sources/pairwise/docs/html/pairwise_8h.html

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   8 <h1>pairwise.h File Reference</h1><code>#include &lt;stdlib.h&gt;</code><br>
   9
  10 <p>
  11 Include dependency graph for pairwise.h:<p><center><img src="pairwise_8h__incl.png" border="0" usemap="#pairwise.h_map" alt="Include dependency graph"></center>
  12
  13 <p>
  14 This graph shows which files directly or indirectly include this file:<p><center><img src="pairwise_8h__dep__incl.png" border="0" usemap="#pairwise.hdep_map" alt="Included by dependency graph"></center>
  15 <map name="pairwise.hdep_map">
  16 <area href="pairwise_8c.html" shape="rect" coords="7,17,79,36" alt="">
  17 </map>
  18
  19 <p>
  20 <a href="pairwise_8h-source.html">Go to the source code of this file.</a><table border=0 cellpadding=0 cellspacing=0>
  21 <tr><td></td></tr>
  22 <tr><td colspan=2><br><h2>Data Structures</h2></td></tr>
  23 <tr><td class="memItemLeft" nowrap align=right valign=top>struct &nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="structfasta.html">fasta</a></td></tr>
  24
  25 <tr><td colspan=2><br><h2>Functions</h2></td></tr>
  26 <tr><td class="memItemLeft" nowrap align=right valign=top>void&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8h.html#a0">fatal_error</a> (char *message)</td></tr>
  27
  28 <tr><td class="memItemLeft" nowrap align=right valign=top>FILE *&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8h.html#a1">xfopen</a> (const char *path, const char *mode)</td></tr>
  29
  30 <tr><td class="memItemLeft" nowrap align=right valign=top>void *&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8h.html#a2">xmalloc</a> (size_t size)</td></tr>
  31
  32 <tr><td class="memItemLeft" nowrap align=right valign=top>void *&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8h.html#a3">xrealloc</a> (void *ptr, size_t size)</td></tr>
  33
  34 <tr><td class="memItemLeft" nowrap align=right valign=top>int&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8h.html#a4">diff</a> (char a, char b)</td></tr>
  35
  36 <tr><td class="memItemLeft" nowrap align=right valign=top>float&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8h.html#a5">pairwise</a> (struct <a class="el" href="structfasta.html">fasta</a> *a, struct <a class="el" href="structfasta.html">fasta</a> *b)</td></tr>
  37
  38 <tr><td class="memItemLeft" nowrap align=right valign=top>void&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8h.html#a6">populate</a> (struct <a class="el" href="structfasta.html">fasta</a> *a)</td></tr>
  39
  40 <tr><td class="memItemLeft" nowrap align=right valign=top>void&nbsp;</td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8h.html#a7">check_length</a> (struct <a class="el" href="structfasta.html">fasta</a> **array)</td></tr>
  41
  42 <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_8h.html#a8">read_fasta</a> (FILE *fh)</td></tr>
  43
  44 </table>
  45 <hr><h2>Function Documentation</h2>
  46 <a name="a7" doxytag="pairwise.h::check_length"></a><p>
  47 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
  48   <tr>
  49     <td class="mdRow">
  50       <table cellpadding="0" cellspacing="0" border="0">
  51         <tr>
  52           <td class="md" nowrap valign="top"> void check_length </td>
  53           <td class="md" valign="top">(&nbsp;</td>
  54           <td class="md" nowrap valign="top">struct <a class="el" href="structfasta.html">fasta</a> **&nbsp;</td>
  55           <td class="mdname1" valign="top" nowrap> <em>array</em>          </td>
  56           <td class="md" valign="top">&nbsp;)&nbsp;</td>
  57           <td class="md" nowrap></td>
  58         </tr>
  59
  60       </table>
  61     </td>
  62   </tr>
  63 </table>
  64 <table cellspacing=5 cellpadding=0 border=0>
  65   <tr>
  66     <td>
  67       &nbsp;
  68     </td>
  69     <td>
  70
  71 <p>
  72
  73 <p>
  74 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>.
