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8 <h1>pairwise.h File Reference</h1><code>#include <stdlib.h></code><br>
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>
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="">
20 <a href="pairwise_8h-source.html">Go to the source code of this file.</a><table border=0 cellpadding=0 cellspacing=0>
22 <tr><td colspan=2><br><h2>Data Structures</h2></td></tr>
23 <tr><td class="memItemLeft" nowrap align=right valign=top>struct </td><td class="memItemRight" valign=bottom><a class="el" href="structfasta.html">fasta</a></td></tr>
25 <tr><td colspan=2><br><h2>Functions</h2></td></tr>
26 <tr><td class="memItemLeft" nowrap align=right valign=top>void </td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8h.html#a0">fatal_error</a> (char *message)</td></tr>
28 <tr><td class="memItemLeft" nowrap align=right valign=top>FILE * </td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8h.html#a1">xfopen</a> (const char *path, const char *mode)</td></tr>
30 <tr><td class="memItemLeft" nowrap align=right valign=top>void * </td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8h.html#a2">xmalloc</a> (size_t size)</td></tr>
32 <tr><td class="memItemLeft" nowrap align=right valign=top>void * </td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8h.html#a3">xrealloc</a> (void *ptr, size_t size)</td></tr>
34 <tr><td class="memItemLeft" nowrap align=right valign=top>int </td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8h.html#a4">diff</a> (char a, char b)</td></tr>
36 <tr><td class="memItemLeft" nowrap align=right valign=top>float </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>
38 <tr><td class="memItemLeft" nowrap align=right valign=top>void </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>
40 <tr><td class="memItemLeft" nowrap align=right valign=top>void </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>
42 <tr><td class="memItemLeft" nowrap align=right valign=top><a class="el" href="structfasta.html">fasta</a> ** </td><td class="memItemRight" valign=bottom><a class="el" href="pairwise_8h.html#a8">read_fasta</a> (FILE *fh)</td></tr>
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">
50 <table cellpadding="0" cellspacing="0" border="0">
52 <td class="md" nowrap valign="top"> void check_length </td>
53 <td class="md" valign="top">( </td>
54 <td class="md" nowrap valign="top">struct <a class="el" href="structfasta.html">fasta</a> ** </td>
55 <td class="mdname1" valign="top" nowrap> <em>array</em> </td>
56 <td class="md" valign="top"> ) </td>
57 <td class="md" nowrap></td>
64 <table cellspacing=5 cellpadding=0 border=0>
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>.
76 References <a class="el" href="pairwise_8c-source.html#l00053">fatal_error()</a>.
78 Referenced by <a class="el" href="pairwise_8c-source.html#l00253">main()</a>.
80 <div class="fragment"><pre>00160 {
81 00161 <span class="keywordtype">int</span> i, length;
83 00163 <span class="keywordflow">if</span> (array[0] != NULL)
84 00164 length = strlen(array[0]->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>;
90 00170 <span class="keywordflow">for</span> (i = 0; array[i] != NULL; i++) {
91 00171 <span class="keywordflow">if</span> (length != strlen(array[i]->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>);
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="">
105 <a name="a4" doxytag="pairwise.h::diff"></a><p>
106 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
109 <table cellpadding="0" cellspacing="0" border="0">
111 <td class="md" nowrap valign="top"> int diff </td>
112 <td class="md" valign="top">( </td>
113 <td class="md" nowrap valign="top">char </td>
114 <td class="mdname" nowrap> <em>a</em>, </td>
119 <td class="md" nowrap>char </td>
120 <td class="mdname" nowrap> <em>b</em></td>
124 <td class="md">) </td>
125 <td class="md" colspan="2"></td>
132 <table cellspacing=5 cellpadding=0 border=0>
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>.
144 Referenced by <a class="el" href="pairwise_8c-source.html#l00106">pairwise()</a>.
146 <div class="fragment"><pre>00092 {
147 00093 <span class="keywordflow">if</span> (a == b && 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;
156 <a name="a0" doxytag="pairwise.h::fatal_error"></a><p>
157 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
160 <table cellpadding="0" cellspacing="0" border="0">
162 <td class="md" nowrap valign="top"> void fatal_error </td>
163 <td class="md" valign="top">( </td>
164 <td class="md" nowrap valign="top">char * </td>
165 <td class="mdname1" valign="top" nowrap> <em>message</em> </td>
166 <td class="md" valign="top"> ) </td>
167 <td class="md" nowrap></td>
174 <table cellspacing=5 cellpadding=0 border=0>
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>.
