit.html#ab9b21171a449e2e88599b398aa46f3ff">More...</a><br /></td></tr>
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<tr class="inherit_header pub_static_attribs_classCSerialObject"><td colspan="2" onclick="javascript:toggleInherit('pub_static_attribs_classCSerialObject')"><img src="closed.png" alt="-"/>&#160;Static Public Attributes inherited from <a class="el" href="classCSerialObject.html">CSerialObject</a></td></tr>
<tr class="memitem:gacf732f6a9f64037d0cad32a72f7522ea inherit pub_static_attribs_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#gacf732f6a9f64037d0cad32a72f7522ea">ms_UnassignedStr</a> = &quot;&lt;*unassigned*&gt;&quot;</td></tr>
<tr class="separator:gacf732f6a9f64037d0cad32a72f7522ea inherit pub_static_attribs_classCSerialObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga6baaf827f8d2e4f98be84d91d511a716 inherit pub_static_attribs_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> char&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#ga6baaf827f8d2e4f98be84d91d511a716">ms_UnassignedByte</a> = char(0xcd)</td></tr>
<tr class="separator:ga6baaf827f8d2e4f98be84d91d511a716 inherit pub_static_attribs_classCSerialObject"><td class="memSeparator" colspan="2">&#160;</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="-"/>&#160;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>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga6b2ef05fc91950a79ed938def4fd705d">eCounterBitsCanBeDeleted</a> = 1 &lt;&lt; 0</td></tr>
<tr class="memdesc:ga6b2ef05fc91950a79ed938def4fd705d inherit pub_static_attribs_classCObject"><td class="mdescLeft">&#160;</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">&#160;</td></tr>
<tr class="memitem:gae6d5b68d219dbdb40e88737873a3488c inherit pub_static_attribs_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__Object.html#ga2e073b6c5b9c29648510bd99ebe00a5c">TCount</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#gae6d5b68d219dbdb40e88737873a3488c">eCounterBitsInPlainHeap</a> = 1 &lt;&lt; 1</td></tr>
<tr class="memdesc:gae6d5b68d219dbdb40e88737873a3488c inherit pub_static_attribs_classCObject"><td class="mdescLeft">&#160;</td><td class="mdescRight">Heap signature was found. <a href="group__Object.html#gae6d5b68d219dbdb40e88737873a3488c">More...</a><br /></td></tr>
<tr class="separator:gae6d5b68d219dbdb40e88737873a3488c inherit pub_static_attribs_classCObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga33e4da9c60adbc3cf2a0ca45ce21a2ba inherit pub_static_attribs_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__Object.html#ga2e073b6c5b9c29648510bd99ebe00a5c">TCount</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga33e4da9c60adbc3cf2a0ca45ce21a2ba">eCounterBitsPlaceMask</a></td></tr>
<tr class="memdesc:ga33e4da9c60adbc3cf2a0ca45ce21a2ba inherit pub_static_attribs_classCObject"><td class="mdescLeft">&#160;</td><td class="mdescRight">Mask for 'in heap' state flags. <a href="group__Object.html#ga33e4da9c60adbc3cf2a0ca45ce21a2ba">More...</a><br /></td></tr>
<tr class="separator:ga33e4da9c60adbc3cf2a0ca45ce21a2ba inherit pub_static_attribs_classCObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga0a412d4ea79669d73671f89cb3e798a2 inherit pub_static_attribs_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#ga0a412d4ea79669d73671f89cb3e798a2">eCounterStep</a> = 1 &lt;&lt; 2</td></tr>
<tr class="memdesc:ga0a412d4ea79669d73671f89cb3e798a2 inherit pub_static_attribs_classCObject"><td class="mdescLeft">&#160;</td><td class="mdescRight">Skip over the "in heap" bits. <a href="group__Object.html#ga0a412d4ea79669d73671f89cb3e798a2">More...</a><br /></td></tr>
<tr class="separator:ga0a412d4ea79669d73671f89cb3e798a2 inherit pub_static_attribs_classCObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gab5880debef7cc7eb2a2891f440cd7569 inherit pub_static_attribs_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__Object.html#ga2e073b6c5b9c29648510bd99ebe00a5c">TCount</a>&#160;</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) &lt;&lt; (sizeof(<a class="el" href="group__Object.html#ga2e073b6c5b9c29648510bd99ebe00a5c">TCount</a>) * 8 - 2)</td></tr>
<tr class="memdesc:gab5880debef7cc7eb2a2891f440cd7569 inherit pub_static_attribs_classCObject"><td class="mdescLeft">&#160;</td><td class="mdescRight">Minimal value for valid objects (reference counter is zero) Must be a single bit value. <a href="group__Object.html#gab5880debef7cc7eb2a2891f440cd7569">More...</a><br /></td></tr>
<tr class="separator:gab5880debef7cc7eb2a2891f440cd7569 inherit pub_static_attribs_classCObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaff6eaaf8b9c4040a05fe2325ab75f44e inherit pub_static_attribs_classCObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__Object.html#ga2e073b6c5b9c29648510bd99ebe00a5c">TCount</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__Object.html#gaff6eaaf8b9c4040a05fe2325ab75f44e">eCounterStateMask</a></td></tr>
<tr class="memdesc:gaff6eaaf8b9c4040a05fe2325ab75f44e inherit pub_static_attribs_classCObject"><td class="mdescLeft">&#160;</td><td class="mdescRight">Valid object, and object in heap. <a href="group__Object.html#gaff6eaaf8b9c4040a05fe2325ab75f44e">More...</a><br /></td></tr>
<tr class="separator:gaff6eaaf8b9c4040a05fe2325ab75f44e inherit pub_static_attribs_classCObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-types"></a>
Private Types</h2></td></tr>
<tr class="memitem:gaf4075ecee2f0ec68fe81fda82d930fa1"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCHit__Base.html">CHit_Base</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gaf4075ecee2f0ec68fe81fda82d930fa1">Tparent</a></td></tr>
<tr class="separator:gaf4075ecee2f0ec68fe81fda82d930fa1"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaf4075ecee2f0ec68fe81fda82d930fa1"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCHit__Base.html">CHit_Base</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaf4075ecee2f0ec68fe81fda82d930fa1">Tparent</a></td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-methods"></a>
Private Member Functions</h2></td></tr>
<tr class="memitem:ga111e81f2c8134f6391c54db668fed02e"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#ga111e81f2c8134f6391c54db668fed02e">CHit</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCHit.html">CHit</a> &amp;<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
<tr class="separator:ga111e81f2c8134f6391c54db668fed02e"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaf2c5606fe7854fb1aa7e6aec148a2eb9"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCHit.html">CHit</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput.html#gaf2c5606fe7854fb1aa7e6aec148a2eb9">operator=</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCHit.html">CHit</a> &amp;<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
<tr class="separator:gaf2c5606fe7854fb1aa7e6aec148a2eb9"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga111e81f2c8134f6391c54db668fed02e"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#ga111e81f2c8134f6391c54db668fed02e">CHit</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCHit.html">CHit</a> &amp;<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