  75 <p>
  76 References <a class="el" href="pairwise_8c-source.html#l00053">fatal_error()</a>.
  77 <p>
  78 Referenced by <a class="el" href="pairwise_8c-source.html#l00253">main()</a>.
  79 <p>
  80 <div class="fragment"><pre>00160                                     {
  81 00161         <span class="keywordtype">int</span> i, length;
  82 00162
  83 00163         <span class="keywordflow">if</span> (array[0] != NULL)
  84 00164                 length = strlen(array[0]-&gt;seq);
  85 00165         <span class="keywordflow">else</span> {
  86 00166                 fprintf(stderr, <span class="stringliteral">"check_length() not passed an array of fasta structs\n"</span>);
  87 00167                 <span class="keywordflow">return</span>;
  88 00168         }
  89 00169
  90 00170         <span class="keywordflow">for</span> (i = 0; array[i] != NULL; i++) {
  91 00171                 <span class="keywordflow">if</span> (length != strlen(array[i]-&gt;seq)) {
  92 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>);
  93 00173                 }
  94 00174         }
  95 00175 }
  96 </pre></div>    </td>
  97   </tr>
  98 </table>
  99
 100 <p>
 101 Here is the call graph for this function:<p><center><img src="pairwise_8h_a7_cgraph.png" border="0" usemap="#pairwise_8h_a7_cgraph_map" alt=""></center>
 102 <map name="pairwise_8h_a7_cgraph_map">
 103 <area href="pairwise_8h.html#a0" shape="rect" coords="160,5,235,23" alt="">
 104 </map>
 105 <a name="a4" doxytag="pairwise.h::diff"></a><p>
 106 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 107   <tr>
 108     <td class="mdRow">
 109       <table cellpadding="0" cellspacing="0" border="0">
 110         <tr>
 111           <td class="md" nowrap valign="top"> int diff </td>
 112           <td class="md" valign="top">(&nbsp;</td>
 113           <td class="md" nowrap valign="top">char&nbsp;</td>
 114           <td class="mdname" nowrap> <em>a</em>, </td>
 115         </tr>
 116         <tr>
 117           <td></td>
 118           <td></td>
 119           <td class="md" nowrap>char&nbsp;</td>
 120           <td class="mdname" nowrap> <em>b</em></td>
 121         </tr>
 122         <tr>
 123           <td></td>
 124           <td class="md">)&nbsp;</td>
 125           <td class="md" colspan="2"></td>
 126         </tr>
 127
 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#l00092">92</a> of file <a class="el" href="pairwise_8c-source.html">pairwise.c</a>.
 143 <p>
 144 Referenced by <a class="el" href="pairwise_8c-source.html#l00106">pairwise()</a>.
 145 <p>
 146 <div class="fragment"><pre>00092                       {
 147 00093         <span class="keywordflow">if</span> (a == b &amp;&amp; a == <span class="charliteral">'-'</span>)
 148 00094                 <span class="keywordflow">return</span> 0;
 149 00095         <span class="keywordflow">if</span> (a == b)
 150 00096                 <span class="keywordflow">return</span> 1;
 151 00097         <span class="keywordflow">return</span> 0;
 152 00098 }
 153 </pre></div>    </td>
 154   </tr>
 155 </table>
 156 <a name="a0" doxytag="pairwise.h::fatal_error"></a><p>
 157 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 158   <tr>
 159     <td class="mdRow">
 160       <table cellpadding="0" cellspacing="0" border="0">
 161         <tr>
 162           <td class="md" nowrap valign="top"> void fatal_error </td>
 163           <td class="md" valign="top">(&nbsp;</td>
 164           <td class="md" nowrap valign="top">char *&nbsp;</td>
 165           <td class="mdname1" valign="top" nowrap> <em>message</em>          </td>
 166           <td class="md" valign="top">&nbsp;)&nbsp;</td>
 167           <td class="md" nowrap></td>
 168         </tr>
 169
 170       </table>
 171     </td>
 172   </tr>
 173 </table>
 174 <table cellspacing=5 cellpadding=0 border=0>
 175   <tr>
 176     <td>
 177       &nbsp;
 178     </td>
 179     <td>
 180
 181 <p>
 182
 183 <p>
 184 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>.
