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<li class="navelem"><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html">src</a></li><li class="navelem"><a class="el" href="dir_078e8be2a200f8a2ce3af8fa572ccadf.html">clustal</a></li> </ul>
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<a href="util_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: util.h 230 2011-04-09 15:37:50Z 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="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include <limits.h></span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#include <string.h></span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor">#include <strings.h></span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#include <stdarg.h></span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="preprocessor">#include <stdbool.h></span></div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> </div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="preprocessor">#ifndef CLUSTALO_UTIL_H</span></div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="preprocessor">#define CLUSTALO_UTIL_H</span></div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> </div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> </div><div class="line"><a name="l00029"></a><span class="lineno"><a class="line" href="util_8h.html#a6d14a9e26af7aad1cb9a4006155be401"> 29</a></span> <span class="preprocessor">#define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__)</span></div><div class="line"><a name="l00030"></a><span class="lineno"><a class="line" href="util_8h.html#a368b61529c2c0bee75519b56256be5e7"> 30</a></span> <span class="preprocessor">#define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__)</span></div><div class="line"><a name="l00031"></a><span class="lineno"><a class="line" href="util_8h.html#a85df19c6ad8d9c4938f58863f9917d4a"> 31</a></span> <span class="preprocessor">#define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__)</span></div><div class="line"><a name="l00032"></a><span class="lineno"><a class="line" href="util_8h.html#a911d2d6bfb17f86eda7d4af941f58051"> 32</a></span> <span class="preprocessor">#define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__))</span></div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> </div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="preprocessor">#ifndef MAX</span></div><div class="line"><a name="l00035"></a><span class="lineno"><a class="line" href="util_8h.html#afa99ec4acc4ecb2dc3c2d05da15d0e3f"> 35</a></span> <span class="preprocessor">#define MAX(a,b) ((a)>(b)?(a):(b))</span></div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor">#ifndef MIN</span></div><div class="line"><a name="l00038"></a><span class="lineno"><a class="line" href="util_8h.html#a3acffbd305ee72dcd4593c0d8af64a4f"> 38</a></span> <span class="preprocessor">#define MIN(a,b) ((a)<(b)?(a):(b))</span></div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> </div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="comment">/* STR_EQ: strings are equal, case sensitive */</span></div><div class="line"><a name="l00042"></a><span class="lineno"><a class="line" href="util_8h.html#a71195150f11cd64ab4de648124a47c1a"> 42</a></span> <span class="preprocessor">#define STR_EQ(a,b) (strcmp((a),(b)) == 0)</span></div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="comment">/* STR_NC_EQ: strings are equal, ignoring case */</span></div><div class="line"><a name="l00044"></a><span class="lineno"><a class="line" href="util_8h.html#a9e6be8088ce9b69a28c20081cabf64a4"> 44</a></span> <span class="preprocessor">#define STR_NC_EQ(a,b) (strcasecmp((a),(b)) == 0)</span></div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span> </div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span> </div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="comment">/* type boolean and false and true defined in stdbool.h */</span></div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="preprocessor">#ifndef TRUE</span></div><div class="line"><a name="l00049"></a><span class="lineno"><a class="line" href="util_8h.html#aa8cecfc5c5c054d2875c03e77b7be15d"> 49</a></span> <span class="preprocessor">#define TRUE true</span></div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="preprocessor">#ifndef FALSE</span></div><div class="line"><a name="l00052"></a><span class="lineno"><a