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<div class="textblock"><code>#include &quot;squid/squid.h&quot;</code><br />
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<p><a href="seq_8h_source.html">Go to the source code of this file.</a></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
Data Structures</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structmseq__t.html">mseq_t</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">structure for storing multiple sequences  <a href="structmseq__t.html#details">More...</a><br /></td></tr>
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Macros</h2></td></tr>
<tr class="memitem:a03dbc4840c83155125914ed849f74416"><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a03dbc4840c83155125914ed849f74416">SEQTYPE_UNKNOWN</a>&#160;&#160;&#160;kOtherSeq</td></tr>
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<tr class="memitem:af455eb393971ad3ce026bda535abc82c"><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#af455eb393971ad3ce026bda535abc82c">SEQTYPE_RNA</a>&#160;&#160;&#160;kRNA</td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="func-members"></a>
Functions</h2></td></tr>
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<tr class="memdesc:a7fa5b7c740c8906424057c112b192088"><td class="mdescLeft">&#160;</td><td class="mdescRight">Stripped down version of squid's alistat.  <a href="#a7fa5b7c740c8906424057c112b192088">More...</a><br /></td></tr>
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<tr class="memitem:a27f31ca0bdcd5b52610651b7e0e52cd7"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a27f31ca0bdcd5b52610651b7e0e52cd7">AddSeq</a> (<a class="el" href="structmseq__t.html">mseq_t</a> **prMSeqDest_p, char *pcSeqName, char *pcSeqRes)</td></tr>
<tr class="memdesc:a27f31ca0bdcd5b52610651b7e0e52cd7"><td class="mdescLeft">&#160;</td><td class="mdescRight">Creates a new sequence entry and appends it to an existing mseq structure.  <a href="#a27f31ca0bdcd5b52610651b7e0e52cd7">More...</a><br /></td></tr>
<tr class="separator:a27f31ca0bdcd5b52610651b7e0e52cd7"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a593f05a8f9329d0409320fed313c720c"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a593f05a8f9329d0409320fed313c720c">SeqSwap</a> (<a class="el" href="structmseq__t.html">mseq_t</a> *mseq, int i, int j)</td></tr>
<tr class="memdesc:a593f05a8f9329d0409320fed313c720c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Swap two sequences in an <a class="el" href="structmseq__t.html" title="structure for storing multiple sequences ">mseq_t</a> structure.  <a href="#a593f05a8f9329d0409320fed313c720c">More...</a><br /></td></tr>
<tr class="separator:a593f05a8f9329d0409320fed313c720c"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a0533ef67eccd9c952b43d53072e9a1f1"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a0533ef67eccd9c952b43d53072e9a1f1">DealignMSeq</a> (<a class="el" href="structmseq__t.html">mseq_t</a> *mseq)</td></tr>
<tr class="memdesc:a0533ef67eccd9c952b43d53072e9a1f1"><td class="mdescLeft">&#160;</td><td class="mdescRight">Dealigns all sequences in mseq structure, updates the sequence length info and sets aligned to FALSE.  <a href="#a0533ef67eccd9c952b43d53072e9a1f1">More...</a><br /></td></tr>
<tr class="separator:a0533ef67eccd9c952b43d53072e9a1f1"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a30c7f4d7600fec2eaa564df74cac731a"><td class="memItemLeft" align="right" valign="top">const char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a30c7f4d7600fec2eaa564df74cac731a">SeqTypeToStr</a> (int seqtype)</td></tr>
<tr class="memdesc:a30c7f4d7600fec2eaa564df74cac731a"><td class="mdescLeft">&#160;</td><td class="mdescRight">convert int-encoded iSeqType to string  <a href="#a30c7f4d7600fec2eaa564df74cac731a">More...</a><br /></td></tr>
<tr class="separator:a30c7f4d7600fec2eaa564df74cac731a"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a853633b9627f9048adf1e5000a6a0916"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a853633b9627f9048adf1e5000a6a0916">ReadSequences</a> (<a class="el" href="structmseq__t.html">mseq_t</a> *prMSeq_p, char *pcSeqFile, int iSeqType, int iSeqFmt, bool bIsProfile, bool bDealignInputSeqs, int iMaxNumSeq, int iMaxSeqLen, char *pcHMMBatch)</td></tr>
<tr class="memdesc:a853633b9627f9048adf1e5000a6a0916"><td class="mdescLeft">&#160;</td><td class="mdescRight">reads sequences from file  <a href="#a853633b9627f9048adf1e5000a6a0916">More...</a><br /></td></tr>
<tr class="separator:a853633b9627f9048adf1e5000a6a0916"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:af60f55dd9f9840f54bf5057d3ab90d42"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#af60f55dd9f9840f54bf5057d3ab90d42">NewMSeq</a> (<a class="el" href="structmseq__t.html">mseq_t</a> **mseq)</td></tr>
<tr class="memdesc:af60f55dd9f9840f54bf5057d3ab90d42"><td class="mdescLeft">&#160;</td><td class="mdescRight">allocate and initialise new <a class="el" href="structmseq__t.html" title="structure for storing multiple sequences ">mseq_t</a>  <a href="#af60f55dd9f9840f54bf5057d3ab90d42">More...</a><br /></td></tr>
<tr class="separator:af60f55dd9f9840f54bf5057d3ab90d42"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:abb8e94cbbfa6f0b8e527f7107c09ae65"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#abb8e94cbbfa6f0b8e527f7107c09ae65">FreeMSeq</a> (<a class="el" href="structmseq__t.html">mseq_t</a> **mseq)</td></tr>