 185 <p>
 186 Referenced by <a class="el" href="pairwise_8c-source.html#l00160">check_length()</a>.
 187 <p>
 188 <div class="fragment"><pre>00053                             {
 189 00054         printf(message);
 190 00055         exit(EXIT_FAILURE);
 191 00056 }
 192 </pre></div>    </td>
 193   </tr>
 194 </table>
 195 <a name="a5" doxytag="pairwise.h::pairwise"></a><p>
 196 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 197   <tr>
 198     <td class="mdRow">
 199       <table cellpadding="0" cellspacing="0" border="0">
 200         <tr>
 201           <td class="md" nowrap valign="top"> float pairwise </td>
 202           <td class="md" valign="top">(&nbsp;</td>
 203           <td class="md" nowrap valign="top">struct <a class="el" href="structfasta.html">fasta</a> *&nbsp;</td>
 204           <td class="mdname" nowrap> <em>a</em>, </td>
 205         </tr>
 206         <tr>
 207           <td></td>
 208           <td></td>
 209           <td class="md" nowrap>struct <a class="el" href="structfasta.html">fasta</a> *&nbsp;</td>
 210           <td class="mdname" nowrap> <em>b</em></td>
 211         </tr>
 212         <tr>
 213           <td></td>
 214           <td class="md">)&nbsp;</td>
 215           <td class="md" colspan="2"></td>
 216         </tr>
 217
 218       </table>
 219     </td>
 220   </tr>
 221 </table>
 222 <table cellspacing=5 cellpadding=0 border=0>
 223   <tr>
 224     <td>
 225       &nbsp;
 226     </td>
 227     <td>
 228
 229 <p>
 230
 231 <p>
 232 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>.
 233 <p>
 234 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>.
 235 <p>
 236 Referenced by <a class="el" href="pairwise_8c-source.html#l00253">main()</a>.
 237 <p>
 238 <div class="fragment"><pre>00106                                             {
 239 00107         <span class="keywordtype">float</span> result;
 240 00108         <span class="keywordtype">int</span> start, end, numres, i, id = 0;
 241 00109
 242 00110         <span class="comment">/* If the sequences don't overlap then the seq ID is 0 */</span>
 243 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>)
 244 00112                 <span class="keywordflow">return</span> 0;
 245 00113
 246 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> );
 247 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> );
 248 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> );
 249 00117
 250 00118         <span class="keywordflow">for</span> (i = start; i &lt; end; i++)
 251 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]);
 252 00120
 253 00121         result = 100 * (<span class="keywordtype">float</span>) id / (<span class="keywordtype">float</span>) numres;
 254 00122
 255 00123         <span class="keywordflow">return</span> result;
 256 00124 }
 257 </pre></div>    </td>
 258   </tr>
 259 </table>
 260
 261 <p>
 262 Here is the call graph for this function:<p><center><img src="pairwise_8h_a5_cgraph.png" border="0" usemap="#pairwise_8h_a5_cgraph_map" alt=""></center>
 263 <map name="pairwise_8h_a5_cgraph_map">
 264 <area href="pairwise_8h.html#a4" shape="rect" coords="131,5,168,23" alt="">
 265 </map>
 266 <a name="a6" doxytag="pairwise.h::populate"></a><p>
 267 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 268   <tr>
 269     <td class="mdRow">
 270       <table cellpadding="0" cellspacing="0" border="0">
 271         <tr>
 272           <td class="md" nowrap valign="top"> void populate </td>
 273           <td class="md" valign="top">(&nbsp;</td>
 274           <td class="md" nowrap valign="top">struct <a class="el" href="structfasta.html">fasta</a> *&nbsp;</td>
 275           <td class="mdname1" valign="top" nowrap> <em>a</em>          </td>
 276           <td class="md" valign="top">&nbsp;)&nbsp;</td>
 277           <td class="md" nowrap></td>
 278         </tr>
 279
 280       </table>
 281     </td>
 282   </tr>
 283 </table>
 284 <table cellspacing=5 cellpadding=0 border=0>
 285   <tr>
 286     <td>
 287       &nbsp;
 288     </td>
 289     <td>
 290
 291 <p>
 292
 293 <p>
 294 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>.
