sources/pairwise/docs/html/pairwise_8c.html

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   8 <h1>pairwise.c File Reference</h1><code>#include &lt;stdio.h&gt;</code><br>
   9 <code>#include &lt;stdlib.h&gt;</code><br>
  10 <code>#include &lt;errno.h&gt;</code><br>
  11 <code>#include &lt;string.h&gt;</code><br>
  12 <code>#include "<a class="el" href="pairwise_8h-source.html">pairwise.h</a>"</code><br>
  13
  14 <p>
  15 Include dependency graph for pairwise.c:<p><center><img src="pairwise_8c__incl.png" border="0" usemap="#pairwise.c_map" alt="Include dependency graph"></center>
  16 <map name="pairwise.c_map">
  17 <area href="pairwise_8h.html" shape="rect" coords="135,86,207,105" alt="">
  18 </map>
  19
  20 <p>
  21 <a href="pairwise_8c-source.html">Go to the source code of this file.</a><table border=0 cellpadding=0 cellspacing=0>
  22 <tr><td></td></tr>
  23 <tr><td colspan=2><br><h2>Defines</h2></td></tr>
  24 <tr><td class="memItemLeft" nowrap align=right valign=top>#define&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8c.html#a0">ARRAY</a>&nbsp;&nbsp;&nbsp;50</td></tr>
  25
  26 <tr><td class="memItemLeft" nowrap align=right valign=top>#define&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8c.html#a1">FILEBUF</a>&nbsp;&nbsp;&nbsp;1000</td></tr>
  27
  28 <tr><td class="memItemLeft" nowrap align=right valign=top>#define&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8c.html#a2">MAX</a>(A, B)&nbsp;&nbsp;&nbsp;((A) &gt; (B) ? (A) : (B))</td></tr>
  29
  30 <tr><td class="memItemLeft" nowrap align=right valign=top>#define&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8c.html#a3">MIN</a>(A, B)&nbsp;&nbsp;&nbsp;((A) &lt; (B) ? (A) : (B))</td></tr>
  31
  32 <tr><td class="memItemLeft" nowrap align=right valign=top>#define&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8c.html#a4">MALLOC</a>(PTR, SIZE)&nbsp;&nbsp;&nbsp;do { PTR = malloc(SIZE); if (PTR == NULL) fatal_sys_error("malloc returned NULL"); } while (0)</td></tr>
  33
  34 <tr><td class="memItemLeft" nowrap align=right valign=top>#define&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8c.html#a5">REALLOC</a>(PTR, SIZE)&nbsp;&nbsp;&nbsp;do { PTR = realloc(PTR, SIZE); if (PTR == NULL &amp;&amp; SIZE != 0) fatal_sys_error("realloc returned NULL"); } while (0)</td></tr>
  35
  36 <tr><td colspan=2><br><h2>Functions</h2></td></tr>
  37 <tr><td class="memItemLeft" nowrap align=right valign=top>void&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8c.html#a6">fatal_error</a> (char *message)</td></tr>
  38
  39 <tr><td class="memItemLeft" nowrap align=right valign=top>void&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8c.html#a7">fatal_sys_error</a> (char *message)</td></tr>
  40
  41 <tr><td class="memItemLeft" nowrap align=right valign=top>FILE *&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8c.html#a8">xfopen</a> (const char *path, const char *mode)</td></tr>
  42
  43 <tr><td class="memItemLeft" nowrap align=right valign=top>void *&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8c.html#a9">xmalloc</a> (size_t size)</td></tr>
  44
  45 <tr><td class="memItemLeft" nowrap align=right valign=top>void *&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8c.html#a10">xrealloc</a> (void *ptr, size_t size)</td></tr>
  46
  47 <tr><td class="memItemLeft" nowrap align=right valign=top>int&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8c.html#a11">diff</a> (char a, char b)</td></tr>
  48
  49 <tr><td class="memItemLeft" nowrap align=right valign=top>float&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8c.html#a12">pairwise</a> (struct <a class="el" href="structfasta.html">fasta</a> *a, struct <a class="el" href="structfasta.html">fasta</a> *b)</td></tr>
  50
  51 <tr><td class="memItemLeft" nowrap align=right valign=top>void&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8c.html#a13">populate</a> (struct <a class="el" href="structfasta.html">fasta</a> *a)</td></tr>
  52
  53 <tr><td class="memItemLeft" nowrap align=right valign=top>void&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8c.html#a14">check_length</a> (struct <a class="el" href="structfasta.html">fasta</a> **array)</td></tr>
  54
  55 <tr><td class="memItemLeft" nowrap align=right valign=top><a class="el" href="structfasta.html">fasta</a> **&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8c.html#a15">read_fasta</a> (FILE *fh)</td></tr>
  56
  57 <tr><td class="memItemLeft" nowrap align=right valign=top>int&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8c.html#a16">main</a> (int argc, char **argv)</td></tr>
  58
  59 </table>
  60 <hr><h2>Define Documentation</h2>
  61 <a name="a0" doxytag="pairwise.c::ARRAY"></a><p>
  62 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
  63   <tr>
  64     <td class="mdRow">
  65       <table cellpadding="0" cellspacing="0" border="0">
  66         <tr>
  67           <td class="md" nowrap valign="top"> #define ARRAY&nbsp;&nbsp;&nbsp;50
  68       </table>
  69     </td>
  70   </tr>
  71 </table>
  72 <table cellspacing=5 cellpadding=0 border=0>
  73   <tr>
  74     <td>
  75       &nbsp;
  76     </td>
  77     <td>
  78
  79 <p>
  80
  81 <p>
  82 Definition at line <a class="el" href="pairwise_8c-source.html#l00029">29</a> of file <a class="el" href="pairwise_8c-source.html">pairwise.c</a>.
  83 <p>
  84 Referenced by <a class="el" href="pairwise_8c-source.html#l00179">read_fasta()</a>.    </td>
  85   </tr>
  86 </table>
  87 <a name="a1" doxytag="pairwise.c::FILEBUF"></a><p>
  88 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
  89   <tr>
  90     <td class="mdRow">
  91       <table cellpadding="0" cellspacing="0" border="0">
  92         <tr>
  93           <td class="md" nowrap valign="top"> #define FILEBUF&nbsp;&nbsp;&nbsp;1000
  94       </table>
  95     </td>
  96   </tr>
  97 </table>
  98 <table cellspacing=5 cellpadding=0 border=0>
  99   <tr>
 100     <td>
 101       &nbsp;
 102     </td>
 103     <td>
 104
 105 <p>
 106
 107 <p>
 108 Definition at line <a class="el" href="pairwise_8c-source.html#l00030">30</a> of file <a class="el" href="pairwise_8c-source.html">pairwise.c</a>.