<tr class="separator:ga111e81f2c8134f6391c54db668fed02e"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gaf2c5606fe7854fb1aa7e6aec148a2eb9"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCHit.html">CHit</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__dataspec__NCBI__BlastOutput2.html#gaf2c5606fe7854fb1aa7e6aec148a2eb9">operator=</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCHit.html">CHit</a> &amp;<a class="el" href="ftds14_2freetds_2tds_2config_8c.html#ac6de4458dc999b0ad86cfcbaaf37222a">value</a>)</td></tr>
<tr class="separator:gaf2c5606fe7854fb1aa7e6aec148a2eb9"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-attribs"></a>
Private Attributes</h2></td></tr>
<tr class="memitem:a48f8efb8c6a21061f14d44ee6fe70d54"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classCEditScript.html">CEditScript</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#a48f8efb8c6a21061f14d44ee6fe70d54">m_EditScript</a></td></tr>
<tr class="memdesc:a48f8efb8c6a21061f14d44ee6fe70d54"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="structTraceback.html">Traceback</a> for this alignment. <a href="classCHit.html#a48f8efb8c6a21061f14d44ee6fe70d54">More...</a><br /></td></tr>
<tr class="separator:a48f8efb8c6a21061f14d44ee6fe70d54"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a144a490ceee55ccbfac5823df6c35aa3"><td class="memItemLeft" align="right" valign="top">vector&lt; <a class="el" href="classCHit.html">CHit</a> * &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCHit.html#a144a490ceee55ccbfac5823df6c35aa3">m_SubHit</a></td></tr>
<tr class="memdesc:a144a490ceee55ccbfac5823df6c35aa3"><td class="mdescLeft">&#160;</td><td class="mdescRight">Subhits for this alignment. <a href="classCHit.html#a144a490ceee55ccbfac5823df6c35aa3">More...</a><br /></td></tr>
<tr class="separator:a144a490ceee55ccbfac5823df6c35aa3"><td class="memSeparator" colspan="2">&#160;</td></tr>
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<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_methods_classCSerialObject"><td colspan="2" onclick="javascript:toggleInherit('pub_static_methods_classCSerialObject')"><img src="closed.png" alt="-"/>&#160;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&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#gab2a92c7a5b5900317294b85e854db07e">SetVerifyDataThread</a> (<a class="el" href="group__GenClassSupport.html#ga58e0144d240fc7ad45518d4c3ba735e1">ESerialVerifyData</a> <a class="el" href="ftds14_2freetds_2dblib_2unittests_2t0002_8c.html#a80ddcf418c95fb872f5eeccb9908b4c7">verify</a>)</td></tr>
<tr class="separator:gab2a92c7a5b5900317294b85e854db07e inherit pub_static_methods_classCSerialObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga2e3bead397d7ec0fffde866cd890267e inherit pub_static_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> void&#160;</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">&#160;</td></tr>
<tr class="memitem:gada3dbb83951d0bed9bde06c6c4ede9e2 inherit pub_static_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#gada3dbb83951d0bed9bde06c6c4ede9e2">UnassignedString</a> (void)</td></tr>
<tr class="separator:gada3dbb83951d0bed9bde06c6c4ede9e2 inherit pub_static_methods_classCSerialObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga123d82fb69550b6418ad5d69e752873a inherit pub_static_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__STL.html#ga88e22aab83a29bae20f5354e89b041e3">CStringUTF8</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#ga123d82fb69550b6418ad5d69e752873a">UnassignedStringUTF8</a> (void)</td></tr>
<tr class="separator:ga123d82fb69550b6418ad5d69e752873a inherit pub_static_methods_classCSerialObject"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga1d897c6ce0f541df2487600cedd9f40a inherit pub_static_methods_classCSerialObject"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> char&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__GenClassSupport.html#ga1d897c6ce0f541df2487600cedd9f40a">UnassignedByte</a> (void)</td></tr>
<tr class="separator:ga1d897c6ce0f541df2487600cedd9f40a inherit pub_static_methods_classCSerialObject"><td class="memSeparator" colspan="2">&#160;</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="-"/>&#160;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&#160;</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">&#160;</td><td class="mdescRight">Define method to throw null pointer exception. <a href="group__Object.html#ga63f363685df177bedf4a7f4ed7797a07">More...</a><br /></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&#160;</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>
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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&#160;</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> &amp;<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">&#160;</td><td class="mdescRight">Set mode from configuration parameter value. <a href="group__Object.html#ga05dafbb430a19e98affa48e669d694f7">More...</a><br /></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="-"/>&#160;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&#160;</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>
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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="-"/>&#160;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&#160;</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">&#160;</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">&#160;</td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>A generalized representation of a pairwise alignment. </p>
<p><a class="el" href="classCHit.html" title="A generalized representation of a pairwise alignment.">CHit</a> &ndash;. </p>
<p class="definition">Definition at line <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00085">85</a> of file <a class="el" href="algo_2cobalt_2hit_8hpp_source.html">hit.hpp</a>.</p>
</div><h2 class="groupheader">Member Typedef Documentation</h2>
<a id="ae7601ab4889718bc6200637d3d2172e5"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ae7601ab4889718bc6200637d3d2172e5">&#9670;&nbsp;</a></span>TSubHit</h2>
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<td class="memname">typedef vector&lt;<a class="el" href="classCHit.html">CHit</a> *&gt; <a class="el" href="classCHit.html#ae7601ab4889718bc6200637d3d2172e5">CHit::TSubHit</a></td>
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<p>Hits can be grouped hierarchically. </p>
<p class="definition">Definition at line <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00093">93</a> of file <a class="el" href="algo_2cobalt_2hit_8hpp_source.html">hit.hpp</a>.</p>
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</div>
<h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
<a id="acbaab500b53a39fa14bdbaa4897feb9a"></a>
<h2 class="memtitle"><span class="permalink"><a href="#acbaab500b53a39fa14bdbaa4897feb9a">&#9670;&nbsp;</a></span>CHit() <span class="overload">[1/5]</span></h2>
