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<li class="navelem"><a class="el" href="dir_0aa59dc4e14f78a2ec16bea9baba3f8e.html">alignment</a></li> </ul>
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<div class="headertitle"><div class="title">alignment.h</div></div>
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<div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span><span class="preprocessor">#pragma once</span></div>
<div class="line"><a id="l00002" name="l00002"></a><span class="lineno"> 2</span><span class="preprocessor">#include &quot;alignmentbase.h&quot;</span></div>
<div class="line"><a id="l00003" name="l00003"></a><span class="lineno"> 3</span> </div>
<div class="line"><a id="l00004" name="l00004"></a><span class="lineno"> 4</span><span class="keyword">namespace </span>cmaple</div>
<div class="line"><a id="l00005" name="l00005"></a><span class="lineno"> 5</span>{</div>
<div class="line"><a id="l00007" name="l00007"></a><span class="lineno"><a class="line" href="classcmaple_1_1_alignment.html"> 7</a></span> <span class="keyword">class </span><a class="code hl_class" href="classcmaple_1_1_alignment.html">Alignment</a> {</div>
<div class="line"><a id="l00008" name="l00008"></a><span class="lineno"> 8</span> <span class="keyword">public</span>:</div>
<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"><a class="line" href="classcmaple_1_1_alignment.html#a6701d29a81fb5dd4149c5c5237b095de"> 15</a></span> <a class="code hl_function" href="classcmaple_1_1_alignment.html#a6701d29a81fb5dd4149c5c5237b095de">Alignment</a>(std::istream&amp; aln_stream, <span class="keyword">const</span> std::string&amp; ref_seq = <span class="stringliteral">&quot;&quot;</span>, <span class="keyword">const</span> std::string&amp; format = <span class="stringliteral">&quot;&quot;</span>, <span class="keyword">const</span> std::string&amp; seqtype = <span class="stringliteral">&quot;&quot;</span>);</div>
<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span> </div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"><a class="line" href="classcmaple_1_1_alignment.html#a857b7e7f683234ec9c0afb54da04e8c0"> 23</a></span> <a class="code hl_function" href="classcmaple_1_1_alignment.html#a857b7e7f683234ec9c0afb54da04e8c0">Alignment</a>(<span class="keyword">const</span> std::string&amp; aln_filename, <span class="keyword">const</span> std::string&amp; ref_seq = <span class="stringliteral">&quot;&quot;</span>, <span class="keyword">const</span> std::string&amp; format = <span class="stringliteral">&quot;&quot;</span>, <span class="keyword">const</span> std::string&amp; seqtype = <span class="stringliteral">&quot;&quot;</span>);</div>
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span> </div>
<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"><a class="line" href="classcmaple_1_1_alignment.html#a36d8b2bbaf72d21162d6e273bb3674e1"> 27</a></span> <a class="code hl_function" href="classcmaple_1_1_alignment.html#a36d8b2bbaf72d21162d6e273bb3674e1">~Alignment</a>();</div>
<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"> 28</span> </div>
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"><a class="line" href="classcmaple_1_1_alignment.html#a0564cc07f4576b5d9332442bb9fd350b"> 33</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classcmaple_1_1_alignment.html#a0564cc07f4576b5d9332442bb9fd350b">write</a>(std::ostream&amp; aln_stream, <span class="keyword">const</span> std::string&amp; format = <span class="stringliteral">&quot;MAPLE&quot;</span>);</div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span> </div>
<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"><a class="line" href="classcmaple_1_1_alignment.html#aa6fde65b30e8f14cc0c1d456701a37c2"> 40</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classcmaple_1_1_alignment.html#aa6fde65b30e8f14cc0c1d456701a37c2">write</a>(<span class="keyword">const</span> std::string&amp; aln_filename, <span class="keyword">const</span> std::string&amp; format = <span class="stringliteral">&quot;MAPLE&quot;</span>, <span class="keyword">const</span> <span class="keywordtype">bool</span> overwrite = <span class="keyword">false</span>);</div>