<tr class="memdesc:abb8e94cbbfa6f0b8e527f7107c09ae65"><td class="mdescLeft">&#160;</td><td class="mdescRight">Frees an <a class="el" href="structmseq__t.html" title="structure for storing multiple sequences ">mseq_t</a> and it's members and zeros all members.  <a href="#abb8e94cbbfa6f0b8e527f7107c09ae65">More...</a><br /></td></tr>
<tr class="separator:abb8e94cbbfa6f0b8e527f7107c09ae65"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a6b124a1118f2276d2a2978227efd0ab4"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a6b124a1118f2276d2a2978227efd0ab4">CopyMSeq</a> (<a class="el" href="structmseq__t.html">mseq_t</a> **prMSeqDest_p, <a class="el" href="structmseq__t.html">mseq_t</a> *prMSeqSrc)</td></tr>
<tr class="memdesc:a6b124a1118f2276d2a2978227efd0ab4"><td class="mdescLeft">&#160;</td><td class="mdescRight">copies an mseq structure  <a href="#a6b124a1118f2276d2a2978227efd0ab4">More...</a><br /></td></tr>
<tr class="separator:a6b124a1118f2276d2a2978227efd0ab4"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a6b1d0d3e408720aa012f66f34f740262"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a6b1d0d3e408720aa012f66f34f740262">LogSqInfo</a> (SQINFO *sqinfo)</td></tr>
<tr class="memdesc:a6b1d0d3e408720aa012f66f34f740262"><td class="mdescLeft">&#160;</td><td class="mdescRight">debug output of sqinfo struct  <a href="#a6b1d0d3e408720aa012f66f34f740262">More...</a><br /></td></tr>
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<tr class="memitem:a720cb218cff78249b898f4c56a9fee6c"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a720cb218cff78249b898f4c56a9fee6c">FindSeqName</a> (char *seqname, <a class="el" href="structmseq__t.html">mseq_t</a> *mseq)</td></tr>
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<tr class="memitem:ad84a0cdc0c49df96ef9ef97a053f841e"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#ad84a0cdc0c49df96ef9ef97a053f841e">WriteAlignment</a> (<a class="el" href="structmseq__t.html">mseq_t</a> *mseq, const char *aln_outfile, int msafile_format, int iWrap, bool bResno)</td></tr>
<tr class="memdesc:ad84a0cdc0c49df96ef9ef97a053f841e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Write alignment to file.  <a href="#ad84a0cdc0c49df96ef9ef97a053f841e">More...</a><br /></td></tr>
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<tr class="memitem:a8a10a512577076df441dc133f7eb13d4"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a8a10a512577076df441dc133f7eb13d4">DealignSeq</a> (char *seq)</td></tr>
<tr class="memdesc:a8a10a512577076df441dc133f7eb13d4"><td class="mdescLeft">&#160;</td><td class="mdescRight">Removes all gap-characters from a sequence.  <a href="#a8a10a512577076df441dc133f7eb13d4">More...</a><br /></td></tr>
<tr class="separator:a8a10a512577076df441dc133f7eb13d4"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a38db9b206246a53873459ff7f1eace06"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a38db9b206246a53873459ff7f1eace06">ShuffleMSeq</a> (<a class="el" href="structmseq__t.html">mseq_t</a> *prMSeq)</td></tr>
<tr class="memdesc:a38db9b206246a53873459ff7f1eace06"><td class="mdescLeft">&#160;</td><td class="mdescRight">Shuffle mseq order.  <a href="#a38db9b206246a53873459ff7f1eace06">More...</a><br /></td></tr>
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<tr class="memitem:a3f29666b8ab80ed563d96fdbfd681e9f"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a3f29666b8ab80ed563d96fdbfd681e9f">SortMSeqByLength</a> (<a class="el" href="structmseq__t.html">mseq_t</a> *prMSeq, const char cOrder)</td></tr>
<tr class="memdesc:a3f29666b8ab80ed563d96fdbfd681e9f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sort sequences by length.  <a href="#a3f29666b8ab80ed563d96fdbfd681e9f">More...</a><br /></td></tr>
<tr class="separator:a3f29666b8ab80ed563d96fdbfd681e9f"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aa7c161c1402bdeb514c97a1ba287819a"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#aa7c161c1402bdeb514c97a1ba287819a">JoinMSeqs</a> (<a class="el" href="structmseq__t.html">mseq_t</a> **prMSeqDest_p, <a class="el" href="structmseq__t.html">mseq_t</a> *prMSeqToAdd)</td></tr>
<tr class="memdesc:aa7c161c1402bdeb514c97a1ba287819a"><td class="mdescLeft">&#160;</td><td class="mdescRight">Appends an mseq structure to an already existing one. filename will be left untouched.  <a href="#aa7c161c1402bdeb514c97a1ba287819a">More...</a><br /></td></tr>
<tr class="separator:aa7c161c1402bdeb514c97a1ba287819a"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a5ffded23e75f2ba58bcfdb024e8d1b92"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a5ffded23e75f2ba58bcfdb024e8d1b92">SeqsAreAligned</a> (<a class="el" href="structmseq__t.html">mseq_t</a> *prMSeq, bool bIsProfile, bool bDealignInputSeqs)</td></tr>
<tr class="memdesc:a5ffded23e75f2ba58bcfdb024e8d1b92"><td class="mdescLeft">&#160;</td><td class="mdescRight">Checks if sequences in given mseq structure are aligned. By definition this is only true, if sequences are of the same length and at least one gap was found.  <a href="#a5ffded23e75f2ba58bcfdb024e8d1b92">More...</a><br /></td></tr>
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<h2 class="groupheader">Macro Definition Documentation</h2>
<a id="af396304082d44225e44933577c320e43"></a>
<h2 class="memtitle"><span class="permalink"><a href="#af396304082d44225e44933577c320e43">&sect;&nbsp;</a></span>AMINOACID_ANY</h2>