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<td class="memname">CHit::CHit </td>
<td>(</td>
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a>&#160;</td>
<td class="paramname"><em>seq1_index</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a>&#160;</td>
<td class="paramname"><em>seq2_index</em>&#160;</td>
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<td>)</td>
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<p>Create an empty alignment. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">seq1_index</td><td>Numerical identifier for first sequence [in] </td></tr>
<tr><td class="paramname">seq2_index</td><td>Numerical identifier for second sequence [in] </td></tr>
</table>
</dd>
</dl>
<p class="definition">Definition at line <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00116">116</a> of file <a class="el" href="algo_2cobalt_2hit_8hpp_source.html">hit.hpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a61fc61e5f9849478788f15bfb8597b4c">&#9670;&nbsp;</a></span>CHit() <span class="overload">[2/5]</span></h2>
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<td class="memname">CHit::CHit </td>
<td>(</td>
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a>&#160;</td>
<td class="paramname"><em>seq1_index</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a>&#160;</td>
<td class="paramname"><em>seq2_index</em>, </td>
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<td class="paramtype"><a class="el" href="structBlastHSP.html">BlastHSP</a> *&#160;</td>
<td class="paramname"><em>hsp</em>&#160;</td>
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<td>)</td>
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<p>Create an alignment from a BLAST hit. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">seq1_index</td><td>Numerical identifier for first sequence [in] </td></tr>
<tr><td class="paramname">seq2_index</td><td>Numerical identifier for second sequence [in] </td></tr>
<tr><td class="paramname">hsp</td><td>A single pairwise alignment from a blast hit [in] </td></tr>
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</dd>
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<p class="definition">Definition at line <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00125">125</a> of file <a class="el" href="algo_2cobalt_2hit_8hpp_source.html">hit.hpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a12f6b6bf0386f8f0e6af136b8f8bdf5e">&#9670;&nbsp;</a></span>CHit() <span class="overload">[3/5]</span></h2>
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<td class="memname">CHit::CHit </td>
<td>(</td>
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a>&#160;</td>
<td class="paramname"><em>seq1_index</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a>&#160;</td>
<td class="paramname"><em>seq2_index</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a>&#160;</td>
<td class="paramname"><em>score</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> objects::CDense_seg &amp;&#160;</td>
<td class="paramname"><em>denseg</em>&#160;</td>
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<p>Create an alignment from a Dense_seg. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">seq1_index</td><td>Numerical identifier for first sequence [in] </td></tr>
<tr><td class="paramname">seq2_index</td><td>Numerical identifier for second sequence [in] </td></tr>
<tr><td class="paramname">score</td><td>The score of the pairwise alignment [in] </td></tr>
<tr><td class="paramname">denseg</td><td>Dense_seg representing a single pairwise alignment from a blast hit [in] </td></tr>
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</dd>
</dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a8236d50dfeab03ac04d0c1f54f7bb2ef">&#9670;&nbsp;</a></span>CHit() <span class="overload">[4/5]</span></h2>
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<td class="memname">CHit::CHit </td>
<td>(</td>
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a>&#160;</td>
<td class="paramname"><em>seq1_index</em>, </td>
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<td></td>
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a>&#160;</td>
<td class="paramname"><em>seq2_index</em>, </td>
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<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a>&#160;</td>
<td class="paramname"><em>score</em>, </td>
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<td></td>
<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> objects::CDense_diag &amp;&#160;</td>
<td class="paramname"><em>dendiag</em>&#160;</td>
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<p>Create an alignment from a Dense_diag. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">seq1_index</td><td>Numerical identifier for first sequence [in] </td></tr>
<tr><td class="paramname">seq2_index</td><td>Numerical identifier for second sequence [in] </td></tr>
<tr><td class="paramname">score</td><td>The score of the pairwise alignment [in] </td></tr>
<tr><td class="paramname">dendiag</td><td>Dense_seg representing a single ungapped pairwise alignment from a blast hit [in] </td></tr>
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</dd>
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<h2 class="memtitle"><span class="permalink"><a href="#a16471ebaf022e9e835aa6fcca9876b46">&#9670;&nbsp;</a></span>CHit() <span class="overload">[5/5]</span></h2>
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<td class="memname">CHit::CHit </td>
<td>(</td>
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a>&#160;</td>
<td class="paramname"><em>seq1_index</em>, </td>
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<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a>&#160;</td>
<td class="paramname"><em>seq2_index</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="base_8hpp.html#a82668c1a5428e2d884d0f0c67d97fdf1">TRange</a>&#160;</td>
<td class="paramname"><em>seq_range1</em>, </td>
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<td class="paramtype"><a class="el" href="base_8hpp.html#a82668c1a5428e2d884d0f0c67d97fdf1">TRange</a>&#160;</td>
<td class="paramname"><em>seq_range2</em>, </td>
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<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a>&#160;</td>
<td class="paramname"><em>score</em>, </td>
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<td class="paramtype"><a class="el" href="classCEditScript.html">CEditScript</a>&#160;</td>
<td class="paramname"><em>edit_script</em>&#160;</td>
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<td>)</td>
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<p>Create an alignment with all specified parameters. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">seq1_index</td><td>Numerical identifier for first sequence [in] </td></tr>
<tr><td class="paramname">seq2_index</td><td>Numerical identifier for second sequence [in] </td></tr>
<tr><td class="paramname">seq_range1</td><td>Offsets on the first sequence [in] </td></tr>