 109 <p>
 110 Referenced by <a class="el" href="pairwise_8c-source.html#l00179">read_fasta()</a>.    </td>
 111   </tr>
 112 </table>
 113 <a name="a4" doxytag="pairwise.c::MALLOC"></a><p>
 114 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 115   <tr>
 116     <td class="mdRow">
 117       <table cellpadding="0" cellspacing="0" border="0">
 118         <tr>
 119           <td class="md" nowrap valign="top"> #define MALLOC</td>
 120           <td class="md" valign="top">(&nbsp;</td>
 121           <td class="md" nowrap valign="top">PTR,         <tr>
 122           <td></td>
 123           <td></td>
 124           <td class="md" nowrap>SIZE&nbsp;</td>
 125           <td class="mdname1" valign="top" nowrap>          </td>
 126           <td class="md" valign="top">&nbsp;)&nbsp;</td>
 127           <td class="md" nowrap>&nbsp;&nbsp;&nbsp;do { PTR = malloc(SIZE); if (PTR == NULL) fatal_sys_error("malloc returned NULL"); } while (0)
 128       </table>
 129     </td>
 130   </tr>
 131 </table>
 132 <table cellspacing=5 cellpadding=0 border=0>
 133   <tr>
 134     <td>
 135       &nbsp;
 136     </td>
 137     <td>
 138
 139 <p>
 140
 141 <p>
 142 Definition at line <a class="el" href="pairwise_8c-source.html#l00045">45</a> of file <a class="el" href="pairwise_8c-source.html">pairwise.c</a>.    </td>
 143   </tr>
 144 </table>
 145 <a name="a2" doxytag="pairwise.c::MAX"></a><p>
 146 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 147   <tr>
 148     <td class="mdRow">
 149       <table cellpadding="0" cellspacing="0" border="0">
 150         <tr>
 151           <td class="md" nowrap valign="top"> #define MAX</td>
 152           <td class="md" valign="top">(&nbsp;</td>
 153           <td class="md" nowrap valign="top">A,         <tr>
 154           <td></td>
 155           <td></td>
 156           <td class="md" nowrap>B&nbsp;</td>
 157           <td class="mdname1" valign="top" nowrap>          </td>
 158           <td class="md" valign="top">&nbsp;)&nbsp;</td>
 159           <td class="md" nowrap>&nbsp;&nbsp;&nbsp;((A) &gt; (B) ? (A) : (B))
 160       </table>
 161     </td>
 162   </tr>
 163 </table>
 164 <table cellspacing=5 cellpadding=0 border=0>
 165   <tr>
 166     <td>
 167       &nbsp;
 168     </td>
 169     <td>
 170
 171 <p>
 172
 173 <p>
 174 Definition at line <a class="el" href="pairwise_8c-source.html#l00035">35</a> of file <a class="el" href="pairwise_8c-source.html">pairwise.c</a>.
 175 <p>
 176 Referenced by <a class="el" href="pairwise_8c-source.html#l00106">pairwise()</a>.    </td>
 177   </tr>
 178 </table>
 179 <a name="a3" doxytag="pairwise.c::MIN"></a><p>
 180 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 181   <tr>
 182     <td class="mdRow">
 183       <table cellpadding="0" cellspacing="0" border="0">
 184         <tr>
 185           <td class="md" nowrap valign="top"> #define MIN</td>
 186           <td class="md" valign="top">(&nbsp;</td>
 187           <td class="md" nowrap valign="top">A,         <tr>
 188           <td></td>
 189           <td></td>
 190           <td class="md" nowrap>B&nbsp;</td>
 191           <td class="mdname1" valign="top" nowrap>          </td>
 192           <td class="md" valign="top">&nbsp;)&nbsp;</td>
 193           <td class="md" nowrap>&nbsp;&nbsp;&nbsp;((A) &lt; (B) ? (A) : (B))
 194       </table>
 195     </td>
 196   </tr>
 197 </table>
 198 <table cellspacing=5 cellpadding=0 border=0>
 199   <tr>
 200     <td>
 201       &nbsp;
 202     </td>
 203     <td>
 204
 205 <p>
 206
 207 <p>
 208 Definition at line <a class="el" href="pairwise_8c-source.html#l00039">39</a> of file <a class="el" href="pairwise_8c-source.html">pairwise.c</a>.
 209 <p>
 210 Referenced by <a class="el" href="pairwise_8c-source.html#l00106">pairwise()</a>.    </td>
 211   </tr>
 212 </table>
 213 <a name="a5" doxytag="pairwise.c::REALLOC"></a><p>
 214 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 215   <tr>
 216     <td class="mdRow">
 217       <table cellpadding="0" cellspacing="0" border="0">
 218         <tr>
 219           <td class="md" nowrap valign="top"> #define REALLOC</td>
 220           <td class="md" valign="top">(&nbsp;</td>
 221           <td class="md" nowrap valign="top">PTR,         <tr>
 222           <td></td>
 223           <td></td>
 224           <td class="md" nowrap>SIZE&nbsp;</td>
 225           <td class="mdname1" valign="top" nowrap>          </td>
 226           <td class="md" valign="top">&nbsp;)&nbsp;</td>
 227           <td class="md" nowrap>&nbsp;&nbsp;&nbsp;do { PTR = realloc(PTR, SIZE); if (PTR == NULL &amp;&amp; SIZE != 0) fatal_sys_error("realloc returned NULL"); } while (0)
 228       </table>
 229     </td>
 230   </tr>
 231 </table>
 232 <table cellspacing=5 cellpadding=0 border=0>
 233   <tr>
 234     <td>
 235       &nbsp;
 236     </td>
 237     <td>
 238
 239 <p>
 240
 241 <p>
 242 Definition at line <a class="el" href="pairwise_8c-source.html#l00049">49</a> of file <a class="el" href="pairwise_8c-source.html">pairwise.c</a>.    </td>
 243   </tr>
 244 </table>
 245 <hr><h2>Function Documentation</h2>
 246 <a name="a14" doxytag="pairwise.c::check_length"></a><p>
 247 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 248   <tr>
 249     <td class="mdRow">
 250       <table cellpadding="0" cellspacing="0" border="0">
 251         <tr>
 252           <td class="md" nowrap valign="top"> void check_length </td>
 253           <td class="md" valign="top">(&nbsp;</td>
 254           <td class="md" nowrap valign="top">struct <a class="el" href="structfasta.html">fasta</a> **&nbsp;</td>
 255           <td class="mdname1" valign="top" nowrap> <em>array</em>          </td>
 256           <td class="md" valign="top">&nbsp;)&nbsp;</td>
 257           <td class="md" nowrap></td>
 258         </tr>
 259
 260       </table>
 261     </td>
 262   </tr>
 263 </table>
 264 <table cellspacing=5 cellpadding=0 border=0>
 265   <tr>
 266     <td>
 267       &nbsp;
 268     </td>
 269     <td>
 270
 271 <p>
 272
 273 <p>
 274 Definition at line <a class="el" href="pairwise_8c-source.html#l00160">160</a> of file <a class="el" href="pairwise_8c-source.html">pairwise.c</a>.