<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span> </div>
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span> <span class="comment">// declare Tree as a friend class</span></div>
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> <span class="keyword">friend</span> <span class="keyword">class </span><a class="code hl_class" href="classcmaple_1_1_tree.html">Tree</a>;</div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> </div>
<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> <span class="keyword">private</span>:</div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> AlignmentBase* aln_base;</div>
<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span> </div>
<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> <span class="keywordtype">void</span> init(std::istream&amp; aln_stream, <span class="keyword">const</span> std::string&amp; ref_seq, <span class="keyword">const</span> std::string&amp; format, <span class="keyword">const</span> std::string&amp; seqtype);</div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> </div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> };</div>
<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</span>}</div>
<div class="ttc" id="aclasscmaple_1_1_alignment_html"><div class="ttname"><a href="classcmaple_1_1_alignment.html">cmaple::Alignment</a></div><div class="ttdef"><b>Definition</b> alignment.h:7</div></div>
<div class="ttc" id="aclasscmaple_1_1_alignment_html_a0564cc07f4576b5d9332442bb9fd350b"><div class="ttname"><a href="classcmaple_1_1_alignment.html#a0564cc07f4576b5d9332442bb9fd350b">cmaple::Alignment::write</a></div><div class="ttdeci">void write(std::ostream &amp;aln_stream, const std::string &amp;format=&quot;MAPLE&quot;)</div><div class="ttdoc">Write the alignment to a stream in FASTA, PHYLIP, or MAPLE format.</div></div>
<div class="ttc" id="aclasscmaple_1_1_alignment_html_a36d8b2bbaf72d21162d6e273bb3674e1"><div class="ttname"><a href="classcmaple_1_1_alignment.html#a36d8b2bbaf72d21162d6e273bb3674e1">cmaple::Alignment::~Alignment</a></div><div class="ttdeci">~Alignment()</div><div class="ttdoc">Destructor.</div></div>
<div class="ttc" id="aclasscmaple_1_1_alignment_html_a6701d29a81fb5dd4149c5c5237b095de"><div class="ttname"><a href="classcmaple_1_1_alignment.html#a6701d29a81fb5dd4149c5c5237b095de">cmaple::Alignment::Alignment</a></div><div class="ttdeci">Alignment(std::istream &amp;aln_stream, const std::string &amp;ref_seq=&quot;&quot;, const std::string &amp;format=&quot;&quot;, const std::string &amp;seqtype=&quot;&quot;)</div><div class="ttdoc">Constructor from a stream of an alignment in FASTA, PHYLIP, or MAPLE format.</div></div>
<div class="ttc" id="aclasscmaple_1_1_alignment_html_a857b7e7f683234ec9c0afb54da04e8c0"><div class="ttname"><a href="classcmaple_1_1_alignment.html#a857b7e7f683234ec9c0afb54da04e8c0">cmaple::Alignment::Alignment</a></div><div class="ttdeci">Alignment(const std::string &amp;aln_filename, const std::string &amp;ref_seq=&quot;&quot;, const std::string &amp;format=&quot;&quot;, const std::string &amp;seqtype=&quot;&quot;)</div><div class="ttdoc">Constructor from an alignment file in FASTA, PHYLIP, or MAPLE format.</div></div>
<div class="ttc" id="aclasscmaple_1_1_alignment_html_aa6fde65b30e8f14cc0c1d456701a37c2"><div class="ttname"><a href="classcmaple_1_1_alignment.html#aa6fde65b30e8f14cc0c1d456701a37c2">cmaple::Alignment::write</a></div><div class="ttdeci">void write(const std::string &amp;aln_filename, const std::string &amp;format=&quot;MAPLE&quot;, const bool overwrite=false)</div><div class="ttdoc">Write the alignment to a file in FASTA, PHYLIP, or MAPLE format.</div></div>
<div class="ttc" id="aclasscmaple_1_1_tree_html"><div class="ttname"><a href="classcmaple_1_1_tree.html">cmaple::Tree</a></div><div class="ttdef"><b>Definition</b> tree.h:9</div></div>
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<div class="textblock">Here are the classes, structs, unions and interfaces with brief descriptions:</div><div class="directory">
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