<tr><td class="paramname">seq_range2</td><td>Offsets on the second sequence [in] </td></tr>
<tr><td class="paramname">score</td><td>The score of the alignment [in] </td></tr>
<tr><td class="paramname">edit_script</td><td><a class="el" href="structTraceback.html">Traceback</a> for the alignment (may be empty) [in] </td></tr>
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</dd>
</dl>
<p class="definition">Definition at line <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00160">160</a> of file <a class="el" href="algo_2cobalt_2hit_8hpp_source.html">hit.hpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ade8d162d4f1bef2580652d39bd7c0f6e">&#9670;&nbsp;</a></span>~CHit()</h2>
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<td class="memname"><a class="el" href="objects_2blastxml2_2Target___8hpp.html#a4a7339111f60ac79dbbc3fda76c89fc1">BEGIN_blastxml2_SCOPE</a> CHit::~CHit </td>
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<p>Destructor. </p>
<p class="definition">Definition at line <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00170">170</a> of file <a class="el" href="algo_2cobalt_2hit_8hpp_source.html">hit.hpp</a>.</p>
<p class="reference">References <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>, and <a class="el" href="dbapi_2driver_2types_8hpp_source.html#l01210">int</a>.</p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a68f59b3a8136766fda92dfdbdb7c8709">&#9670;&nbsp;</a></span>AddUpSubHits()</h2>
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<td class="memname">void CHit::AddUpSubHits </td>
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<p>Sum the score of all subhits, and make the sequence ranges the union of the ranges of all subhits. </p>
<p><a class="el" href="structTraceback.html">Traceback</a> is ignored </p>
<p class="definition">Definition at line <a class="el" href="hit_8cpp_source.html#l00087">87</a> of file <a class="el" href="hit_8cpp_source.html">hit.cpp</a>.</p>
<p class="reference">References <a class="el" href="test__assert__impl_8h_source.html#l00173">_ASSERT</a>, <a class="el" href="range_8hpp_source.html#l00345">COpenRange&lt; Position &gt;::CombineWith()</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00195">HasSubHits()</a>, <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>, <a class="el" href="dbapi_2driver_2types_8hpp_source.html#l01210">int</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00104">m_Score</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00107">m_SeqRange1</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00110">m_SeqRange2</a>, and <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00268">m_SubHit</a>.</p>
<p class="reference">Referenced by <a class="el" href="hitlist_8cpp_source.html#l00221">CHitList::MatchOverlappingSubHits()</a>, and <a class="el" href="rps_8cpp_source.html#l00114">CMultiAligner::x_RealignBlocks()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a4fd3a163bfa7ecb665a664dbe0ca618f">&#9670;&nbsp;</a></span>Clone()</h2>
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<td class="memname"><a class="el" href="classCHit.html">CHit</a> * CHit::Clone </td>
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<p>Produce an independent copy of a <a class="el" href="classCHit.html" title="A generalized representation of a pairwise alignment.">CHit</a>. </p>
<dl class="section return"><dt>Returns</dt><dd>Pointer to the copy </dd></dl>
<p class="definition">Definition at line <a class="el" href="hit_8cpp_source.html#l00378">378</a> of file <a class="el" href="hit_8cpp_source.html">hit.cpp</a>.</p>
<p class="reference">References <a class="el" href="blastxml_2Hit_8hpp_source.html#l00086">CHit()</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00185">GetSubHit()</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00195">HasSubHits()</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00180">InsertSubHit()</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00267">m_EditScript</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00104">m_Score</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00097">m_SeqIndex1</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00101">m_SeqIndex2</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00107">m_SeqRange1</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00110">m_SeqRange2</a>, and <a class="el" href="ncbimisc_8hpp_source.html#l00822">NON_CONST_ITERATE</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#aadb02ad4a88803334256c94d8a02810d">&#9670;&nbsp;</a></span>GetEditScript()</h2>
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<td class="memname"><a class="el" href="classCEditScript.html">CEditScript</a>&amp; CHit::GetEditScript </td>
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<p>Retrieve the traceback associated with a <a class="el" href="classCHit.html" title="A generalized representation of a pairwise alignment.">CHit</a>. </p>
<dl class="section return"><dt>Returns</dt><dd>The traceback </dd></dl>
<p class="definition">Definition at line <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00190">190</a> of file <a class="el" href="algo_2cobalt_2hit_8hpp_source.html">hit.hpp</a>.</p>
<p class="reference">Referenced by <a class="el" href="hitlist_8cpp_source.html#l00098">CHitList::MakeCanonical()</a>, <a class="el" href="hit_8cpp_source.html#l00285">ResolveSubHitConflicts()</a>, <a class="el" href="rps_8cpp_source.html#l00512">CMultiAligner::x_AssignRPSResFreqs()</a>, <a class="el" href="prog_8cpp_source.html#l00700">CMultiAligner::x_FindInClusterConstraints()</a>, and <a class="el" href="rps_8cpp_source.html#l00114">CMultiAligner::x_RealignBlocks()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a000263cc1e4c7f20a7414020b7ec33c9">&#9670;&nbsp;</a></span>GetRangeFromSeq1()</h2>
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<td class="memname">void CHit::GetRangeFromSeq1 </td>
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<td class="paramname"><em>seq_range1</em>, </td>
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<td class="paramtype"><a class="el" href="base_8hpp.html#a82668c1a5428e2d884d0f0c67d97fdf1">TRange</a> &amp;&#160;</td>
<td class="paramname"><em>new_seq_range1</em>, </td>
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<p>Retrieve the seq2 range corresponding to a specified seq1 range. </p>
<p>Assumes traceback is valid </p><dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">seq_range1</td><td>The target range on the first sequence [in] </td></tr>
<tr><td class="paramname">new_seq_range1</td><td>If seq_range1 starts or ends in a gap on seq_range2, the range is shortened to exclude the gap and seq_range1 is cropped to compensate [out] </td></tr>
<tr><td class="paramname">seq_range2</td><td>The corresponding range on the second sequence [out] </td></tr>
<tr><td class="paramname">traceback_range</td><td>The range of traceback operations corresponding to seq_range1 and new_seq_range2 [out] </td></tr>
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<p class="definition">Definition at line <a class="el" href="hit_8cpp_source.html#l00145">145</a> of file <a class="el" href="hit_8cpp_source.html">hit.cpp</a>.</p>