 275 <p>
 276 References <a class="el" href="pairwise_8c-source.html#l00053">fatal_error()</a>.
 277 <p>
 278 Referenced by <a class="el" href="pairwise_8c-source.html#l00253">main()</a>.
 279 <p>
 280 <div class="fragment"><pre>00160                                     {
 281 00161         <span class="keywordtype">int</span> i, length;
 282 00162
 283 00163         <span class="keywordflow">if</span> (array[0] != NULL)
 284 00164                 length = strlen(array[0]-&gt;seq);
 285 00165         <span class="keywordflow">else</span> {
 286 00166                 fprintf(stderr, <span class="stringliteral">"check_length() not passed an array of fasta structs\n"</span>);
 287 00167                 <span class="keywordflow">return</span>;
 288 00168         }
 289 00169
 290 00170         <span class="keywordflow">for</span> (i = 0; array[i] != NULL; i++) {
 291 00171                 <span class="keywordflow">if</span> (length != strlen(array[i]-&gt;seq)) {
 292 00172                         <a class="code" href="pairwise_8c.html#a6">fatal_error</a>(<span class="stringliteral">"Not all of the sequences are the same length\n"</span>);
 293 00173                 }
 294 00174         }
 295 00175 }
 296 </pre></div>    </td>
 297   </tr>
 298 </table>
 299
 300 <p>
 301 Here is the call graph for this function:<p><center><img src="pairwise_8c_a14_cgraph.png" border="0" usemap="#pairwise_8c_a14_cgraph_map" alt=""></center>
 302 <map name="pairwise_8c_a14_cgraph_map">
 303 <area href="pairwise_8h.html#a0" shape="rect" coords="160,5,235,23" alt="">
 304 </map>
 305 <a name="a11" doxytag="pairwise.c::diff"></a><p>
 306 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 307   <tr>
 308     <td class="mdRow">
 309       <table cellpadding="0" cellspacing="0" border="0">
 310         <tr>
 311           <td class="md" nowrap valign="top"> int diff </td>
 312           <td class="md" valign="top">(&nbsp;</td>
 313           <td class="md" nowrap valign="top">char&nbsp;</td>
 314           <td class="mdname" nowrap> <em>a</em>, </td>
 315         </tr>
 316         <tr>
 317           <td></td>
 318           <td></td>
 319           <td class="md" nowrap>char&nbsp;</td>
 320           <td class="mdname" nowrap> <em>b</em></td>
 321         </tr>
 322         <tr>
 323           <td></td>
 324           <td class="md">)&nbsp;</td>
 325           <td class="md" colspan="2"></td>
 326         </tr>
 327
 328       </table>
 329     </td>
 330   </tr>
 331 </table>
 332 <table cellspacing=5 cellpadding=0 border=0>
 333   <tr>
 334     <td>
 335       &nbsp;
 336     </td>
 337     <td>
 338
 339 <p>
 340
 341 <p>
 342 Definition at line <a class="el" href="pairwise_8c-source.html#l00092">92</a> of file <a class="el" href="pairwise_8c-source.html">pairwise.c</a>.
 343 <p>
 344 Referenced by <a class="el" href="pairwise_8c-source.html#l00106">pairwise()</a>.
 345 <p>
 346 <div class="fragment"><pre>00092                       {
 347 00093         <span class="keywordflow">if</span> (a == b &amp;&amp; a == <span class="charliteral">'-'</span>)
 348 00094                 <span class="keywordflow">return</span> 0;
 349 00095         <span class="keywordflow">if</span> (a == b)
 350 00096                 <span class="keywordflow">return</span> 1;
 351 00097         <span class="keywordflow">return</span> 0;
 352 00098 }
 353 </pre></div>    </td>
 354   </tr>
 355 </table>
 356 <a name="a6" doxytag="pairwise.c::fatal_error"></a><p>
 357 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 358   <tr>
 359     <td class="mdRow">
 360       <table cellpadding="0" cellspacing="0" border="0">
 361         <tr>
 362           <td class="md" nowrap valign="top"> void fatal_error </td>
 363           <td class="md" valign="top">(&nbsp;</td>
 364           <td class="md" nowrap valign="top">char *&nbsp;</td>
 365           <td class="mdname1" valign="top" nowrap> <em>message</em>          </td>
 366           <td class="md" valign="top">&nbsp;)&nbsp;</td>
 367           <td class="md" nowrap></td>
 368         </tr>
 369
 370       </table>
 371     </td>
 372   </tr>
 373 </table>
 374 <table cellspacing=5 cellpadding=0 border=0>
 375   <tr>
 376     <td>
 377       &nbsp;
 378     </td>
 379     <td>
 380
 381 <p>
 382
 383 <p>
 384 Definition at line <a class="el" href="pairwise_8c-source.html#l00053">53</a> of file <a class="el" href="pairwise_8c-source.html">pairwise.c</a>.
 385 <p>
 386 Referenced by <a class="el" href="pairwise_8c-source.html#l00160">check_length()</a>.
 387 <p>
 388 <div class="fragment"><pre>00053                             {
 389 00054         printf(message);
 390 00055         exit(EXIT_FAILURE);
 391 00056 }
 392 </pre></div>    </td>
 393   </tr>
 394 </table>
 395 <a name="a7" doxytag="pairwise.c::fatal_sys_error"></a><p>
 396 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 397   <tr>
 398     <td class="mdRow">
 399       <table cellpadding="0" cellspacing="0" border="0">
 400         <tr>
 401           <td class="md" nowrap valign="top"> void fatal_sys_error </td>
 402           <td class="md" valign="top">(&nbsp;</td>
 403           <td class="md" nowrap valign="top">char *&nbsp;</td>
 404           <td class="mdname1" valign="top" nowrap> <em>message</em>          </td>
 405           <td class="md" valign="top">&nbsp;)&nbsp;</td>
 406           <td class="md" nowrap></td>
 407         </tr>
 408
 409       </table>
 410     </td>
 411   </tr>
 412 </table>
 413 <table cellspacing=5 cellpadding=0 border=0>
 414   <tr>
 415     <td>
 416       &nbsp;
 417     </td>
 418     <td>
 419
 420 <p>
 421
 422 <p>
 423 Definition at line <a class="el" href="pairwise_8c-source.html#l00059">59</a> of file <a class="el" href="pairwise_8c-source.html">pairwise.c</a>.