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          <td class="memname">#define AMINOACID_ANY&#160;&#160;&#160;'X'</td>
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<a id="acf7121d916e81f2ee9ac83680434bb9a"></a>
<h2 class="memtitle"><span class="permalink"><a href="#acf7121d916e81f2ee9ac83680434bb9a">&sect;&nbsp;</a></span>NUCLEOTIDE_ANY</h2>

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          <td class="memname">#define NUCLEOTIDE_ANY&#160;&#160;&#160;'N'</td>
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<a id="a5e07e6c291f096c3e6b6e8cda4efb37b"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a5e07e6c291f096c3e6b6e8cda4efb37b">&sect;&nbsp;</a></span>SEQTYPE_DNA</h2>

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          <td class="memname">#define SEQTYPE_DNA&#160;&#160;&#160;kDNA</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a193343bb1bec0dd172e9b24b9b13c077">&sect;&nbsp;</a></span>SEQTYPE_PROTEIN</h2>

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          <td class="memname">#define SEQTYPE_PROTEIN&#160;&#160;&#160;kAmino</td>
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<h2 class="memtitle"><span class="permalink"><a href="#af455eb393971ad3ce026bda535abc82c">&sect;&nbsp;</a></span>SEQTYPE_RNA</h2>

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          <td class="memname">#define SEQTYPE_RNA&#160;&#160;&#160;kRNA</td>
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<a id="a03dbc4840c83155125914ed849f74416"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a03dbc4840c83155125914ed849f74416">&sect;&nbsp;</a></span>SEQTYPE_UNKNOWN</h2>