<p class="reference">References <a class="el" href="test__assert__impl_8h_source.html#l00173">_ASSERT</a>, <a class="el" href="base_8hpp_source.html#l00085">CLocalRange&lt; Position &gt;::Contains()</a>, <a class="el" href="traceback_8cpp_source.html#l00270">CEditScript::FindOffsetFromSeq1()</a>, <a class="el" href="Range___8hpp_source.html#l00222">CRange_Base::GetFrom()</a>, <a class="el" href="Range___8hpp_source.html#l00269">CRange_Base::GetTo()</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00267">m_EditScript</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00107">m_SeqRange1</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00110">m_SeqRange2</a>, <a class="el" href="Range___8hpp_source.html#l00231">CRange_Base::SetFrom()</a>, and <a class="el" href="Range___8hpp_source.html#l00278">CRange_Base::SetTo()</a>.</p>
<p class="reference">Referenced by <a class="el" href="hit_8cpp_source.html#l00285">ResolveSubHitConflicts()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a61e3b2b920739aa249b9af31d7aab92b">&#9670;&nbsp;</a></span>GetRangeFromSeq2()</h2>
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<td class="memname">void CHit::GetRangeFromSeq2 </td>
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<td class="paramname"><em>seq_range2</em>, </td>
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<p>Retrieve the seq1 range corresponding to a specified seq2 range. </p>
<p>Assumes traceback is valid </p><dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">seq_range2</td><td>The target range on the second sequence [in] </td></tr>
<tr><td class="paramname">seq_range1</td><td>The corresponding range on the first sequence [out] </td></tr>
<tr><td class="paramname">new_seq_range2</td><td>If seq_range2 starts or ends in a gap on seq_range1, the range is shortened to exclude the gap and seq_range2 is cropped to compensate [out] </td></tr>
<tr><td class="paramname">traceback_range</td><td>The range of traceback operations corresponding to seq_range1 and new_seq_range2 [out] </td></tr>
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<p class="definition">Definition at line <a class="el" href="hit_8cpp_source.html#l00109">109</a> of file <a class="el" href="hit_8cpp_source.html">hit.cpp</a>.</p>
<p class="reference">References <a class="el" href="test__assert__impl_8h_source.html#l00173">_ASSERT</a>, <a class="el" href="base_8hpp_source.html#l00085">CLocalRange&lt; Position &gt;::Contains()</a>, <a class="el" href="traceback_8cpp_source.html#l00196">CEditScript::FindOffsetFromSeq2()</a>, <a class="el" href="Range___8hpp_source.html#l00222">CRange_Base::GetFrom()</a>, <a class="el" href="Range___8hpp_source.html#l00269">CRange_Base::GetTo()</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00267">m_EditScript</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00107">m_SeqRange1</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00110">m_SeqRange2</a>, <a class="el" href="Range___8hpp_source.html#l00231">CRange_Base::SetFrom()</a>, and <a class="el" href="Range___8hpp_source.html#l00278">CRange_Base::SetTo()</a>.</p>
<p class="reference">Referenced by <a class="el" href="hitlist_8cpp_source.html#l00162">x_MatchSubHits()</a>, and <a class="el" href="rps_8cpp_source.html#l00114">CMultiAligner::x_RealignBlocks()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a0ff84da4f65908f9dabcc0f1348798b5">&#9670;&nbsp;</a></span>GetSubHit()</h2>
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<td class="memname"><a class="el" href="classCHit.html#ae7601ab4889718bc6200637d3d2172e5">TSubHit</a>&amp; CHit::GetSubHit </td>
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<p>Retrieve a list of subhits. </p>
<dl class="section return"><dt>Returns</dt><dd>The list of subhits </dd></dl>
<p class="definition">Definition at line <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00185">185</a> of file <a class="el" href="algo_2cobalt_2hit_8hpp_source.html">hit.hpp</a>.</p>
<p class="reference">Referenced by <a class="el" href="hit_8cpp_source.html#l00378">Clone()</a>, <a class="el" href="hitlist_8cpp_source.html#l00098">CHitList::MakeCanonical()</a>, <a class="el" href="hitlist_8cpp_source.html#l00221">CHitList::MatchOverlappingSubHits()</a>, <a class="el" href="rps_8cpp_source.html#l00512">CMultiAligner::x_AssignRPSResFreqs()</a>, <a class="el" href="prog_8cpp_source.html#l00382">CMultiAligner::x_FindConstraints()</a>, <a class="el" href="rps_8cpp_source.html#l00866">CMultiAligner::x_FindDomainHits()</a>, <a class="el" href="prog_8cpp_source.html#l00094">x_HitToConstraints()</a>, and <a class="el" href="blast_8cpp_source.html#l00095">CMultiAligner::x_MakeFillerBlocks()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ae0212e09bf44bac32deedfc7317c01bf">&#9670;&nbsp;</a></span>HasSubHits()</h2>
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<td class="memname"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> CHit::HasSubHits </td>
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<p>Query if a <a class="el" href="classCHit.html" title="A generalized representation of a pairwise alignment.">CHit</a> has a hierarchy of subhits available. </p>
<dl class="section return"><dt>Returns</dt><dd>true if subhits are available </dd></dl>
<p class="definition">Definition at line <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00195">195</a> of file <a class="el" href="algo_2cobalt_2hit_8hpp_source.html">hit.hpp</a>.</p>
<p class="reference">Referenced by <a class="el" href="hit_8cpp_source.html#l00087">AddUpSubHits()</a>, <a class="el" href="hit_8cpp_source.html#l00378">Clone()</a>, <a class="el" href="hitlist_8cpp_source.html#l00098">CHitList::MakeCanonical()</a>, <a class="el" href="hitlist_8cpp_source.html#l00221">CHitList::MatchOverlappingSubHits()</a>, <a class="el" href="rps_8cpp_source.html#l00512">CMultiAligner::x_AssignRPSResFreqs()</a>, <a class="el" href="prog_8cpp_source.html#l00382">CMultiAligner::x_FindConstraints()</a>, <a class="el" href="prog_8cpp_source.html#l00094">x_HitToConstraints()</a>, <a class="el" href="blast_8cpp_source.html#l00095">CMultiAligner::x_MakeFillerBlocks()</a>, and <a class="el" href="rps_8cpp_source.html#l00114">CMultiAligner::x_RealignBlocks()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a60d366a793bd4c751c1d1a14a7b41dae">&#9670;&nbsp;</a></span>InsertSubHit()</h2>
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<td class="memname">void CHit::InsertSubHit </td>
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<p>Add a to a <a class="el" href="classCHit.html" title="A generalized representation of a pairwise alignment.">CHit</a>'s list of subhits. </p>
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<tr><td class="paramname">hit</td><td>The hit to add [in] </td></tr>
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<p class="definition">Definition at line <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00180">180</a> of file <a class="el" href="algo_2cobalt_2hit_8hpp_source.html">hit.hpp</a>.</p>