 295 <p>
 296 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>.
 297 <p>
 298 Referenced by <a class="el" href="pairwise_8c-source.html#l00179">read_fasta()</a>.
 299 <p>
 300 <div class="fragment"><pre>00133                            {
 301 00134         <span class="keywordtype">int</span> i;
 302 00135         <span class="keywordtype">int</span> len = strlen(a-&gt;<a class="code" href="structfasta.html#o1">seq</a>);
 303 00136
 304 00137         a-&gt;<a class="code" href="structfasta.html#o4">numres</a> = 0;
 305 00138
 306 00139         <span class="keywordflow">for</span> (i = 0; i &lt;= len; i++) {
 307 00140                 <span class="keywordflow">if</span> (a-&gt;<a class="code" href="structfasta.html#o1">seq</a>[i] != <span class="charliteral">'-'</span>) {
 308 00141                         a-&gt;<a class="code" href="structfasta.html#o2">start</a> = i;
 309 00142                         <span class="keywordflow">break</span>;
 310 00143                 }
 311 00144         }
 312 00145         <span class="keywordflow">for</span> (i = len; i &gt; 0; i--) {
 313 00146                 <span class="keywordflow">if</span> (a-&gt;<a class="code" href="structfasta.html#o1">seq</a>[i] != <span class="charliteral">'-'</span>) {
 314 00147                         a-&gt;<a class="code" href="structfasta.html#o3">end</a> = i;
 315 00148                         <span class="keywordflow">break</span>;
 316 00149                 }
 317 00150         }
 318 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++) {
 319 00152                 <span class="keywordflow">if</span> (a-&gt;<a class="code" href="structfasta.html#o1">seq</a>[i] != <span class="charliteral">'-'</span>) {
 320 00153                         a-&gt;<a class="code" href="structfasta.html#o4">numres</a>++;
 321 00154                 }
 322 00155         }
 323 00156 }
 324 </pre></div>    </td>
 325   </tr>
 326 </table>
 327 <a name="a8" doxytag="pairwise.h::read_fasta"></a><p>
 328 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 329   <tr>
 330     <td class="mdRow">
 331       <table cellpadding="0" cellspacing="0" border="0">
 332         <tr>
 333           <td class="md" nowrap valign="top"> struct <a class="el" href="structfasta.html">fasta</a>** read_fasta </td>
 334           <td class="md" valign="top">(&nbsp;</td>
 335           <td class="md" nowrap valign="top">FILE *&nbsp;</td>
 336           <td class="mdname1" valign="top" nowrap> <em>fh</em>          </td>
 337           <td class="md" valign="top">&nbsp;)&nbsp;</td>
 338           <td class="md" nowrap></td>
 339         </tr>
 340
 341       </table>
 342     </td>
 343   </tr>
 344 </table>
 345 <table cellspacing=5 cellpadding=0 border=0>
 346   <tr>
 347     <td>
 348       &nbsp;
 349     </td>
 350     <td>
 351
 352 <p>
 353
 354 <p>
 355 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>.
 356 <p>
 357 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>.
 358 <p>
 359 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>.