 424 <p>
 425 Referenced by <a class="el" href="pairwise_8c-source.html#l00065">xfopen()</a>, <a class="el" href="pairwise_8c-source.html#l00074">xmalloc()</a>, and <a class="el" href="pairwise_8c-source.html#l00083">xrealloc()</a>.
 426 <p>
 427 <div class="fragment"><pre>00059                                 {
 428 00060         perror(message);
 429 00061         exit(EXIT_FAILURE);
 430 00062 }
 431 </pre></div>    </td>
 432   </tr>
 433 </table>
 434 <a name="a16" doxytag="pairwise.c::main"></a><p>
 435 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 436   <tr>
 437     <td class="mdRow">
 438       <table cellpadding="0" cellspacing="0" border="0">
 439         <tr>
 440           <td class="md" nowrap valign="top"> int main </td>
 441           <td class="md" valign="top">(&nbsp;</td>
 442           <td class="md" nowrap valign="top">int&nbsp;</td>
 443           <td class="mdname" nowrap> <em>argc</em>, </td>
 444         </tr>
 445         <tr>
 446           <td></td>
 447           <td></td>
 448           <td class="md" nowrap>char **&nbsp;</td>
 449           <td class="mdname" nowrap> <em>argv</em></td>
 450         </tr>
 451         <tr>
 452           <td></td>
 453           <td class="md">)&nbsp;</td>
 454           <td class="md" colspan="2"></td>
 455         </tr>
 456
 457       </table>
 458     </td>
 459   </tr>
 460 </table>
 461 <table cellspacing=5 cellpadding=0 border=0>
 462   <tr>
 463     <td>
 464       &nbsp;
 465     </td>
 466     <td>
 467
 468 <p>
 469
 470 <p>
 471 Definition at line <a class="el" href="pairwise_8c-source.html#l00253">253</a> of file <a class="el" href="pairwise_8c-source.html">pairwise.c</a>.
 472 <p>
 473 References <a class="el" href="pairwise_8c-source.html#l00160">check_length()</a>, <a class="el" href="pairwise_8c-source.html#l00106">pairwise()</a>, <a class="el" href="pairwise_8c-source.html#l00179">read_fasta()</a>, and <a class="el" href="pairwise_8c-source.html#l00065">xfopen()</a>.
 474 <p>
 475 <div class="fragment"><pre>00253                              {
 476 00254         FILE *fh;
 477 00255         <span class="keyword">struct </span><a class="code" href="structfasta.html">fasta</a> **array;
 478 00256         <span class="keywordtype">int</span> i = 0, j;
 479 00257
 480 00258         <span class="comment">/* Read in the FASTA file */</span>
 481 00259         <span class="keywordflow">if</span> (argc == 2)
 482 00260                 fh = <a class="code" href="pairwise_8c.html#a8">xfopen</a>(argv[1], <span class="stringliteral">"r"</span>);
 483 00261         <span class="keywordflow">else</span>
 484 00262                 fh = stdin;
 485 00263
 486 00264         array = <a class="code" href="pairwise_8c.html#a15">read_fasta</a>(fh);
 487 00265         fclose(fh);
 488 00266
 489 00267         <a class="code" href="pairwise_8c.html#a14">check_length</a>(array);
 490 00268
 491 00269         <span class="comment">/* start the OC output */</span>
 492 00270         <span class="keywordflow">while</span> (array[i] != NULL)
 493 00271                 i++;
 494 00272
 495 00273         fprintf(stdout, <span class="stringliteral">"%i\n"</span>, i);
 496 00274
 497 00275         <span class="keywordflow">for</span> (i = 0; array[i] != NULL; i++)
 498 00276                 fprintf(stdout, <span class="stringliteral">"%s\n"</span>, array[i]-&gt;id);
 499 00277
 500 00278         <span class="comment">/* do the pairwise comparison */</span>
 501 00279         <span class="keywordflow">for</span> (i = 0; array[i] != NULL; i++) {
 502 00280                 <span class="keywordflow">for</span> (j = i + 1; array[j] != NULL; j++) {
 503 00281                         printf(<span class="stringliteral">"%f\n"</span>, <a class="code" href="pairwise_8c.html#a12">pairwise</a>(array[i], array[j]));
 504 00282                 }
 505 00283         }
 506 00284
 507 00285         <span class="keywordflow">return</span> EXIT_SUCCESS;
 508 00286 }
 509 </pre></div>    </td>
 510   </tr>
 511 </table>
 512
 513 <p>
 514 Here is the call graph for this function:<p><center><img src="pairwise_8c_a16_cgraph.png" border="0" usemap="#pairwise_8c_a16_cgraph_map" alt=""></center>
 515 <map name="pairwise_8c_a16_cgraph_map">
 516 <area href="pairwise_8h.html#a7" shape="rect" coords="108,5,201,24" alt="">
 517 <area href="pairwise_8h.html#a5" shape="rect" coords="124,48,185,67" alt="">
 518 <area href="pairwise_8h.html#a8" shape="rect" coords="116,209,193,228" alt="">
 519 <area href="pairwise_8h.html#a1" shape="rect" coords="263,92,316,111" alt="">
 520 <area href="pairwise_8h.html#a0" shape="rect" coords="252,5,327,24" alt="">
 521 <area href="pairwise_8h.html#a4" shape="rect" coords="271,48,308,67" alt="">
 522 <area href="pairwise_8h.html#a6" shape="rect" coords="377,153,444,172" alt="">
 523 <area href="pairwise_8c.html#a15" shape="rect" coords="251,209,328,228" alt="">
 524 <area href="pairwise_8c.html#a9" shape="rect" coords="381,252,440,271" alt="">
 525 <area href="pairwise_8h.html#a3" shape="rect" coords="380,209,441,228" alt="">
 526 <area href="pairwise_8c.html#a7" shape="rect" coords="492,209,596,228" alt="">
 527 </map>
 528 <a name="a12" doxytag="pairwise.c::pairwise"></a><p>
 529 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 530   <tr>
 531     <td class="mdRow">
 532       <table cellpadding="0" cellspacing="0" border="0">
 533         <tr>
 534           <td class="md" nowrap valign="top"> float pairwise </td>
 535           <td class="md" valign="top">(&nbsp;</td>
 536           <td class="md" nowrap valign="top">struct <a class="el" href="structfasta.html">fasta</a> *&nbsp;</td>
 537           <td class="mdname" nowrap> <em>a</em>, </td>
 538         </tr>
 539         <tr>
 540           <td></td>
 541           <td></td>
 542           <td class="md" nowrap>struct <a class="el" href="structfasta.html">fasta</a> *&nbsp;</td>
 543           <td class="mdname" nowrap> <em>b</em></td>
 544         </tr>
 545         <tr>
 546           <td></td>
 547           <td class="md">)&nbsp;</td>
 548           <td class="md" colspan="2"></td>
 549         </tr>
 550
 551       </table>
 552     </td>
 553   </tr>
 554 </table>
 555 <table cellspacing=5 cellpadding=0 border=0>
 556   <tr>
 557     <td>
 558       &nbsp;
 559     </td>
 560     <td>
 561
 562 <p>
 563
 564 <p>
 565 Definition at line <a class="el" href="pairwise_8c-source.html#l00106">106</a> of file <a class="el" href="pairwise_8c-source.html">pairwise.c</a>.