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          <td class="memname">#define SEQTYPE_UNKNOWN&#160;&#160;&#160;kOtherSeq</td>
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<p>int-encoded sequence types. these are in sync with squid's seqtypes and only used for convenience here </p>

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<h2 class="groupheader">Function Documentation</h2>
<a id="a27f31ca0bdcd5b52610651b7e0e52cd7"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a27f31ca0bdcd5b52610651b7e0e52cd7">&sect;&nbsp;</a></span>AddSeq()</h2>

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          <td class="memname">void AddSeq </td>
          <td>(</td>
          <td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> **&#160;</td>
          <td class="paramname"><em>prMSeqDest_p</em>, </td>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">char *&#160;</td>
          <td class="paramname"><em>pcSeqName</em>, </td>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">char *&#160;</td>
          <td class="paramname"><em>pcSeqRes</em>&#160;</td>
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        <tr>
          <td></td>
          <td>)</td>
          <td></td><td></td>
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<p>Creates a new sequence entry and appends it to an existing mseq structure. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[out]</td><td class="paramname">prMSeqDest_p</td><td>Already existing and initialised mseq structure </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">pcSeqName</td><td>sequence name of the sequence to add </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">pcSeqRes</td><td>the actual sequence (residues) to add</td></tr>
  </table>
  </dd>
</dl>
<dl class="section note"><dt>Note</dt><dd>Don't forget to update the align and type flag if necessary!</dd></dl>
<p>FIXME allow adding of more features </p>

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<h2 class="memtitle"><span class="permalink"><a href="#a7fa5b7c740c8906424057c112b192088">&sect;&nbsp;</a></span>AliStat()</h2>

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          <td class="memname">void AliStat </td>
          <td>(</td>
          <td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> *&#160;</td>
          <td class="paramname"><em>prMSeq</em>, </td>
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        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">bool&#160;</td>
          <td class="paramname"><em>bSampling</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">bool&#160;</td>
          <td class="paramname"><em>bReportAll</em>&#160;</td>
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          <td></td>
          <td>)</td>
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<p>Stripped down version of squid's alistat. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in]</td><td class="paramname">prMSeq</td><td>The alignment to analyse </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">bSampling</td><td>For many sequences: samples from pool </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">bReportAll</td><td>Report identities for all sequence pairs</td></tr>
  </table>
  </dd>
</dl>
<p>Don't have to worry about sequence case because our version of PairwiseIdentity is case insensitive </p>
<p>mseq to squid msa</p>
<p>FIXME code overlap with WriteAlignment. Make it a function and take code there (contains more comments) as template</p>

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<h2 class="memtitle"><span class="permalink"><a href="#a6b124a1118f2276d2a2978227efd0ab4">&sect;&nbsp;</a></span>CopyMSeq()</h2>

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          <td class="memname">void CopyMSeq </td>
          <td>(</td>
          <td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> **&#160;</td>
          <td class="paramname"><em>prMSeqDest_p</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> *&#160;</td>
          <td class="paramname"><em>prMSeqSrc</em>&#160;</td>
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          <td></td>
          <td>)</td>
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<p>copies an mseq structure </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[out]</td><td class="paramname">prMSeqDest_p</td><td>Copy of mseq structure </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">prMSeqSrc</td><td>Source mseq structure to copy</td></tr>
  </table>
  </dd>
</dl>
<dl class="section note"><dt>Note</dt><dd>caller has to free copy by calling <a class="el" href="seq_8c.html#abb8e94cbbfa6f0b8e527f7107c09ae65" title="Frees an mseq_t and it&#39;s members and zeros all members. ">FreeMSeq()</a> </dd></dl>

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<a id="a0533ef67eccd9c952b43d53072e9a1f1"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a0533ef67eccd9c952b43d53072e9a1f1">&sect;&nbsp;</a></span>DealignMSeq()</h2>

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          <td class="memname">void DealignMSeq </td>
          <td>(</td>
          <td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> *&#160;</td>
          <td class="paramname"><em>mseq</em></td><td>)</td>
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<p>Dealigns all sequences in mseq structure, updates the sequence length info and sets aligned to FALSE. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[out]</td><td class="paramname">mseq</td><td>The mseq structure to dealign </td></tr>
  </table>
  </dd>
</dl>