 360 <p>
 361 <div class="fragment"><pre>00179                       {
 362 00180         <span class="keywordtype">int</span> i, j, k, c, filesize = 1;
 363 00181         <span class="keywordtype">char</span> *file;
 364 00182         <span class="keyword">struct </span><a class="code" href="structfasta.html">fasta</a> **array;
 365 00183
 366 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 *));
 367 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>));
 368 00186
 369 00187         <span class="comment">/* Allocate initial space for the file */</span>
 370 00188         file = <a class="code" href="pairwise_8c.html#a10">xrealloc</a>(file, <span class="keyword">sizeof</span>(<span class="keywordtype">char</span>) * filesize);
 371 00189         file[filesize] = <span class="charliteral">'\0'</span>;
 372 00190
 373 00191         <span class="comment">/* Read in the file */</span>
 374 00192         <span class="keywordflow">while</span> ((c = getc(fh)) != EOF) {
 375 00193                 <span class="keywordflow">if</span> (filesize % <a class="code" href="pairwise_8c.html#a1">FILEBUF</a>)
 376 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));
 377 00195
 378 00196                 file[filesize] = c;
 379 00197                 filesize++;
 380 00198         }
 381 00199
 382 00200         <span class="comment">/* Parse the FASTA file into an array of structures */</span>
 383 00201         <span class="keywordflow">for</span> (i = 0, j = 0, k = 0; i &lt; filesize; i++) {
 384 00202                 <span class="keywordflow">if</span> (file[i] == <span class="charliteral">'&gt;'</span>) {
 385 00203                         <span class="keywordflow">if</span> (j % <a class="code" href="pairwise_8c.html#a0">ARRAY</a> == 0)
 386 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>));
 387 00205
 388 00206                         array[j] = (<span class="keyword">struct </span>fasta *) <a class="code" href="pairwise_8c.html#a9">xmalloc</a>(sizeof(struct fasta));
 389 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>));
 390 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>));
 391 00209                         array[j]-&gt;<a class="code" href="structfasta.html#o4">numres</a> = 0;
 392 00210
 393 00211                         i++;
 394 00212                         <span class="keywordflow">while</span> (file[i] != <span class="charliteral">'\0'</span> &amp;&amp; file[i] != <span class="charliteral">'\n'</span>) {
 395 00213                                 <span class="keywordflow">if</span> (k % <a class="code" href="pairwise_8c.html#a0">ARRAY</a> == 0)
 396 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));
 397 00215                                 array[j]-&gt;<a class="code" href="structfasta.html#o0">id</a>[k] = file[i];
 398 00216                                 k++; i++;
 399 00217                         }
 400 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));
 401 00219                         array[j]-&gt;<a class="code" href="structfasta.html#o0">id</a>[k] = <span class="charliteral">'\0'</span>;
 402 00220                         k = 0;
 403 00221
 404 00222                         <span class="keywordflow">while</span> (file[i] != <span class="charliteral">'\0'</span> &amp;&amp; file[i] != <span class="charliteral">'&gt;'</span>) {
 405 00223                                 <span class="keywordflow">if</span> (file[i] == <span class="charliteral">'\n'</span>) {
 406 00224                                         i++;
 407 00225                                         <span class="keywordflow">continue</span>;
 408 00226                                 }
 409 00227                                 <span class="keywordflow">if</span> (k % <a class="code" href="pairwise_8c.html#a0">ARRAY</a> == 0)
 410 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));
 411 00229                                 array[j]-&gt;<a class="code" href="structfasta.html#o1">seq</a>[k] = file[i];
 412 00230                                 k++; i++;
 413 00231                         }
 414 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));
 415 00233                         array[j]-&gt;<a class="code" href="structfasta.html#o1">seq</a>[k] = <span class="charliteral">'\0'</span>;
 416 00234                         k = 0;
 417 00235                         i--;
 418 00236                         j++;
 419 00237                 }