 566 <p>
 567 References <a class="el" href="pairwise_8c-source.html#l00092">diff()</a>, <a class="el" href="pairwise_8h-source.html#l00007">fasta::end</a>, <a class="el" href="pairwise_8c-source.html#l00035">MAX</a>, <a class="el" href="pairwise_8c-source.html#l00039">MIN</a>, <a class="el" href="pairwise_8h-source.html#l00008">fasta::numres</a>, <a class="el" href="pairwise_8h-source.html#l00005">fasta::seq</a>, and <a class="el" href="pairwise_8h-source.html#l00006">fasta::start</a>.
 568 <p>
 569 Referenced by <a class="el" href="pairwise_8c-source.html#l00253">main()</a>.
 570 <p>
 571 <div class="fragment"><pre>00106                                             {
 572 00107         <span class="keywordtype">float</span> result;
 573 00108         <span class="keywordtype">int</span> start, end, numres, i, id = 0;
 574 00109
 575 00110         <span class="comment">/* If the sequences don't overlap then the seq ID is 0 */</span>
 576 00111         <span class="keywordflow">if</span> (a-&gt;<a class="code" href="structfasta.html#o3">end</a> &lt; b-&gt;<a class="code" href="structfasta.html#o2">start</a> || a-&gt;<a class="code" href="structfasta.html#o2">start</a> &gt; b-&gt;<a class="code" href="structfasta.html#o3">end</a>)
 577 00112                 <span class="keywordflow">return</span> 0;
 578 00113
 579 00114         start = <a class="code" href="pairwise_8c.html#a3">MIN</a>( a-&gt;<a class="code" href="structfasta.html#o2">start</a>, b-&gt;<a class="code" href="structfasta.html#o2">start</a> );
 580 00115         end = <a class="code" href="pairwise_8c.html#a2">MAX</a>( a-&gt;<a class="code" href="structfasta.html#o3">end</a>, b-&gt;<a class="code" href="structfasta.html#o3">end</a> );
 581 00116         numres = <a class="code" href="pairwise_8c.html#a2">MAX</a>( a-&gt;<a class="code" href="structfasta.html#o4">numres</a>, b-&gt;<a class="code" href="structfasta.html#o4">numres</a> );
 582 00117
 583 00118         <span class="keywordflow">for</span> (i = start; i &lt; end; i++)
 584 00119                 id += <a class="code" href="pairwise_8c.html#a11">diff</a>(a-&gt;<a class="code" href="structfasta.html#o1">seq</a>[i], b-&gt;<a class="code" href="structfasta.html#o1">seq</a>[i]);
 585 00120
 586 00121         result = 100 * (<span class="keywordtype">float</span>) id / (<span class="keywordtype">float</span>) numres;
 587 00122
 588 00123         <span class="keywordflow">return</span> result;
 589 00124 }
 590 </pre></div>    </td>
 591   </tr>
 592 </table>
 593
 594 <p>
 595 Here is the call graph for this function:<p><center><img src="pairwise_8c_a12_cgraph.png" border="0" usemap="#pairwise_8c_a12_cgraph_map" alt=""></center>
 596 <map name="pairwise_8c_a12_cgraph_map">
 597 <area href="pairwise_8h.html#a4" shape="rect" coords="131,5,168,23" alt="">
 598 </map>
 599 <a name="a13" doxytag="pairwise.c::populate"></a><p>
 600 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 601   <tr>
 602     <td class="mdRow">
 603       <table cellpadding="0" cellspacing="0" border="0">
 604         <tr>
 605           <td class="md" nowrap valign="top"> void populate </td>
 606           <td class="md" valign="top">(&nbsp;</td>
 607           <td class="md" nowrap valign="top">struct <a class="el" href="structfasta.html">fasta</a> *&nbsp;</td>
 608           <td class="mdname1" valign="top" nowrap> <em>a</em>          </td>
 609           <td class="md" valign="top">&nbsp;)&nbsp;</td>
 610           <td class="md" nowrap></td>
 611         </tr>
 612
 613       </table>
 614     </td>
 615   </tr>
 616 </table>
 617 <table cellspacing=5 cellpadding=0 border=0>
 618   <tr>
 619     <td>
 620       &nbsp;
 621     </td>
 622     <td>
 623
 624 <p>
 625
 626 <p>
 627 Definition at line <a class="el" href="pairwise_8c-source.html#l00133">133</a> of file <a class="el" href="pairwise_8c-source.html">pairwise.c</a>.
 628 <p>
 629 References <a class="el" href="pairwise_8h-source.html#l00007">fasta::end</a>, <a class="el" href="pairwise_8h-source.html#l00008">fasta::numres</a>, <a class="el" href="pairwise_8h-source.html#l00005">fasta::seq</a>, and <a class="el" href="pairwise_8h-source.html#l00006">fasta::start</a>.