<p class="reference">Referenced by <a class="el" href="hit_8cpp_source.html#l00378">Clone()</a>, <a class="el" href="hitlist_8cpp_source.html#l00221">CHitList::MatchOverlappingSubHits()</a>, <a class="el" href="prog_8cpp_source.html#l00382">CMultiAligner::x_FindConstraints()</a>, and <a class="el" href="rps_8cpp_source.html#l00114">CMultiAligner::x_RealignBlocks()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a45aef14f14da8664ca53393631ce4922">&#9670;&nbsp;</a></span>ResolveSubHitConflicts()</h2>
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<td class="memname">void CHit::ResolveSubHitConflicts </td>
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<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> **&#160;</td>
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<td class="paramtype"><a class="el" href="group__AlgoAlignRoot.html#ga52f93d4188f6edb1940043ae7a67605b">CNWAligner::TScore</a>&#160;</td>
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<p>If pairs of subhits have overlapping ranges, either delete one or change one so that the overlap is avoided. </p>
<p>Only the sequence 1 range is checked for overlap; in practice, the hits refer to block alignments derived from RPS blast results, and sequence 2 is an RPS database sequence. It is sequence 1 that matters for later processing </p><dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">seq1</td><td>The sequence data corresponding to the first sequence [in] </td></tr>
<tr><td class="paramname">seq2_pssm</td><td>The PSSM for the second sequence [in] </td></tr>
<tr><td class="paramname">gap_open</td><td>Penalty for opening a gap [in] </td></tr>
<tr><td class="paramname">gap_extend</td><td>Penalty for extending a gap [in] </td></tr>
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<p class="definition">Definition at line <a class="el" href="hit_8cpp_source.html#l00285">285</a> of file <a class="el" href="hit_8cpp_source.html">hit.cpp</a>.</p>
<p class="reference">References <a class="el" href="blastxml_2Hit_8hpp_source.html#l00086">CHit()</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00190">GetEditScript()</a>, <a class="el" href="Range___8hpp_source.html#l00222">CRange_Base::GetFrom()</a>, <a class="el" href="hit_8cpp_source.html#l00145">GetRangeFromSeq1()</a>, <a class="el" href="traceback_8cpp_source.html#l00343">CEditScript::GetScore()</a>, <a class="el" href="Range___8hpp_source.html#l00269">CRange_Base::GetTo()</a>, <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00104">m_Score</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00097">m_SeqIndex1</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00101">m_SeqIndex2</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00107">m_SeqRange1</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00110">m_SeqRange2</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00268">m_SubHit</a>, <a class="el" href="traceback_8cpp_source.html#l00153">CEditScript::MakeEditScript()</a>, <a class="el" href="base_8hpp_source.html#l00100">CLocalRange&lt; Position &gt;::StrictlyBelow()</a>, and <a class="el" href="hit_8cpp_source.html#l00222">x_RemoveEnvelopedSubHits()</a>.</p>
<p class="reference">Referenced by <a class="el" href="rps_8cpp_source.html#l00114">CMultiAligner::x_RealignBlocks()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a377dc4366e7dfe8d7ce50e75c0ee268e">&#9670;&nbsp;</a></span>VerifyHit()</h2>
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<td class="memname">void CHit::VerifyHit </td>
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<p>Perform basic integrity checks on a <a class="el" href="classCHit.html" title="A generalized representation of a pairwise alignment.">CHit</a>. </p>
<p class="definition">Definition at line <a class="el" href="hit_8cpp_source.html#l00180">180</a> of file <a class="el" href="hit_8cpp_source.html">hit.cpp</a>.</p>
<p class="reference">References <a class="el" href="test__assert__impl_8h_source.html#l00173">_ASSERT</a>, <a class="el" href="range_8hpp_source.html#l00148">COpenRange&lt; Position &gt;::Empty()</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00267">m_EditScript</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00107">m_SeqRange1</a>, <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00110">m_SeqRange2</a>, and <a class="el" href="traceback_8cpp_source.html#l00475">CEditScript::VerifyScript()</a>.</p>
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<h2 class="groupheader">Member Data Documentation</h2>
<a id="ab9b21171a449e2e88599b398aa46f3ff"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ab9b21171a449e2e88599b398aa46f3ff">&#9670;&nbsp;</a></span>kMinHitSize</h2>
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<td class="memname"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> CHit::kMinHitSize = 2</td>
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<p>Not always used, but useful to avoid extremely small hits. </p>
<p class="definition">Definition at line <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00090">90</a> of file <a class="el" href="algo_2cobalt_2hit_8hpp_source.html">hit.hpp</a>.</p>
<p class="reference">Referenced by <a class="el" href="blast_8cpp_source.html#l00095">CMultiAligner::x_MakeFillerBlocks()</a>, <a class="el" href="hitlist_8cpp_source.html#l00162">x_MatchSubHits()</a>, and <a class="el" href="rps_8cpp_source.html#l00114">CMultiAligner::x_RealignBlocks()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a48f8efb8c6a21061f14d44ee6fe70d54">&#9670;&nbsp;</a></span>m_EditScript</h2>
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<td class="memname"><a class="el" href="classCEditScript.html">CEditScript</a> CHit::m_EditScript</td>
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<p><a class="el" href="structTraceback.html">Traceback</a> for this alignment. </p>
<p class="definition">Definition at line <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00267">267</a> of file <a class="el" href="algo_2cobalt_2hit_8hpp_source.html">hit.hpp</a>.</p>
<p class="reference">Referenced by <a class="el" href="hit_8cpp_source.html#l00378">Clone()</a>, <a class="el" href="hit_8cpp_source.html#l00145">GetRangeFromSeq1()</a>, <a class="el" href="hit_8cpp_source.html#l00109">GetRangeFromSeq2()</a>, and <a class="el" href="hit_8cpp_source.html#l00180">VerifyHit()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a84670daf0a817644571023bbf6311147">&#9670;&nbsp;</a></span>m_Score</h2>
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<td class="memname"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> CHit::m_Score</td>
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<p>Score of alignment. </p>
<p class="definition">Definition at line <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00104">104</a> of file <a class="el" href="algo_2cobalt_2hit_8hpp_source.html">hit.hpp</a>.</p>