 420 00238         }
 421 00239
 422 00240         free(file);
 423 00241         array = (<span class="keyword">struct </span>fasta **) <a class="code" href="pairwise_8c.html#a10">xrealloc</a>(array, sizeof(struct fasta *) * j);
 424 00242         array[j] = NULL;
 425 00243
 426 00244         <span class="comment">/* find the start and end points for the alignments */</span>
 427 00245         <span class="keywordflow">for</span> (i = 0; array[i] != NULL; i++) {
 428 00246                 <a class="code" href="pairwise_8c.html#a13">populate</a>(array[i]);
 429 00247         }
 430 00248
 431 00249         <span class="keywordflow">return</span> array;
 432 00250 }
 433 </pre></div>    </td>
 434   </tr>
 435 </table>
 436
 437 <p>
 438 Here is the call graph for this function:<p><center><img src="pairwise_8h_a8_cgraph.png" border="0" usemap="#pairwise_8h_a8_cgraph_map" alt=""></center>
 439 <map name="pairwise_8h_a8_cgraph_map">
 440 <area href="pairwise_8h.html#a6" shape="rect" coords="273,45,340,63" alt="">
 441 <area href="pairwise_8c.html#a15" shape="rect" coords="147,79,224,98" alt="">
 442 <area href="pairwise_8c.html#a9" shape="rect" coords="277,150,336,169" alt="">
 443 <area href="pairwise_8h.html#a3" shape="rect" coords="276,107,337,126" alt="">
 444 <area href="pairwise_8c.html#a7" shape="rect" coords="388,129,492,147" alt="">
 445 </map>
 446 <a name="a1" doxytag="pairwise.h::xfopen"></a><p>
 447 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 448   <tr>
 449     <td class="mdRow">
 450       <table cellpadding="0" cellspacing="0" border="0">
 451         <tr>
 452           <td class="md" nowrap valign="top"> FILE* xfopen </td>
 453           <td class="md" valign="top">(&nbsp;</td>
 454           <td class="md" nowrap valign="top">const char *&nbsp;</td>
 455           <td class="mdname" nowrap> <em>path</em>, </td>
 456         </tr>
 457         <tr>
 458           <td></td>
 459           <td></td>
 460           <td class="md" nowrap>const char *&nbsp;</td>
 461           <td class="mdname" nowrap> <em>mode</em></td>
 462         </tr>
 463         <tr>
 464           <td></td>
 465           <td class="md">)&nbsp;</td>
 466           <td class="md" colspan="2"></td>
 467         </tr>
 468
 469       </table>
 470     </td>
 471   </tr>
 472 </table>
 473 <table cellspacing=5 cellpadding=0 border=0>
 474   <tr>
 475     <td>
 476       &nbsp;
 477     </td>
 478     <td>
 479
 480 <p>
 481
 482 <p>
 483 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>.
 484 <p>
 485 References <a class="el" href="pairwise_8c-source.html#l00059">fatal_sys_error()</a>.
 486 <p>
 487 Referenced by <a class="el" href="pairwise_8c-source.html#l00253">main()</a>.
 488 <p>
 489 <div class="fragment"><pre>00065                                             {
 490 00066         FILE *fh;
 491 00067         fh = fopen(path, mode);
 492 00068         <span class="keywordflow">if</span> (fh == NULL)
 493 00069                 <a class="code" href="pairwise_8c.html#a7">fatal_sys_error</a>(<span class="stringliteral">"fopen returned NULL"</span>);
 494 00070         <span class="keywordflow">return</span> fh;
 495 00071 }
 496 </pre></div>    </td>
 497   </tr>
 498 </table>
 499
 500 <p>
 501 Here is the call graph for this function:<p><center><img src="pairwise_8h_a1_cgraph.png" border="0" usemap="#pairwise_8h_a1_cgraph_map" alt=""></center>
 502 <map name="pairwise_8h_a1_cgraph_map">
 503 <area href="pairwise_8c.html#a7" shape="rect" coords="121,5,225,23" alt="">
 504 </map>
 505 <a name="a2" doxytag="pairwise.h::xmalloc"></a><p>
 506 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 507   <tr>
 508     <td class="mdRow">
 509       <table cellpadding="0" cellspacing="0" border="0">
 510         <tr>
 511           <td class="md" nowrap valign="top"> void* xmalloc </td>
 512           <td class="md" valign="top">(&nbsp;</td>
 513           <td class="md" nowrap valign="top">size_t&nbsp;</td>
 514           <td class="mdname1" valign="top" nowrap> <em>size</em>          </td>
 515           <td class="md" valign="top">&nbsp;)&nbsp;</td>
 516           <td class="md" nowrap></td>
 517         </tr>
 518
 519       </table>
 520     </td>
 521   </tr>
 522 </table>
 523 <table cellspacing=5 cellpadding=0 border=0>
 524   <tr>
 525     <td>
 526       &nbsp;
 527     </td>
 528     <td>
 529
 530 <p>
 531
 532 <p>
 533 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>.