186 Referenced by <a class="el" href="pairwise_8c-source.html#l00160">check_length()</a>.
188 <div class="fragment"><pre>00053 {
189 00054 printf(message);
190 00055 exit(EXIT_FAILURE);
195 <a name="a5" doxytag="pairwise.h::pairwise"></a><p>
196 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
199 <table cellpadding="0" cellspacing="0" border="0">
201 <td class="md" nowrap valign="top"> float pairwise </td>
202 <td class="md" valign="top">( </td>
203 <td class="md" nowrap valign="top">struct <a class="el" href="structfasta.html">fasta</a> * </td>
204 <td class="mdname" nowrap> <em>a</em>, </td>
209 <td class="md" nowrap>struct <a class="el" href="structfasta.html">fasta</a> * </td>
210 <td class="mdname" nowrap> <em>b</em></td>
214 <td class="md">) </td>
215 <td class="md" colspan="2"></td>
222 <table cellspacing=5 cellpadding=0 border=0>
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>.
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>.
236 Referenced by <a class="el" href="pairwise_8c-source.html#l00253">main()</a>.
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;
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-><a class="code" href="structfasta.html#o3">end</a> < b-><a class="code" href="structfasta.html#o2">start</a> || a-><a class="code" href="structfasta.html#o2">start</a> > b-><a class="code" href="structfasta.html#o3">end</a>)
244 00112 <span class="keywordflow">return</span> 0;
246 00114 start = <a class="code" href="pairwise_8c.html#a3">MIN</a>( a-><a class="code" href="structfasta.html#o2">start</a>, b-><a class="code" href="structfasta.html#o2">start</a> );
247 00115 end = <a class="code" href="pairwise_8c.html#a2">MAX</a>( a-><a class="code" href="structfasta.html#o3">end</a>, b-><a class="code" href="structfasta.html#o3">end</a> );
248 00116 numres = <a class="code" href="pairwise_8c.html#a2">MAX</a>( a-><a class="code" href="structfasta.html#o4">numres</a>, b-><a class="code" href="structfasta.html#o4">numres</a> );
250 00118 <span class="keywordflow">for</span> (i = start; i < end; i++)
251 00119 id += <a class="code" href="pairwise_8c.html#a11">diff</a>(a-><a class="code" href="structfasta.html#o1">seq</a>[i], b-><a class="code" href="structfasta.html#o1">seq</a>[i]);
253 00121 result = 100 * (<span class="keywordtype">float</span>) id / (<span class="keywordtype">float</span>) numres;
255 00123 <span class="keywordflow">return</span> result;
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="">
266 <a name="a6" doxytag="pairwise.h::populate"></a><p>
267 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
270 <table cellpadding="0" cellspacing="0" border="0">
272 <td class="md" nowrap valign="top"> void populate </td>
273 <td class="md" valign="top">( </td>
274 <td class="md" nowrap valign="top">struct <a class="el" href="structfasta.html">fasta</a> * </td>
275 <td class="mdname1" valign="top" nowrap> <em>a</em> </td>
276 <td class="md" valign="top"> ) </td>
277 <td class="md" nowrap></td>
284 <table cellspacing=5 cellpadding=0 border=0>
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>.
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>.
298 Referenced by <a class="el" href="pairwise_8c-source.html#l00179">read_fasta()</a>.
300 <div class="fragment"><pre>00133 {
301 00134 <span class="keywordtype">int</span> i;
302 00135 <span class="keywordtype">int</span> len = strlen(a-><a class="code" href="structfasta.html#o1">seq</a>);
304 00137 a-><a class="code" href="structfasta.html#o4">numres</a> = 0;
306 00139 <span class="keywordflow">for</span> (i = 0; i <= len; i++) {
307 00140 <span class="keywordflow">if</span> (a-><a class="code" href="structfasta.html#o1">seq</a>[i] != <span class="charliteral">'-'</span>) {
308 00141 a-><a class="code" href="structfasta.html#o2">start</a> = i;
309 00142 <span class="keywordflow">break</span>;
312 00145 <span class="keywordflow">for</span> (i = len; i > 0; i--) {
313 00146 <span class="keywordflow">if</span> (a-><a class="code" href="structfasta.html#o1">seq</a>[i] != <span class="charliteral">'-'</span>) {
314 00147 a-><a class="code" href="structfasta.html#o3">end</a> = i;
315 00148 <span class="keywordflow">break</span>;
318 00151 <span class="keywordflow">for</span> (i = a-><a class="code" href="structfasta.html#o2">start</a>; i < a-><a class="code" href="structfasta.html#o3">end</a>; i++) {
319 00152 <span class="keywordflow">if</span> (a-><a class="code" href="structfasta.html#o1">seq</a>[i] != <span class="charliteral">'-'</span>) {
320 00153 a-><a class="code" href="structfasta.html#o4">numres</a>++;
327 <a name="a8" doxytag="pairwise.h::read_fasta"></a><p>
328 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
331 <table cellpadding="0" cellspacing="0" border="0">
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">( </td>
335 <td class="md" nowrap valign="top">FILE * </td>
336 <td class="mdname1" valign="top" nowrap> <em>fh</em> </td>
337 <td class="md" valign="top"> ) </td>
338 <td class="md" nowrap></td>
345 <table cellspacing=5 cellpadding=0 border=0>
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>.