<p class="reference">Referenced by <a class="el" href="hit_8cpp_source.html#l00087">AddUpSubHits()</a>, <a class="el" href="hit_8cpp_source.html#l00378">Clone()</a>, <a class="el" href="cobalt__unit__test_8cpp_source.html#l00162">CMultiAlignerTest::CompareDomainHits()</a>, <a class="el" href="dist_8cpp_source.html#l00156">CDistances::ComputeMatrix()</a>, <a class="el" href="hitlist_8cpp_source.html#l00221">CHitList::MatchOverlappingSubHits()</a>, <a class="el" href="hit_8cpp_source.html#l00285">ResolveSubHitConflicts()</a>, <a class="el" href="seg_8cpp_source.html#l00120">CMultiAligner::x_FindAlignmentSubsets()</a>, <a class="el" href="seg_8cpp_source.html#l00175">CMultiAligner::x_FindConsistentHitSubset()</a>, <a class="el" href="prog_8cpp_source.html#l00382">CMultiAligner::x_FindConstraints()</a>, <a class="el" href="rps_8cpp_source.html#l00866">CMultiAligner::x_FindDomainHits()</a>, <a class="el" href="prog_8cpp_source.html#l00700">CMultiAligner::x_FindInClusterConstraints()</a>, <a class="el" href="blast_8cpp_source.html#l00306">CMultiAligner::x_FindLocalHits()</a>, <a class="el" href="blast_8cpp_source.html#l00481">CMultiAligner::x_FindLocalInClusterHits()</a>, <a class="el" href="phi_8cpp_source.html#l00062">CMultiAligner::x_FindPatternHits()</a>, <a class="el" href="rps_8cpp_source.html#l00411">CMultiAligner::x_FindRPSHits()</a>, <a class="el" href="hitlist_8cpp_source.html#l00162">x_MatchSubHits()</a>, <a class="el" href="hit_8cpp_source.html#l00222">x_RemoveEnvelopedSubHits()</a>, and <a class="el" href="rps_8cpp_source.html#l00664">CMultiAligner::x_SetDomainHits()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#aae6d0920a29f57838fb2b4a115dee6ba">&#9670;&nbsp;</a></span>m_SeqIndex1</h2>
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<td class="memname"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> CHit::m_SeqIndex1</td>
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<p>Numerical identifier for first sequence in alignment. </p>
<p class="definition">Definition at line <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00097">97</a> of file <a class="el" href="algo_2cobalt_2hit_8hpp_source.html">hit.hpp</a>.</p>
<p class="reference">Referenced by <a class="el" href="hit_8cpp_source.html#l00378">Clone()</a>, <a class="el" href="cobalt__unit__test_8cpp_source.html#l00162">CMultiAlignerTest::CompareDomainHits()</a>, <a class="el" href="dist_8cpp_source.html#l00156">CDistances::ComputeMatrix()</a>, <a class="el" href="hitlist_8cpp_source.html#l00098">CHitList::MakeCanonical()</a>, <a class="el" href="hitlist_8cpp_source.html#l00221">CHitList::MatchOverlappingSubHits()</a>, <a class="el" href="hit_8cpp_source.html#l00285">ResolveSubHitConflicts()</a>, <a class="el" href="cobalt_8cpp_source.html#l00513">CMultiAligner::x_AlignMSAs()</a>, <a class="el" href="rps_8cpp_source.html#l00512">CMultiAligner::x_AssignRPSResFreqs()</a>, <a class="el" href="prog_8cpp_source.html#l01812">CMultiAligner::x_BuildAlignmentIterative()</a>, <a class="el" href="seg_8cpp_source.html#l00120">CMultiAligner::x_FindAlignmentSubsets()</a>, <a class="el" href="seg_8cpp_source.html#l00175">CMultiAligner::x_FindConsistentHitSubset()</a>, <a class="el" href="prog_8cpp_source.html#l00382">CMultiAligner::x_FindConstraints()</a>, <a class="el" href="rps_8cpp_source.html#l00866">CMultiAligner::x_FindDomainHits()</a>, <a class="el" href="prog_8cpp_source.html#l00700">CMultiAligner::x_FindInClusterConstraints()</a>, <a class="el" href="blast_8cpp_source.html#l00306">CMultiAligner::x_FindLocalHits()</a>, <a class="el" href="blast_8cpp_source.html#l00481">CMultiAligner::x_FindLocalInClusterHits()</a>, <a class="el" href="phi_8cpp_source.html#l00062">CMultiAligner::x_FindPatternHits()</a>, <a class="el" href="cobalt_8cpp_source.html#l00744">CMultiAligner::x_FindQueryClusters()</a>, <a class="el" href="rps_8cpp_source.html#l00411">CMultiAligner::x_FindRPSHits()</a>, <a class="el" href="dist_8cpp_source.html#l00074">CDistances::x_GetSelfScores()</a>, <a class="el" href="blast_8cpp_source.html#l00095">CMultiAligner::x_MakeFillerBlocks()</a>, <a class="el" href="hitlist_8cpp_source.html#l00162">x_MatchSubHits()</a>, <a class="el" href="rps_8cpp_source.html#l00114">CMultiAligner::x_RealignBlocks()</a>, <a class="el" href="rps_8cpp_source.html#l00664">CMultiAligner::x_SetDomainHits()</a>, and <a class="el" href="cobalt_8cpp_source.html#l00159">CMultiAligner::x_ValidateUserHits()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ab0ea5f8851a79f17da18404a9f7c00af">&#9670;&nbsp;</a></span>m_SeqIndex2</h2>
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<td class="memname"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> CHit::m_SeqIndex2</td>
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<p>Numerical identifier for second sequence in alignment. </p>
<p class="definition">Definition at line <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00101">101</a> of file <a class="el" href="algo_2cobalt_2hit_8hpp_source.html">hit.hpp</a>.</p>
<p class="reference">Referenced by <a class="el" href="hit_8cpp_source.html#l00378">Clone()</a>, <a class="el" href="cobalt__unit__test_8cpp_source.html#l00162">CMultiAlignerTest::CompareDomainHits()</a>, <a class="el" href="dist_8cpp_source.html#l00156">CDistances::ComputeMatrix()</a>, <a class="el" href="hitlist_8cpp_source.html#l00098">CHitList::MakeCanonical()</a>, <a class="el" href="hitlist_8cpp_source.html#l00221">CHitList::MatchOverlappingSubHits()</a>, <a class="el" href="hit_8cpp_source.html#l00285">ResolveSubHitConflicts()</a>, <a class="el" href="cobalt_8cpp_source.html#l00513">CMultiAligner::x_AlignMSAs()</a>, <a class="el" href="rps_8cpp_source.html#l00512">CMultiAligner::x_AssignRPSResFreqs()</a>, <a class="el" href="prog_8cpp_source.html#l01812">CMultiAligner::x_BuildAlignmentIterative()</a>, <a class="el" href="seg_8cpp_source.html#l00120">CMultiAligner::x_FindAlignmentSubsets()</a>, <a class="el" href="seg_8cpp_source.html#l00175">CMultiAligner::x_FindConsistentHitSubset()</a>, <a class="el" href="prog_8cpp_source.html#l00382">CMultiAligner::x_FindConstraints()</a>, <a class="el" href="rps_8cpp_source.html#l00866">CMultiAligner::x_FindDomainHits()</a>, <a class="el" href="prog_8cpp_source.html#l00700">CMultiAligner::x_FindInClusterConstraints()</a>, <a class="el" href="blast_8cpp_source.html#l00306">CMultiAligner::x_FindLocalHits()</a>, <a class="el" href="blast_8cpp_source.html#l00481">CMultiAligner::x_FindLocalInClusterHits()</a>, <a class="el" href="phi_8cpp_source.html#l00062">CMultiAligner::x_FindPatternHits()</a>, <a class="el" href="cobalt_8cpp_source.html#l00744">CMultiAligner::x_FindQueryClusters()</a>, <a class="el" href="rps_8cpp_source.html#l00411">CMultiAligner::x_FindRPSHits()</a>, <a class="el" href="dist_8cpp_source.html#l00074">CDistances::x_GetSelfScores()</a>, <a class="el" href="blast_8cpp_source.html#l00095">CMultiAligner::x_MakeFillerBlocks()</a>, <a class="el" href="rps_8cpp_source.html#l00114">CMultiAligner::x_RealignBlocks()</a>, <a class="el" href="rps_8cpp_source.html#l00664">CMultiAligner::x_SetDomainHits()</a>, and <a class="el" href="cobalt_8cpp_source.html#l00159">CMultiAligner::x_ValidateUserHits()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ab47f81d0ca3eaaa1891c7770ae0af530">&#9670;&nbsp;</a></span>m_SeqRange1</h2>