 630 <p>
 631 Referenced by <a class="el" href="pairwise_8c-source.html#l00179">read_fasta()</a>.
 632 <p>
 633 <div class="fragment"><pre>00133                            {
 634 00134         <span class="keywordtype">int</span> i;
 635 00135         <span class="keywordtype">int</span> len = strlen(a-&gt;<a class="code" href="structfasta.html#o1">seq</a>);
 636 00136
 637 00137         a-&gt;<a class="code" href="structfasta.html#o4">numres</a> = 0;
 638 00138
 639 00139         <span class="keywordflow">for</span> (i = 0; i &lt;= len; i++) {
 640 00140                 <span class="keywordflow">if</span> (a-&gt;<a class="code" href="structfasta.html#o1">seq</a>[i] != <span class="charliteral">'-'</span>) {
 641 00141                         a-&gt;<a class="code" href="structfasta.html#o2">start</a> = i;
 642 00142                         <span class="keywordflow">break</span>;
 643 00143                 }
 644 00144         }
 645 00145         <span class="keywordflow">for</span> (i = len; i &gt; 0; i--) {
 646 00146                 <span class="keywordflow">if</span> (a-&gt;<a class="code" href="structfasta.html#o1">seq</a>[i] != <span class="charliteral">'-'</span>) {
 647 00147                         a-&gt;<a class="code" href="structfasta.html#o3">end</a> = i;
 648 00148                         <span class="keywordflow">break</span>;
 649 00149                 }
 650 00150         }
 651 00151         <span class="keywordflow">for</span> (i = a-&gt;<a class="code" href="structfasta.html#o2">start</a>; i &lt; a-&gt;<a class="code" href="structfasta.html#o3">end</a>; i++) {
 652 00152                 <span class="keywordflow">if</span> (a-&gt;<a class="code" href="structfasta.html#o1">seq</a>[i] != <span class="charliteral">'-'</span>) {
 653 00153                         a-&gt;<a class="code" href="structfasta.html#o4">numres</a>++;
 654 00154                 }
 655 00155         }
 656 00156 }
 657 </pre></div>    </td>
 658   </tr>
 659 </table>
 660 <a name="a15" doxytag="pairwise.c::read_fasta"></a><p>
 661 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 662   <tr>
 663     <td class="mdRow">
 664       <table cellpadding="0" cellspacing="0" border="0">
 665         <tr>
 666           <td class="md" nowrap valign="top"> struct <a class="el" href="structfasta.html">fasta</a>** read_fasta </td>
 667           <td class="md" valign="top">(&nbsp;</td>
 668           <td class="md" nowrap valign="top">FILE *&nbsp;</td>
 669           <td class="mdname1" valign="top" nowrap> <em>fh</em>          </td>
 670           <td class="md" valign="top">&nbsp;)&nbsp;</td>
 671           <td class="md" nowrap></td>
 672         </tr>
 673
 674       </table>
 675     </td>
 676   </tr>
 677 </table>
 678 <table cellspacing=5 cellpadding=0 border=0>
 679   <tr>
 680     <td>
 681       &nbsp;
 682     </td>
 683     <td>
 684
 685 <p>
 686
 687 <p>
 688 Definition at line <a class="el" href="pairwise_8c-source.html#l00179">179</a> of file <a class="el" href="pairwise_8c-source.html">pairwise.c</a>.
 689 <p>
 690 References <a class="el" href="pairwise_8c-source.html#l00029">ARRAY</a>, <a class="el" href="pairwise_8c-source.html#l00030">FILEBUF</a>, <a class="el" href="pairwise_8h-source.html#l00004">fasta::id</a>, <a class="el" href="pairwise_8h-source.html#l00008">fasta::numres</a>, <a class="el" href="pairwise_8c-source.html#l00133">populate()</a>, <a class="el" href="pairwise_8c-source.html#l00179">read_fasta()</a>, <a class="el" href="pairwise_8h-source.html#l00005">fasta::seq</a>, <a class="el" href="pairwise_8c-source.html#l00074">xmalloc()</a>, and <a class="el" href="pairwise_8c-source.html#l00083">xrealloc()</a>.
 691 <p>
 692 Referenced by <a class="el" href="pairwise_8c-source.html#l00253">main()</a>, and <a class="el" href="pairwise_8c-source.html#l00179">read_fasta()</a>.
 693 <p>
 694 <div class="fragment"><pre>00179                       {
 695 00180         <span class="keywordtype">int</span> i, j, k, c, filesize = 1;
 696 00181         <span class="keywordtype">char</span> *file;
 697 00182         <span class="keyword">struct </span><a class="code" href="structfasta.html">fasta</a> **array;
 698 00183
 699 00184         array = (<span class="keyword">struct </span><a class="code" href="structfasta.html">fasta</a> **) <a class="code" href="pairwise_8c.html#a9">xmalloc</a>(<a class="code" href="pairwise_8c.html#a0">ARRAY</a> * sizeof(struct fasta *));
 700 00185         file = (<span class="keywordtype">char</span> *) <a class="code" href="pairwise_8c.html#a9">xmalloc</a>(<span class="keyword">sizeof</span>(<span class="keywordtype">char</span>));
 701 00186
 702 00187         <span class="comment">/* Allocate initial space for the file */</span>
 703 00188         file = <a class="code" href="pairwise_8c.html#a10">xrealloc</a>(file, <span class="keyword">sizeof</span>(<span class="keywordtype">char</span>) * filesize);
 704 00189         file[filesize] = <span class="charliteral">'\0'</span>;
 705 00190
 706 00191         <span class="comment">/* Read in the file */</span>
 707 00192         <span class="keywordflow">while</span> ((c = getc(fh)) != EOF) {
 708 00193                 <span class="keywordflow">if</span> (filesize % <a class="code" href="pairwise_8c.html#a1">FILEBUF</a>)
 709 00194                         file = <a class="code" href="pairwise_8c.html#a10">xrealloc</a>(file, <span class="keyword">sizeof</span>(<span class="keywordtype">char</span>) * (FILEBUF + filesize));
 710 00195
 711 00196                 file[filesize] = c;
 712 00197                 filesize++;
 713 00198         }
 714 00199
 715 00200         <span class="comment">/* Parse the FASTA file into an array of structures */</span>
 716 00201         <span class="keywordflow">for</span> (i = 0, j = 0, k = 0; i &lt; filesize; i++) {
 717 00202                 <span class="keywordflow">if</span> (file[i] == <span class="charliteral">'&gt;'</span>) {
 718 00203                         <span class="keywordflow">if</span> (j % <a class="code" href="pairwise_8c.html#a0">ARRAY</a> == 0)
 719 00204                                 array = (<span class="keyword">struct </span>fasta **) <a class="code" href="pairwise_8c.html#a10">xrealloc</a>(array, sizeof(struct fasta *) * (j + <a class="code" href="pairwise_8c.html#a0">ARRAY</a>));
 720 00205
 721 00206                         array[j] = (<span class="keyword">struct </span>fasta *) <a class="code" href="pairwise_8c.html#a9">xmalloc</a>(sizeof(struct fasta));