class="line" href="util_8h.html#aa93f0eb578d23995850d61f7d61c55c1"> 52</a></span> <span class="preprocessor">#define FALSE false</span></div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span> </div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <span class="comment">/* clashes with hhalign</span></div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span> <span class="comment">#define FAIL -1</span></div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span> <span class="comment">#define OK 0</span></div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span> <span class="comment">*/</span></div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span> </div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span> </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> <span class="comment">/* don't use the following directly; use macros provided above instead</span></div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span> <span class="comment"> */</span></div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span> <span class="keywordtype">void</span> *<a class="code" href="util_8h.html#a5fc3d869ab98caf740b58539efef01bb">CkMalloc</a>(<span class="keywordtype">size_t</span> size, <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keyword">function</span>, <span class="keyword">const</span> <span class="keywordtype">int</span> line);</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span> <span class="keywordtype">void</span> *<a class="code" href="util_8h.html#a4a66f56360f9c91a4845bdf9c192e08a">CkCalloc</a>(<span class="keywordtype">size_t</span> count, <span class="keywordtype">size_t</span> size, <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keyword">function</span>, <span class="keyword">const</span> <span class="keywordtype">int</span> line);</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span> <span class="keywordtype">void</span> *<a class="code" href="util_8h.html#a14acb2efac545e46035708957463d9e2">CkRealloc</a>(<span class="keywordtype">void</span> *ptr, <span class="keywordtype">size_t</span> bytes, <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keyword">function</span>, <span class="keyword">const</span> <span class="keywordtype">int</span> line);</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span> <span class="keywordtype">void</span> *<a class="code" href="util_8h.html#abcad90d2861523f68945f04b7bf81752">CkFree</a>(<span class="keywordtype">void</span> *ptr, <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keyword">function</span>, <span class="keyword">const</span> <span class="keywordtype">int</span> line);</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span> <span class="keywordtype">char</span> *<a class="code" href="util_8h.html#a4d6fde7b9604e0301c18f68b252db010">CkStrdup</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *s);</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span> <span class="keywordtype">void</span> <a class="code" href="util_8h.html#a3270ec7cb14ad135fe11e6d1712fcd4c">PermutationArray</a>(<span class="keywordtype">int</span> **array, <span class="keyword">const</span> <span class="keywordtype">int</span> len);</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span> <span class="keywordtype">void</span> <a class="code" href="util_8h.html#aa5ee9504afc548239113fc564b3a735e">RandomUniqueIntArray</a>(<span class="keywordtype">int</span> *array, <span class="keyword">const</span> <span class="keywordtype">int</span> array_len, <span class="keyword">const</span> <span class="keywordtype">int</span> max_value);</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span> <span class="keywordtype">int</span> <a class="code" href="util_8h.html#a5a87ce594ee9e2157ccdefee1273372c">IntCmp</a>(<span class="keyword">const</span> <span class="keywordtype">void</span> *a, <span class="keyword">const</span> <span class="keywordtype">void</span> *b);</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span> <span class="keywordtype">bool</span> <a class="code" href="util_8h.html#a9543f691bc0adaaec4000d133809657a">FileIsWritable</a>(<span class="keywordtype">char</span> *pcFileName);</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span> <span class="keywordtype">void</span> <a class="code" href="util_8h.html#a85ba9f38ea0620e5202479103159297b">QSortAndTrackIndex</a>(<span class="keywordtype">int</span> *piSortedIndices, <span