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<td class="memname"><a class="el" href="base_8hpp.html#a82668c1a5428e2d884d0f0c67d97fdf1">TRange</a> CHit::m_SeqRange1</td>
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<p>The range of offsets on the first sequence. </p>
<p class="definition">Definition at line <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00107">107</a> of file <a class="el" href="algo_2cobalt_2hit_8hpp_source.html">hit.hpp</a>.</p>
<p class="reference">Referenced by <a class="el" href="hit_8cpp_source.html#l00087">AddUpSubHits()</a>, <a class="el" href="hit_8cpp_source.html#l00378">Clone()</a>, <a class="el" href="cobalt__unit__test_8cpp_source.html#l00162">CMultiAlignerTest::CompareDomainHits()</a>, <a class="el" href="hit_8cpp_source.html#l00145">GetRangeFromSeq1()</a>, <a class="el" href="hit_8cpp_source.html#l00109">GetRangeFromSeq2()</a>, <a class="el" href="hitlist_8cpp_source.html#l00098">CHitList::MakeCanonical()</a>, <a class="el" href="hitlist_8cpp_source.html#l00221">CHitList::MatchOverlappingSubHits()</a>, <a class="el" href="hit_8cpp_source.html#l00285">ResolveSubHitConflicts()</a>, <a class="el" href="hit_8cpp_source.html#l00180">VerifyHit()</a>, <a class="el" href="prog_8cpp_source.html#l00051">x_AddConstraint()</a>, <a class="el" href="rps_8cpp_source.html#l00512">CMultiAligner::x_AssignRPSResFreqs()</a>, <a class="el" href="prog_8cpp_source.html#l01812">CMultiAligner::x_BuildAlignmentIterative()</a>, <a class="el" href="seg_8cpp_source.html#l00052">CMultiAligner::x_FindBestPath()</a>, <a class="el" href="seg_8cpp_source.html#l00175">CMultiAligner::x_FindConsistentHitSubset()</a>, <a class="el" href="prog_8cpp_source.html#l00382">CMultiAligner::x_FindConstraints()</a>, <a class="el" href="rps_8cpp_source.html#l00866">CMultiAligner::x_FindDomainHits()</a>, <a class="el" href="prog_8cpp_source.html#l00700">CMultiAligner::x_FindInClusterConstraints()</a>, <a class="el" href="blast_8cpp_source.html#l00306">CMultiAligner::x_FindLocalHits()</a>, <a class="el" href="blast_8cpp_source.html#l00481">CMultiAligner::x_FindLocalInClusterHits()</a>, <a class="el" href="phi_8cpp_source.html#l00062">CMultiAligner::x_FindPatternHits()</a>, <a class="el" href="rps_8cpp_source.html#l00411">CMultiAligner::x_FindRPSHits()</a>, <a class="el" href="dist_8cpp_source.html#l00074">CDistances::x_GetSelfScores()</a>, <a class="el" href="blast_8cpp_source.html#l00095">CMultiAligner::x_MakeFillerBlocks()</a>, <a class="el" href="rps_8cpp_source.html#l00114">CMultiAligner::x_RealignBlocks()</a>, <a class="el" href="hit_8cpp_source.html#l00222">x_RemoveEnvelopedSubHits()</a>, <a class="el" href="rps_8cpp_source.html#l00664">CMultiAligner::x_SetDomainHits()</a>, and <a class="el" href="cobalt_8cpp_source.html#l00159">CMultiAligner::x_ValidateUserHits()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ad3dfe32864b86dde081aa629561b9fc6">&#9670;&nbsp;</a></span>m_SeqRange2</h2>
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<td class="memname"><a class="el" href="base_8hpp.html#a82668c1a5428e2d884d0f0c67d97fdf1">TRange</a> CHit::m_SeqRange2</td>
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<p>The range of offsets on the second sequence. </p>
<p class="definition">Definition at line <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00110">110</a> of file <a class="el" href="algo_2cobalt_2hit_8hpp_source.html">hit.hpp</a>.</p>
<p class="reference">Referenced by <a class="el" href="hit_8cpp_source.html#l00087">AddUpSubHits()</a>, <a class="el" href="hit_8cpp_source.html#l00378">Clone()</a>, <a class="el" href="cobalt__unit__test_8cpp_source.html#l00162">CMultiAlignerTest::CompareDomainHits()</a>, <a class="el" href="hit_8cpp_source.html#l00145">GetRangeFromSeq1()</a>, <a class="el" href="hit_8cpp_source.html#l00109">GetRangeFromSeq2()</a>, <a class="el" href="hitlist_8cpp_source.html#l00098">CHitList::MakeCanonical()</a>, <a class="el" href="hitlist_8cpp_source.html#l00221">CHitList::MatchOverlappingSubHits()</a>, <a class="el" href="hit_8cpp_source.html#l00285">ResolveSubHitConflicts()</a>, <a class="el" href="hit_8cpp_source.html#l00180">VerifyHit()</a>, <a class="el" href="prog_8cpp_source.html#l00051">x_AddConstraint()</a>, <a class="el" href="rps_8cpp_source.html#l00512">CMultiAligner::x_AssignRPSResFreqs()</a>, <a class="el" href="seg_8cpp_source.html#l00052">CMultiAligner::x_FindBestPath()</a>, <a class="el" href="seg_8cpp_source.html#l00175">CMultiAligner::x_FindConsistentHitSubset()</a>, <a class="el" href="prog_8cpp_source.html#l00382">CMultiAligner::x_FindConstraints()</a>, <a class="el" href="rps_8cpp_source.html#l00866">CMultiAligner::x_FindDomainHits()</a>, <a class="el" href="prog_8cpp_source.html#l00700">CMultiAligner::x_FindInClusterConstraints()</a>, <a class="el" href="blast_8cpp_source.html#l00306">CMultiAligner::x_FindLocalHits()</a>, <a class="el" href="blast_8cpp_source.html#l00481">CMultiAligner::x_FindLocalInClusterHits()</a>, <a class="el" href="phi_8cpp_source.html#l00062">CMultiAligner::x_FindPatternHits()</a>, <a class="el" href="rps_8cpp_source.html#l00411">CMultiAligner::x_FindRPSHits()</a>, <a class="el" href="dist_8cpp_source.html#l00074">CDistances::x_GetSelfScores()</a>, <a class="el" href="blast_8cpp_source.html#l00095">CMultiAligner::x_MakeFillerBlocks()</a>, <a class="el" href="hitlist_8cpp_source.html#l00162">x_MatchSubHits()</a>, <a class="el" href="rps_8cpp_source.html#l00114">CMultiAligner::x_RealignBlocks()</a>, <a class="el" href="rps_8cpp_source.html#l00664">CMultiAligner::x_SetDomainHits()</a>, and <a class="el" href="cobalt_8cpp_source.html#l00159">CMultiAligner::x_ValidateUserHits()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a144a490ceee55ccbfac5823df6c35aa3">&#9670;&nbsp;</a></span>m_SubHit</h2>
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<td class="memname">vector&lt;<a class="el" href="classCHit.html">CHit</a> *&gt; CHit::m_SubHit</td>
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<p>Subhits for this alignment. </p>
<p class="definition">Definition at line <a class="el" href="algo_2cobalt_2hit_8hpp_source.html#l00268">268</a> of file <a class="el" href="algo_2cobalt_2hit_8hpp_source.html">hit.hpp</a>.</p>
<p class="reference">Referenced by <a class="el" href="hit_8cpp_source.html#l00087">AddUpSubHits()</a>, and <a class="el" href="hit_8cpp_source.html#l00285">ResolveSubHitConflicts()</a>.</p>
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<hr/>The documentation for this class was generated from the following files:<ul>
<li>include/algo/cobalt/<a class="el" href="algo_2cobalt_2hit_8hpp_source.html">hit.hpp</a></li>
<li>src/algo/cobalt/<a class="el" href="hit_8cpp_source.html">hit.cpp</a></li>
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<address style="align: right;"><small>Modified on Fri Sep 20 14:58:07 2024 by modify_doxy.py rev. 669887</small></address>
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