 722 00207                         array[j]-&gt;<a class="code" href="structfasta.html#o0">id</a> = (<span class="keywordtype">char</span> *) <a class="code" href="pairwise_8c.html#a9">xmalloc</a>(<span class="keyword">sizeof</span>(<span class="keywordtype">char</span>));
 723 00208                         array[j]-&gt;<a class="code" href="structfasta.html#o1">seq</a> = (<span class="keywordtype">char</span> *) <a class="code" href="pairwise_8c.html#a9">xmalloc</a>(<span class="keyword">sizeof</span>(<span class="keywordtype">char</span>));
 724 00209                         array[j]-&gt;<a class="code" href="structfasta.html#o4">numres</a> = 0;
 725 00210
 726 00211                         i++;
 727 00212                         <span class="keywordflow">while</span> (file[i] != <span class="charliteral">'\0'</span> &amp;&amp; file[i] != <span class="charliteral">'\n'</span>) {
 728 00213                                 <span class="keywordflow">if</span> (k % <a class="code" href="pairwise_8c.html#a0">ARRAY</a> == 0)
 729 00214                                         array[j]-&gt;<a class="code" href="structfasta.html#o0">id</a> = (<span class="keywordtype">char</span> *) <a class="code" href="pairwise_8c.html#a10">xrealloc</a>(array[j]-&gt;id, <span class="keyword">sizeof</span>(<span class="keywordtype">char</span>) * (ARRAY + k));
 730 00215                                 array[j]-&gt;<a class="code" href="structfasta.html#o0">id</a>[k] = file[i];
 731 00216                                 k++; i++;
 732 00217                         }
 733 00218                         array[j]-&gt;<a class="code" href="structfasta.html#o0">id</a> = (<span class="keywordtype">char</span> *) <a class="code" href="pairwise_8c.html#a10">xrealloc</a>(array[j]-&gt;id, <span class="keyword">sizeof</span>(<span class="keywordtype">char</span>) * (ARRAY + k));
 734 00219                         array[j]-&gt;<a class="code" href="structfasta.html#o0">id</a>[k] = <span class="charliteral">'\0'</span>;
 735 00220                         k = 0;
 736 00221
 737 00222                         <span class="keywordflow">while</span> (file[i] != <span class="charliteral">'\0'</span> &amp;&amp; file[i] != <span class="charliteral">'&gt;'</span>) {
 738 00223                                 <span class="keywordflow">if</span> (file[i] == <span class="charliteral">'\n'</span>) {
 739 00224                                         i++;
 740 00225                                         <span class="keywordflow">continue</span>;
 741 00226                                 }
 742 00227                                 <span class="keywordflow">if</span> (k % <a class="code" href="pairwise_8c.html#a0">ARRAY</a> == 0)
 743 00228                                         array[j]-&gt;<a class="code" href="structfasta.html#o1">seq</a> = (<span class="keywordtype">char</span> *) <a class="code" href="pairwise_8c.html#a10">xrealloc</a>(array[j]-&gt;seq, <span class="keyword">sizeof</span>(<span class="keywordtype">char</span>) * (ARRAY + k));
 744 00229                                 array[j]-&gt;<a class="code" href="structfasta.html#o1">seq</a>[k] = file[i];
 745 00230                                 k++; i++;
 746 00231                         }
 747 00232                         array[j]-&gt;<a class="code" href="structfasta.html#o1">seq</a> = (<span class="keywordtype">char</span> *) <a class="code" href="pairwise_8c.html#a10">xrealloc</a>(array[j]-&gt;seq, <span class="keyword">sizeof</span>(<span class="keywordtype">char</span>) * (ARRAY + k));
 748 00233                         array[j]-&gt;<a class="code" href="structfasta.html#o1">seq</a>[k] = <span class="charliteral">'\0'</span>;
 749 00234                         k = 0;
 750 00235                         i--;
 751 00236                         j++;
 752 00237                 }
 753 00238         }
 754 00239
 755 00240         free(file);
 756 00241         array = (<span class="keyword">struct </span>fasta **) <a class="code" href="pairwise_8c.html#a10">xrealloc</a>(array, sizeof(struct fasta *) * j);
 757 00242         array[j] = NULL;
 758 00243
 759 00244         <span class="comment">/* find the start and end points for the alignments */</span>
 760 00245         <span class="keywordflow">for</span> (i = 0; array[i] != NULL; i++) {
 761 00246                 <a class="code" href="pairwise_8c.html#a13">populate</a>(array[i]);
 762 00247         }
 763 00248
 764 00249         <span class="keywordflow">return</span> array;
 765 00250 }
 766 </pre></div>    </td>
 767   </tr>
 768 </table>
 769
 770 <p>
 771 Here is the call graph for this function:<p><center><img src="pairwise_8c_a15_cgraph.png" border="0" usemap="#pairwise_8c_a15_cgraph_map" alt=""></center>
 772 <map name="pairwise_8c_a15_cgraph_map">
 773 <area href="pairwise_8h.html#a6" shape="rect" coords="145,5,212,24" alt="">
 774 <area href="pairwise_8c.html#a9" shape="rect" coords="149,48,208,67" alt="">
 775 <area href="pairwise_8h.html#a3" shape="rect" coords="148,91,209,109" alt="">
 776 <area href="pairwise_8c.html#a7" shape="rect" coords="260,69,364,88" alt="">
 777 </map>
 778 <a name="a8" doxytag="pairwise.c::xfopen"></a><p>
 779 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 780   <tr>
 781     <td class="mdRow">
 782       <table cellpadding="0" cellspacing="0" border="0">
 783         <tr>
 784           <td class="md" nowrap valign="top"> FILE* xfopen </td>
 785           <td class="md" valign="top">(&nbsp;</td>
 786           <td class="md" nowrap valign="top">const char *&nbsp;</td>
 787           <td class="mdname" nowrap> <em>path</em>, </td>
 788         </tr>
 789         <tr>
 790           <td></td>
 791           <td></td>
 792           <td class="md" nowrap>const char *&nbsp;</td>
 793           <td class="mdname" nowrap> <em>mode</em></td>
 794         </tr>
 795         <tr>
 796           <td></td>
 797           <td class="md">)&nbsp;</td>
 798           <td class="md" colspan="2"></td>
 799         </tr>
 800
 801       </table>
 802     </td>
 803   </tr>
 804 </table>
 805 <table cellspacing=5 cellpadding=0 border=0>
 806   <tr>
 807     <td>
 808       &nbsp;
 809     </td>
 810     <td>
 811
 812 <p>
 813
 814 <p>
 815 Definition at line <a class="el" href="pairwise_8c-source.html#l00065">65</a> of file <a class="el" href="pairwise_8c-source.html">pairwise.c</a>.