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<a id="a8a10a512577076df441dc133f7eb13d4"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a8a10a512577076df441dc133f7eb13d4">&sect;&nbsp;</a></span>DealignSeq()</h2>

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          <td class="memname">void DealignSeq </td>
          <td>(</td>
          <td class="paramtype">char *&#160;</td>
          <td class="paramname"><em>seq</em></td><td>)</td>
          <td></td>
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<p>Removes all gap-characters from a sequence. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[out]</td><td class="paramname">seq</td><td>Sequence to dealign</td></tr>
  </table>
  </dd>
</dl>
<dl class="section note"><dt>Note</dt><dd>seq will not be reallocated </dd></dl>

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<h2 class="memtitle"><span class="permalink"><a href="#a720cb218cff78249b898f4c56a9fee6c">&sect;&nbsp;</a></span>FindSeqName()</h2>

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          <td class="memname">int FindSeqName </td>
          <td>(</td>
          <td class="paramtype">char *&#160;</td>
          <td class="paramname"><em>seqname</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> *&#160;</td>
          <td class="paramname"><em>mseq</em>&#160;</td>
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        <tr>
          <td></td>
          <td>)</td>
          <td></td><td></td>
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<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in]</td><td class="paramname">seqname</td><td>The sequence name to search for </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">mseq</td><td>The multiple sequence structure to search in</td></tr>
  </table>
  </dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>-1 on failure, sequence index of matching name otherwise</dd></dl>
<dl class="section warning"><dt>Warning</dt><dd>If sequence name happens to be used twice, only the first one will be reported back </dd></dl>

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<a id="abb8e94cbbfa6f0b8e527f7107c09ae65"></a>
<h2 class="memtitle"><span class="permalink"><a href="#abb8e94cbbfa6f0b8e527f7107c09ae65">&sect;&nbsp;</a></span>FreeMSeq()</h2>

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          <td class="memname">void FreeMSeq </td>
          <td>(</td>
          <td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> **&#160;</td>
          <td class="paramname"><em>mseq</em></td><td>)</td>
          <td></td>
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      </table>
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<p>Frees an <a class="el" href="structmseq__t.html" title="structure for storing multiple sequences ">mseq_t</a> and it's members and zeros all members. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in]</td><td class="paramname">mseq</td><td>mseq_to to free</td></tr>
  </table>
  </dd>
</dl>
<dl class="section note"><dt>Note</dt><dd>use in conjunction with <a class="el" href="seq_8c.html#a7dcd309007c753f509c6589475229c11" title="allocate and initialise new mseq_t ">NewMSeq()</a> </dd></dl>
<dl class="section see"><dt>See also</dt><dd>new_mseq </dd></dl>

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<h2 class="memtitle"><span class="permalink"><a href="#aa7c161c1402bdeb514c97a1ba287819a">&sect;&nbsp;</a></span>JoinMSeqs()</h2>

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          <td class="memname">void JoinMSeqs </td>
          <td>(</td>
          <td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> **&#160;</td>
          <td class="paramname"><em>prMSeqDest_p</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> *&#160;</td>
          <td class="paramname"><em>prMSeqToAdd</em>&#160;</td>
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          <td></td>
          <td>)</td>
          <td></td><td></td>
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<p>Appends an mseq structure to an already existing one. filename will be left untouched. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in]</td><td class="paramname">prMSeqDest_p</td><td>MSeq structure to which to append to </td></tr>
    <tr><td class="paramdir">[out]</td><td class="paramname">prMSeqToAdd</td><td>MSeq structure which is to append </td></tr>
  </table>
  </dd>
</dl>

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<h2 class="memtitle"><span class="permalink"><a href="#a6b1d0d3e408720aa012f66f34f740262">&sect;&nbsp;</a></span>LogSqInfo()</h2>

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          <td class="memname">void LogSqInfo </td>
          <td>(</td>
          <td class="paramtype">SQINFO *&#160;</td>
          <td class="paramname"><em>sqinfo</em></td><td>)</td>
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<p>debug output of sqinfo struct </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in]</td><td class="paramname">sqinfo</td><td>Squid's SQINFO struct for a certain seqeuence</td></tr>
  </table>
  </dd>
</dl>
<dl class="section note"><dt>Note</dt><dd>useful for debugging only </dd></dl>

