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<a href="symmatrix_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*********************************************************************</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * Clustal Omega - Multiple sequence alignment</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> *</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * Copyright (C) 2010 University College Dublin</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * Clustal-Omega is free software; you can redistribute it and/or</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * modify it under the terms of the GNU General Public License as</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> * published by the Free Software Foundation; either version 2 of the</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * License, or (at your option) any later version.</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> *</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * This file is part of Clustal-Omega.</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> *</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> ********************************************************************/</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> </div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">/*</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment"> * RCS $Id: symmatrix.h 288 2013-07-29 13:15:50Z andreas $</span></div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment"> */</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> </div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor">#ifndef CLUSTALO_SYMMATRIX_H</span></div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor">#define CLUSTALO_SYMMATRIX_H</span></div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> </div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="comment">/* ugly, but necessary for cross-checking of names in distmat and</span></div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="comment"> * mseq */</span></div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include "<a class="code" href="seq_8h.html">seq.h</a>"</span></div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span> </div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> </div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span> </div><div class="line"><a name="l00048"></a><span class="lineno"><a class="line" href="structsymmatrix__t.html"> 48</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span>{</div><div class="line"><a name="l00049"></a><span class="lineno"><a class="line" href="structsymmatrix__t.html#a3dbed8b3a7cb590f03b5d3d656511841"> 49</a></span>  <span class="keywordtype">int</span> <a class="code" href="structsymmatrix__t.html#a3dbed8b3a7cb590f03b5d3d656511841">nrows</a>; </div><div class="line"><a name="l00050"></a><span class="lineno"><a class="line" href="structsymmatrix__t.html#a1339443759d7731a087bb3540e21418f"> 50</a></span>  <span class="keywordtype">int</span> <a class="code" href="structsymmatrix__t.html#a1339443759d7731a087bb3540e21418f">ncols</a>; </div><div class="line"><a name="l00059"></a><span class="lineno"><a class="line" href="structsymmatrix__t.html#aed934a8755f15b45442a3f57ef5c54e6"> 59</a></span>  <span class="keywordtype">double</span> **<a class="code" href="structsymmatrix__t.html#aed934a8755f15b45442a3f57ef5c54e6">data</a>; </div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span> } <a class="code" href="structsymmatrix__t.html">symmatrix_t</a>;</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span> </div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span> </div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span> </div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span> <span class="keyword">extern</span> <span class="keywordtype">int</span></div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span> <a class="code" href="symmatrix_8h.html#aa162f43d7e26247677dd70d12c0fc59e">NewSymMatrix</a>(<a class="code" href="structsymmatrix__t.html">symmatrix_t</a> **symmat, <span class="keyword">const</span> <span class="keywordtype">int</span> nrows, <span class="keyword">const</span> <span class="keywordtype">int</span> ncols);</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span> </div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span> <span class="keyword">extern</span> <span class="keywordtype">void</span></div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span> <a class="code" href="symmatrix_8h.html#a379c2a8bacd01fef2c90f8a7dbe594a7">SymMatrixSetValue</a>(<a class="code" href="structsymmatrix__t.html">symmatrix_t</a> *symmat, <span class="keyword">const</span> <span class="keywordtype">int</span> i, <span class="keyword">const</span> <span class="keywordtype">int</span> j, <span class="keyword">const</span> <span class="keywordtype">double</span> value);</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span> </div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span> <span class="keyword">extern</span> <span class="keywordtype">double</span></div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span> <a class="code" href="symmatrix_8h.html#a4efc1a13a578c075e5a11e4829f98ad0">SymMatrixGetValue</a>(<a class="code" href="structsymmatrix__t.html">symmatrix_t</a> *symmat, <span class="keyword">const</span> <span class="keywordtype">int</span> i, <span class="keyword">const</span> <span class="keywordtype">int</span> j);</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span> </div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span> <span class="keyword">extern</span> <span class="keywordtype">void</span></div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span> <a class="code" href="symmatrix_8h.html#a0d2451af4a6eabc193ad2909602bb554">SymMatrixGetValueP</a>(<span class="keywordtype">double</span> **value, <a class="code" href="structsymmatrix__t.html">symmatrix_t</a> *symmat, <span class="keyword">const</span> <span class="keywordtype">int</span> i, <span class="keyword">const</span> <span class="keywordtype">int</span> j);</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span> </div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span> <span