 816 <p>
 817 References <a class="el" href="pairwise_8c-source.html#l00059">fatal_sys_error()</a>.
 818 <p>
 819 Referenced by <a class="el" href="pairwise_8c-source.html#l00253">main()</a>.
 820 <p>
 821 <div class="fragment"><pre>00065                                             {
 822 00066         FILE *fh;
 823 00067         fh = fopen(path, mode);
 824 00068         <span class="keywordflow">if</span> (fh == NULL)
 825 00069                 <a class="code" href="pairwise_8c.html#a7">fatal_sys_error</a>(<span class="stringliteral">"fopen returned NULL"</span>);
 826 00070         <span class="keywordflow">return</span> fh;
 827 00071 }
 828 </pre></div>    </td>
 829   </tr>
 830 </table>
 831
 832 <p>
 833 Here is the call graph for this function:<p><center><img src="pairwise_8c_a8_cgraph.png" border="0" usemap="#pairwise_8c_a8_cgraph_map" alt=""></center>
 834 <map name="pairwise_8c_a8_cgraph_map">
 835 <area href="pairwise_8c.html#a7" shape="rect" coords="121,5,225,23" alt="">
 836 </map>
 837 <a name="a9" doxytag="pairwise.c::xmalloc"></a><p>
 838 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 839   <tr>
 840     <td class="mdRow">
 841       <table cellpadding="0" cellspacing="0" border="0">
 842         <tr>
 843           <td class="md" nowrap valign="top"> void* xmalloc </td>
 844           <td class="md" valign="top">(&nbsp;</td>
 845           <td class="md" nowrap valign="top">size_t&nbsp;</td>
 846           <td class="mdname1" valign="top" nowrap> <em>size</em>          </td>
 847           <td class="md" valign="top">&nbsp;)&nbsp;</td>
 848           <td class="md" nowrap></td>
 849         </tr>
 850
 851       </table>
 852     </td>
 853   </tr>
 854 </table>
 855 <table cellspacing=5 cellpadding=0 border=0>
 856   <tr>
 857     <td>
 858       &nbsp;
 859     </td>
 860     <td>
 861
 862 <p>
 863
 864 <p>
 865 Definition at line <a class="el" href="pairwise_8c-source.html#l00074">74</a> of file <a class="el" href="pairwise_8c-source.html">pairwise.c</a>.
 866 <p>
 867 References <a class="el" href="pairwise_8c-source.html#l00059">fatal_sys_error()</a>.
 868 <p>
 869 Referenced by <a class="el" href="pairwise_8c-source.html#l00179">read_fasta()</a>.
 870 <p>
 871 <div class="fragment"><pre>00074                       {
 872 00075         <span class="keywordtype">void</span> *ptr;
 873 00076         ptr = (<span class="keywordtype">void</span> *) malloc(size);
 874 00077         <span class="keywordflow">if</span> (ptr == NULL)
 875 00078                 <a class="code" href="pairwise_8c.html#a7">fatal_sys_error</a>(<span class="stringliteral">"malloc returned NULL"</span>);
 876 00079         <span class="keywordflow">return</span> ptr;
 877 00080 }
 878 </pre></div>    </td>
 879   </tr>
 880 </table>
 881
 882 <p>
 883 Here is the call graph for this function:<p><center><img src="pairwise_8c_a9_cgraph.png" border="0" usemap="#pairwise_8c_a9_cgraph_map" alt=""></center>
 884 <map name="pairwise_8c_a9_cgraph_map">
 885 <area href="pairwise_8c.html#a7" shape="rect" coords="127,5,231,23" alt="">
 886 </map>
 887 <a name="a10" doxytag="pairwise.c::xrealloc"></a><p>
 888 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 889   <tr>
 890     <td class="mdRow">
 891       <table cellpadding="0" cellspacing="0" border="0">
 892         <tr>
 893           <td class="md" nowrap valign="top"> void* xrealloc </td>
 894           <td class="md" valign="top">(&nbsp;</td>
 895           <td class="md" nowrap valign="top">void *&nbsp;</td>
 896           <td class="mdname" nowrap> <em>ptr</em>, </td>
 897         </tr>
 898         <tr>
 899           <td></td>
 900           <td></td>
 901           <td class="md" nowrap>size_t&nbsp;</td>
 902           <td class="mdname" nowrap> <em>size</em></td>
 903         </tr>
 904         <tr>
 905           <td></td>
 906           <td class="md">)&nbsp;</td>
 907           <td class="md" colspan="2"></td>
 908         </tr>
 909
 910       </table>
 911     </td>
 912   </tr>
 913 </table>
 914 <table cellspacing=5 cellpadding=0 border=0>
 915   <tr>
 916     <td>
 917       &nbsp;
 918     </td>
 919     <td>
 920
 921 <p>
 922
 923 <p>
 924 Definition at line <a class="el" href="pairwise_8c-source.html#l00083">83</a> of file <a class="el" href="pairwise_8c-source.html">pairwise.c</a>.
 925 <p>
 926 References <a class="el" href="pairwise_8c-source.html#l00059">fatal_sys_error()</a>.
 927 <p>
 928 Referenced by <a class="el" href="pairwise_8c-source.html#l00179">read_fasta()</a>.
 929 <p>
 930 <div class="fragment"><pre>00083                                   {
 931 00084         ptr = (<span class="keywordtype">void</span> *) realloc(ptr, size);
 932 00085         <span class="keywordflow">if</span> (ptr == NULL &amp;&amp; size != 0)
 933 00086                 <a class="code" href="pairwise_8c.html#a7">fatal_sys_error</a>(<span class="stringliteral">"realloc returned NULL"</span>);
 934 00087         <span class="keywordflow">return</span> ptr;
 935 00088 }
 936 </pre></div>    </td>
 937   </tr>
 938 </table>
 939
 940 <p>
 941 Here is the call graph for this function:<p><center><img src="pairwise_8c_a10_cgraph.png" border="0" usemap="#pairwise_8c_a10_cgraph_map" alt=""></center>
 942 <map name="pairwise_8c_a10_cgraph_map">
 943 <area href="pairwise_8c.html#a7" shape="rect" coords="127,5,231,23" alt="">
 944 </map>
 945 <hr size="1"><address style="align: right;"><small>Generated on Thu Jul 24 12:17:51 2003 for pairwise by
 946 <a href="http://www.doxygen.org/index.html">
 947 <img src="doxygen.png" alt="doxygen" align="middle" border=0 >
 948 </a>1.3.2 </small></address>
 949 </body>
 950 </html>