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<h2 class="memtitle"><span class="permalink"><a href="#af60f55dd9f9840f54bf5057d3ab90d42">&sect;&nbsp;</a></span>NewMSeq()</h2>

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          <td class="memname">void NewMSeq </td>
          <td>(</td>
          <td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> **&#160;</td>
          <td class="paramname"><em>prMSeq</em></td><td>)</td>
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<p>allocate and initialise new <a class="el" href="structmseq__t.html" title="structure for storing multiple sequences ">mseq_t</a> </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[out]</td><td class="paramname">prMSeq</td><td>newly allocated and initialised <a class="el" href="structmseq__t.html" title="structure for storing multiple sequences ">mseq_t</a></td></tr>
  </table>
  </dd>
</dl>
<dl class="section note"><dt>Note</dt><dd>caller has to free by calling <a class="el" href="seq_8c.html#abb8e94cbbfa6f0b8e527f7107c09ae65" title="Frees an mseq_t and it&#39;s members and zeros all members. ">FreeMSeq()</a></dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="seq_8c.html#abb8e94cbbfa6f0b8e527f7107c09ae65" title="Frees an mseq_t and it&#39;s members and zeros all members. ">FreeMSeq</a> </dd></dl>

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<h2 class="memtitle"><span class="permalink"><a href="#a853633b9627f9048adf1e5000a6a0916">&sect;&nbsp;</a></span>ReadSequences()</h2>

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          <td class="memname">int ReadSequences </td>
          <td>(</td>
          <td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> *&#160;</td>
          <td class="paramname"><em>prMSeq</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">char *&#160;</td>
          <td class="paramname"><em>seqfile</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">int&#160;</td>
          <td class="paramname"><em>iSeqType</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">int&#160;</td>
          <td class="paramname"><em>iSeqFmt</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">bool&#160;</td>
          <td class="paramname"><em>bIsProfile</em>, </td>
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        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">bool&#160;</td>
          <td class="paramname"><em>bDealignInputSeqs</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">int&#160;</td>
          <td class="paramname"><em>iMaxNumSeq</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">int&#160;</td>
          <td class="paramname"><em>iMaxSeqLen</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">char *&#160;</td>
          <td class="paramname"><em>pcHMMBatch</em>&#160;</td>
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        <tr>
          <td></td>
          <td>)</td>
          <td></td><td></td>
        </tr>
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<p>reads sequences from file </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[out]</td><td class="paramname">prMSeq</td><td>Multiple sequence struct. Must be preallocated. FIXME: would make more sense to allocate it here. </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">seqfile</td><td>Sequence file name. If '-' sequence will be read from stdin. </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">iSeqType</td><td>int-encoded sequence type. Set to SEQTYPE_UNKNOWN for autodetect (guessed from first sequence) </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">iMaxNumSeq</td><td>Return an error, if more than iMaxNumSeq have been read </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">iMaxSeqLen</td><td>Return an error, if a seq longer than iMaxSeqLen has been read</td></tr>
  </table>
  </dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>0 on success, -1 on error</dd></dl>
<dl class="section note"><dt>Note</dt><dd><ul>
<li>Depends heavily on squid</li>
<li>Sequence file format will be guessed</li>
<li>If supported by squid, gzipped files can be read as well. </li>
</ul>
</dd></dl>

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<h2 class="memtitle"><span class="permalink"><a href="#a5ffded23e75f2ba58bcfdb024e8d1b92">&sect;&nbsp;</a></span>SeqsAreAligned()</h2>

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          <td class="memname">bool SeqsAreAligned </td>
          <td>(</td>
          <td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> *&#160;</td>
          <td class="paramname"><em>prMSeq</em>, </td>
        </tr>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">bool&#160;</td>
          <td class="paramname"><em>bIsProfile</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">bool&#160;</td>
          <td class="paramname"><em>bDealignInputSeqs</em>&#160;</td>
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          <td></td>
          <td>)</td>
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<p>Checks if sequences in given mseq structure are aligned. By definition this is only true, if sequences are of the same length and at least one gap was found. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in]</td><td class="paramname">prMSeq</td><td>Sequences to check</td></tr>
  </table>
  </dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>TRUE if sequences are aligned, FALSE if not </dd></dl>

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<h2 class="memtitle"><span class="permalink"><a href="#a593f05a8f9329d0409320fed313c720c">&sect;&nbsp;</a></span>SeqSwap()</h2>