class="keyword">extern</span> <span class="keywordtype">void</span></div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span> <a class="code" href="symmatrix_8h.html#ac29198776330bc1f22420d98cfc2e7b4">FreeSymMatrix</a>(<a class="code" href="structsymmatrix__t.html">symmatrix_t</a> **symmat);</div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span> </div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span> <span class="keyword">extern</span> <span class="keywordtype">void</span></div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span> <a class="code" href="symmatrix_8h.html#a1c1c44553c88b5c88093b444d4901be3">SymMatrixPrint</a>(<a class="code" href="structsymmatrix__t.html">symmatrix_t</a> *symmat, <span class="keywordtype">char</span> **labels, <span class="keyword">const</span> <span class="keywordtype">char</span> *path, <span class="keywordtype">bool</span> bPercID);</div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span> </div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span> <span class="keyword">extern</span> <span class="keywordtype">int</span></div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span> <a class="code" href="symmatrix_8h.html#a5373394faadcb8147eb297b610b651fa">SymMatrixRead</a>(<span class="keywordtype">char</span> *pcFileIn, <a class="code" href="structsymmatrix__t.html">symmatrix_t</a> **prSymMat_p, <a class="code" href="structmseq__t.html">mseq_t</a> *prMSeq);</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span> <span class="preprocessor">#endif</span></div><div class="ttc" id="structsymmatrix__t_html"><div class="ttname"><a href="structsymmatrix__t.html">symmatrix_t</a></div><div class="ttdoc">symmetric matrix structure </div><div class="ttdef"><b>Definition:</b> symmatrix.h:48</div></div>
<div class="ttc" id="symmatrix_8h_html_a379c2a8bacd01fef2c90f8a7dbe594a7"><div class="ttname"><a href="symmatrix_8h.html#a379c2a8bacd01fef2c90f8a7dbe594a7">SymMatrixSetValue</a></div><div class="ttdeci">void SymMatrixSetValue(symmatrix_t *symmat, const int i, const int j, const double value)</div><div class="ttdoc">Sets symmat data of given index to given value. </div><div class="ttdef"><b>Definition:</b> symmatrix.c:176</div></div>
<div class="ttc" id="symmatrix_8h_html_a5373394faadcb8147eb297b610b651fa"><div class="ttname"><a href="symmatrix_8h.html#a5373394faadcb8147eb297b610b651fa">SymMatrixRead</a></div><div class="ttdeci">int SymMatrixRead(char *pcFileIn, symmatrix_t **prSymMat_p, mseq_t *prMSeq)</div><div class="ttdoc">Read a distance matrix in phylip format. </div><div class="ttdef"><b>Definition:</b> symmatrix.c:399</div></div>
<div class="ttc" id="symmatrix_8h_html_ac29198776330bc1f22420d98cfc2e7b4"><div class="ttname"><a href="symmatrix_8h.html#ac29198776330bc1f22420d98cfc2e7b4">FreeSymMatrix</a></div><div class="ttdeci">void FreeSymMatrix(symmatrix_t **symmat)</div><div class="ttdoc">Frees memory allocated by data members of symmat and symmat itself. </div><div class="ttdef"><b>Definition:</b> symmatrix.c:277</div></div>
<div class="ttc" id="symmatrix_8h_html_a1c1c44553c88b5c88093b444d4901be3"><div class="ttname"><a href="symmatrix_8h.html#a1c1c44553c88b5c88093b444d4901be3">SymMatrixPrint</a></div><div class="ttdeci">void SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path, bool bPercID)</div><div class="ttdoc">Print out a symmat in phylip style. Distances are printed on one line per sequence/object. Since we also support matrices with rows<cols, the first line can also be nrows by ncolumns instead of just nrows. </div><div class="ttdef"><b>Definition:</b> symmatrix.c:316</div></div>
<div class="ttc" id="symmatrix_8h_html_aa162f43d7e26247677dd70d12c0fc59e"><div class="ttname"><a href="symmatrix_8h.html#aa162f43d7e26247677dd70d12c0fc59e">NewSymMatrix</a></div><div class="ttdeci">int NewSymMatrix(symmatrix_t **symmat, const int nrows, const int ncols)</div><div class="ttdoc">Allocates symmat and its members and initialises them. Data will be calloced, i.e. initialised with zeros. </div><div class="ttdef"><b>Definition:</b> symmatrix.c:68</div></div>
<div class="ttc" id="structsymmatrix__t_html_a1339443759d7731a087bb3540e21418f"><div class="ttname"><a href="structsymmatrix__t.html#a1339443759d7731a087bb3540e21418f">symmatrix_t::ncols</a></div><div class="ttdeci">int ncols</div><div class="ttdef"><b>Definition:</b> symmatrix.h:50</div></div>
<div class="ttc" id="symmatrix_8h_html_a4efc1a13a578c075e5a11e4829f98ad0"><div class="ttname"><a href="symmatrix_8h.html#a4efc1a13a578c075e5a11e4829f98ad0">SymMatrixGetValue</a></div><div class="ttdeci">double SymMatrixGetValue(symmatrix_t *symmat, const int i, const int j)</div><div class="ttdoc">Returns element of symmat corresponding to given indices. </div><div class="ttdef"><b>Definition:</b> symmatrix.c:209</div></div>
<div class="ttc" id="seq_8h_html"><div class="ttname"><a href="seq_8h.html">seq.h</a></div></div>
<div class="ttc" id="structsymmatrix__t_html_a3dbed8b3a7cb590f03b5d3d656511841"><div class="ttname"><a href="structsymmatrix__t.html#a3dbed8b3a7cb590f03b5d3d656511841">symmatrix_t::nrows</a></div><div class="ttdeci">int nrows</div><div class="ttdef"><b>Definition:</b> symmatrix.h:49</div></div>
<div class="ttc" id="structsymmatrix__t_html_aed934a8755f15b45442a3f57ef5c54e6"><div class="ttname"><a href="structsymmatrix__t.html#aed934a8755f15b45442a3f57ef5c54e6">symmatrix_t::data</a></div><div class="ttdeci">double ** data</div><div class="ttdef"><b>Definition:</b> symmatrix.h:59</div></div>
<div class="ttc" id="structmseq__t_html"><div class="ttname"><a href="structmseq__t.html">mseq_t</a></div><div class="ttdoc">structure for storing multiple sequences </div><div class="ttdef"><b>Definition:</b> seq.h:47</div></div>
<div class="ttc" id="symmatrix_8h_html_a0d2451af4a6eabc193ad2909602bb554"><div class="ttname"><a href="symmatrix_8h.html#a0d2451af4a6eabc193ad2909602bb554">SymMatrixGetValueP</a></div><div class="ttdeci">void SymMatrixGetValueP(double **value, symmatrix_t *symmat, const int i, const int j)</div><div class="ttdoc">Returns a pointer to an element of symmat corresponding to given indices. </div><div class="ttdef"><b>Definition:</b> symmatrix.c:248</div></div>
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