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>.
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>.
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;
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>));
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>;
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));
378 00196 file[filesize] = c;
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 < filesize; i++) {
384 00202 <span class="keywordflow">if</span> (file[i] == <span class="charliteral">'>'</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>));
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]-><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]-><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]-><a class="code" href="structfasta.html#o4">numres</a> = 0;
394 00212 <span class="keywordflow">while</span> (file[i] != <span class="charliteral">'\0'</span> && 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]-><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]->id, <span class="keyword">sizeof</span>(<span class="keywordtype">char</span>) * (ARRAY + k));
397 00215 array[j]-><a class="code" href="structfasta.html#o0">id</a>[k] = file[i];
400 00218 array[j]-><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]->id, <span class="keyword">sizeof</span>(<span class="keywordtype">char</span>) * (ARRAY + k));
401 00219 array[j]-><a class="code" href="structfasta.html#o0">id</a>[k] = <span class="charliteral">'\0'</span>;
404 00222 <span class="keywordflow">while</span> (file[i] != <span class="charliteral">'\0'</span> && file[i] != <span class="charliteral">'>'</span>) {
405 00223 <span class="keywordflow">if</span> (file[i] == <span class="charliteral">'\n'</span>) {
407 00225 <span class="keywordflow">continue</span>;
409 00227 <span class="keywordflow">if</span> (k % <a class="code" href="pairwise_8c.html#a0">ARRAY</a> == 0)
410 00228 array[j]-><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]->seq, <span class="keyword">sizeof</span>(<span class="keywordtype">char</span>) * (ARRAY + k));
411 00229 array[j]-><a class="code" href="structfasta.html#o1">seq</a>[k] = file[i];
414 00232 array[j]-><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]->seq, <span class="keyword">sizeof</span>(<span class="keywordtype">char</span>) * (ARRAY + k));
415 00233 array[j]-><a class="code" href="structfasta.html#o1">seq</a>[k] = <span class="charliteral">'\0'</span>;
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;
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]);
431 00249 <span class="keywordflow">return</span> array;
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="">
446 <a name="a1" doxytag="pairwise.h::xfopen"></a><p>
447 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
450 <table cellpadding="0" cellspacing="0" border="0">
452 <td class="md" nowrap valign="top"> FILE* xfopen </td>
453 <td class="md" valign="top">( </td>
454 <td class="md" nowrap valign="top">const char * </td>
455 <td class="mdname" nowrap> <em>path</em>, </td>
460 <td class="md" nowrap>const char * </td>
461 <td class="mdname" nowrap> <em>mode</em></td>
465 <td class="md">) </td>
466 <td class="md" colspan="2"></td>
473 <table cellspacing=5 cellpadding=0 border=0>
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>.
485 References <a class="el" href="pairwise_8c-source.html#l00059">fatal_sys_error()</a>.
487 Referenced by <a class="el" href="pairwise_8c-source.html#l00253">main()</a>.
489 <div class="fragment"><pre>00065 {
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;
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="">
505 <a name="a2" doxytag="pairwise.h::xmalloc"></a><p>
506 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
509 <table cellpadding="0" cellspacing="0" border="0">
511 <td class="md" nowrap valign="top"> void* xmalloc </td>
512 <td class="md" valign="top">( </td>
513 <td class="md" nowrap valign="top">size_t </td>
514 <td class="mdname1" valign="top" nowrap> <em>size</em> </td>
515 <td class="md" valign="top"> ) </td>
516 <td class="md" nowrap></td>
523 <table cellspacing=5 cellpadding=0 border=0>
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>.
535 References <a class="el" href="pairwise_8c-source.html#l00059">fatal_sys_error()</a>.
537 Referenced by <a class="el" href="pairwise_8c-source.html#l00179">read_fasta()</a>.
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;
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="">
555 <a name="a3" doxytag="pairwise.h::xrealloc"></a><p>
556 <table class="mdTable" width="100%" cellpadding="2" cellspacing="0">
559 <table cellpadding="0" cellspacing="0" border="0">
561 <td class="md" nowrap valign="top"> void* xrealloc </td>
562 <td class="md" valign="top">( </td>
563 <td class="md" nowrap valign="top">void * </td>
564 <td class="mdname" nowrap> <em>ptr</em>, </td>
569 <td class="md" nowrap>size_t </td>
570 <td class="mdname" nowrap> <em>size</em></td>
574 <td class="md">) </td>
575 <td class="md" colspan="2"></td>
582 <table cellspacing=5 cellpadding=0 border=0>
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>.
594 References <a class="el" href="pairwise_8c-source.html#l00059">fatal_sys_error()</a>.
596 Referenced by <a class="el" href="pairwise_8c-source.html#l00179">read_fasta()</a>.
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 && 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;
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="">
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>