class="keywordtype">int</span> *piArrayToSort,</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> uArrayLen, <span class="keyword">const</span> <span class="keywordtype">char</span> cOrder, <span class="keyword">const</span> <span class="keywordtype">bool</span> bOverwriteArrayToSort);</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="preprocessor">#endif</span></div><div class="ttc" id="util_8h_html_abcad90d2861523f68945f04b7bf81752"><div class="ttname"><a href="util_8h.html#abcad90d2861523f68945f04b7bf81752">CkFree</a></div><div class="ttdeci">void * CkFree(void *ptr, const char *function, const int line)</div><div class="ttdoc">Frees memory. </div><div class="ttdef"><b>Definition:</b> util.c:180</div></div>
<div class="ttc" id="util_8h_html_a4d6fde7b9604e0301c18f68b252db010"><div class="ttname"><a href="util_8h.html#a4d6fde7b9604e0301c18f68b252db010">CkStrdup</a></div><div class="ttdeci">char * CkStrdup(const char *s)</div><div class="ttdoc">safe version of strdup </div><div class="ttdef"><b>Definition:</b> util.c:207</div></div>
<div class="ttc" id="util_8h_html_a5fc3d869ab98caf740b58539efef01bb"><div class="ttname"><a href="util_8h.html#a5fc3d869ab98caf740b58539efef01bb">CkMalloc</a></div><div class="ttdeci">void * CkMalloc(size_t size, const char *function, const int line)</div><div class="ttdoc">Allocates memory (malloc) </div><div class="ttdef"><b>Definition:</b> util.c:79</div></div>
<div class="ttc" id="util_8h_html_a14acb2efac545e46035708957463d9e2"><div class="ttname"><a href="util_8h.html#a14acb2efac545e46035708957463d9e2">CkRealloc</a></div><div class="ttdeci">void * CkRealloc(void *ptr, size_t bytes, const char *function, const int line)</div><div class="ttdoc">Reallocates memory. </div><div class="ttdef"><b>Definition:</b> util.c:148</div></div>
<div class="ttc" id="util_8h_html_a3270ec7cb14ad135fe11e6d1712fcd4c"><div class="ttname"><a href="util_8h.html#a3270ec7cb14ad135fe11e6d1712fcd4c">PermutationArray</a></div><div class="ttdeci">void PermutationArray(int **array, const int len)</div><div class="ttdoc">Creates an int array of size len with len-1 random but unique integers with values 0–len-1...</div><div class="ttdef"><b>Definition:</b> util.c:237</div></div>
<div class="ttc" id="util_8h_html_a85ba9f38ea0620e5202479103159297b"><div class="ttname"><a href="util_8h.html#a85ba9f38ea0620e5202479103159297b">QSortAndTrackIndex</a></div><div class="ttdeci">void QSortAndTrackIndex(int *piSortedIndices, int *piArrayToSort, const int uArrayLen, const char cOrder, const bool bOverwriteArrayToSort)</div><div class="ttdoc">Sort a given int array in ascending or descending order, while keeping track of the element order...</div><div class="ttdef"><b>Definition:</b> util.c:403</div></div>
<div class="ttc" id="util_8h_html_aa5ee9504afc548239113fc564b3a735e"><div class="ttname"><a href="util_8h.html#aa5ee9504afc548239113fc564b3a735e">RandomUniqueIntArray</a></div><div class="ttdeci">void RandomUniqueIntArray(int *array, const int array_len, const int max_value)</div><div class="ttdoc">Creates an array filled with random, but unique ints of given range. Implementation of the Floyd algo...</div><div class="ttdef"><b>Definition:</b> util.c:293</div></div>
<div class="ttc" id="util_8h_html_a5a87ce594ee9e2157ccdefee1273372c"><div class="ttname"><a href="util_8h.html#a5a87ce594ee9e2157ccdefee1273372c">IntCmp</a></div><div class="ttdeci">int IntCmp(const void *a, const void *b)</div><div class="ttdoc">int comparison function for qsort </div><div class="ttdef"><b>Definition:</b> util.c:329</div></div>
<div class="ttc" id="util_8h_html_a9543f691bc0adaaec4000d133809657a"><div class="ttname"><a href="util_8h.html#a9543f691bc0adaaec4000d133809657a">FileIsWritable</a></div><div class="ttdeci">bool FileIsWritable(char *pcFileName)</div><div class="ttdoc">Test if file is writable. File may or may not exist. </div><div class="ttdef"><b>Definition:</b> util.c:466</div></div>
<div class="ttc" id="util_8h_html_a4a66f56360f9c91a4845bdf9c192e08a"><div class="ttname"><a href="util_8h.html#a4a66f56360f9c91a4845bdf9c192e08a">CkCalloc</a></div><div class="ttdeci">void * CkCalloc(size_t count, size_t size, const char *function, const int line)</div><div class="ttdoc">Allocates memory (calloc). Memory will be set to zero. </div><div class="ttdef"><b>Definition:</b> util.c:114</div></div>
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