 534 <p>
 535 References <a class="el" href="pairwise_8c-source.html#l00059">fatal_sys_error()</a>.
 536 <p>
 537 Referenced by <a class="el" href="pairwise_8c-source.html#l00179">read_fasta()</a>.
 538 <p>
 539 <div class="fragment"><pre>00074                       {
 540 00075         <span class="keywordtype">void</span> *ptr;
 541 00076         ptr = (<span class="keywordtype">void</span> *) malloc(size);
 542 00077         <span class="keywordflow">if</span> (ptr == NULL)
 543 00078                 <a class="code" href="pairwise_8c.html#a7">fatal_sys_error</a>(<span class="stringliteral">"malloc returned NULL"</span>);
 544 00079         <span class="keywordflow">return</span> ptr;
 545 00080 }
 546 </pre></div>    </td>
 547   </tr>
 548 </table>
 549
 550 <p>
 551 Here is the call graph for this function:<p><center><img src="pairwise_8h_a2_cgraph.png" border="0" usemap="#pairwise_8h_a2_cgraph_map" alt=""></center>
 552 <map name="pairwise_8h_a2_cgraph_map">
 553 <area href="pairwise_8c.html#a7" shape="rect" coords="127,5,231,23" alt="">
 554 </map>
 555 <a name="a3" doxytag="pairwise.h::xrealloc"></a><p>
 556 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
 557   <tr>
 558     <td class="mdRow">
 559       <table cellpadding="0" cellspacing="0" border="0">
 560         <tr>
 561           <td class="md" nowrap valign="top"> void* xrealloc </td>
 562           <td class="md" valign="top">(&nbsp;</td>
 563           <td class="md" nowrap valign="top">void *&nbsp;</td>
 564           <td class="mdname" nowrap> <em>ptr</em>, </td>
 565         </tr>
 566         <tr>
 567           <td></td>
 568           <td></td>
 569           <td class="md" nowrap>size_t&nbsp;</td>
 570           <td class="mdname" nowrap> <em>size</em></td>
 571         </tr>
 572         <tr>
 573           <td></td>
 574           <td class="md">)&nbsp;</td>
 575           <td class="md" colspan="2"></td>
 576         </tr>
 577
 578       </table>
 579     </td>
 580   </tr>
 581 </table>
 582 <table cellspacing=5 cellpadding=0 border=0>
 583   <tr>
 584     <td>
 585       &nbsp;
 586     </td>
 587     <td>
 588
 589 <p>
 590
 591 <p>
 592 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>.
 593 <p>
 594 References <a class="el" href="pairwise_8c-source.html#l00059">fatal_sys_error()</a>.
 595 <p>
 596 Referenced by <a class="el" href="pairwise_8c-source.html#l00179">read_fasta()</a>.
 597 <p>
 598 <div class="fragment"><pre>00083                                   {
 599 00084         ptr = (<span class="keywordtype">void</span> *) realloc(ptr, size);
 600 00085         <span class="keywordflow">if</span> (ptr == NULL &amp;&amp; size != 0)
 601 00086                 <a class="code" href="pairwise_8c.html#a7">fatal_sys_error</a>(<span class="stringliteral">"realloc returned NULL"</span>);
 602 00087         <span class="keywordflow">return</span> ptr;
 603 00088 }
 604 </pre></div>    </td>
 605   </tr>
 606 </table>
 607
 608 <p>
 609 Here is the call graph for this function:<p><center><img src="pairwise_8h_a3_cgraph.png" border="0" usemap="#pairwise_8h_a3_cgraph_map" alt=""></center>
 610 <map name="pairwise_8h_a3_cgraph_map">
 611 <area href="pairwise_8c.html#a7" shape="rect" coords="127,5,231,23" alt="">
 612 </map>
 613 <hr size="1"><address style="align: right;"><small>Generated on Thu Jul 24 12:17:51 2003 for pairwise by
 614 <a href="http://www.doxygen.org/index.html">
 615 <img src="doxygen.png" alt="doxygen" align="middle" border=0 >
 616 </a>1.3.2 </small></address>
 617 </body>
 618 </html>