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          <td class="memname">void SeqSwap </td>
          <td>(</td>
          <td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> *&#160;</td>
          <td class="paramname"><em>prMSeq</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">int&#160;</td>
          <td class="paramname"><em>i</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">int&#160;</td>
          <td class="paramname"><em>j</em>&#160;</td>
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          <td></td>
          <td>)</td>
          <td></td><td></td>
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<p>Swap two sequences in an <a class="el" href="structmseq__t.html" title="structure for storing multiple sequences ">mseq_t</a> structure. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[out]</td><td class="paramname">prMSeq</td><td>Multiple sequence struct </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">i</td><td>Index of first sequence </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">j</td><td>Index of seconds sequence </td></tr>
  </table>
  </dd>
</dl>

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<h2 class="memtitle"><span class="permalink"><a href="#a30c7f4d7600fec2eaa564df74cac731a">&sect;&nbsp;</a></span>SeqTypeToStr()</h2>

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          <td class="memname">const char* SeqTypeToStr </td>
          <td>(</td>
          <td class="paramtype">int&#160;</td>
          <td class="paramname"><em>iSeqType</em></td><td>)</td>
          <td></td>
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<p>convert int-encoded iSeqType to string </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in]</td><td class="paramname">iSeqType</td><td>int-encoded sequence type</td></tr>
  </table>
  </dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>character pointer describing the sequence type </dd></dl>

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<h2 class="memtitle"><span class="permalink"><a href="#a38db9b206246a53873459ff7f1eace06">&sect;&nbsp;</a></span>ShuffleMSeq()</h2>

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          <td class="memname">void ShuffleMSeq </td>
          <td>(</td>
          <td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> *&#160;</td>
          <td class="paramname"><em>mseq</em></td><td>)</td>
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<p>Shuffle mseq order. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[out]</td><td class="paramname">mseq</td><td>mseq structure to shuffle </td></tr>
  </table>
  </dd>
</dl>

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<h2 class="memtitle"><span class="permalink"><a href="#a3f29666b8ab80ed563d96fdbfd681e9f">&sect;&nbsp;</a></span>SortMSeqByLength()</h2>

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          <td class="memname">void SortMSeqByLength </td>
          <td>(</td>
          <td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> *&#160;</td>
          <td class="paramname"><em>prMSeq</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const char&#160;</td>
          <td class="paramname"><em>cOrder</em>&#160;</td>
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        <tr>
          <td></td>
          <td>)</td>
          <td></td><td></td>
        </tr>
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<p>Sort sequences by length. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[out]</td><td class="paramname">prMSeq</td><td>mseq to sort by length </td></tr>
    <tr><td class="paramdir">[out]</td><td class="paramname">cOrder</td><td>Sorting order. 'd' for descending, 'a' for ascending. </td></tr>
  </table>
  </dd>
</dl>

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<h2 class="memtitle"><span class="permalink"><a href="#ad84a0cdc0c49df96ef9ef97a053f841e">&sect;&nbsp;</a></span>WriteAlignment()</h2>

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          <td class="memname">int WriteAlignment </td>
          <td>(</td>
          <td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> *&#160;</td>
          <td class="paramname"><em>mseq</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const char *&#160;</td>
          <td class="paramname"><em>pcAlnOutfile</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">int&#160;</td>
          <td class="paramname"><em>outfmt</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">int&#160;</td>
          <td class="paramname"><em>iWrap</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">bool&#160;</td>
          <td class="paramname"><em>bResno</em>&#160;</td>
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          <td></td>
          <td>)</td>
          <td></td><td></td>
        </tr>
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<p>Write alignment to file. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in]</td><td class="paramname">mseq</td><td>The <a class="el" href="structmseq__t.html" title="structure for storing multiple sequences ">mseq_t</a> struct containing the aligned sequences </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">pcAlnOutfile</td><td>The name of the output file </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">outfmt</td><td>The alignment output format (defined in squid.h) </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">iWrap</td><td>length of line for Clustal/Fasta format</td></tr>
  </table>
  </dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>Non-zero on error</dd></dl>
<dl class="section note"><dt>Note</dt><dd>We create a temporary squid MSA struct in here because we never use it within clustal. We might be better of using the old clustal output routines instead. </dd></dl>

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