X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=sources%2Fpairwise%2Fdocs%2Fhtml%2Fpairwise_8c.html;fp=sources%2Fpairwise%2Fdocs%2Fhtml%2Fpairwise_8c.html;h=f37eaf5af3303c754f11c4a16fb44e6cba35dd5a;hb=81362e35a140cd040e948b921053e74267f8a6e3;hp=0000000000000000000000000000000000000000;hpb=2cf032f4b987ba747c04159965aed78e3820d942;p=jpred.git diff --git a/sources/pairwise/docs/html/pairwise_8c.html b/sources/pairwise/docs/html/pairwise_8c.html new file mode 100644 index 0000000..f37eaf5 --- /dev/null +++ b/sources/pairwise/docs/html/pairwise_8c.html @@ -0,0 +1,950 @@ + + +pairwise: pairwise.c File Reference + + + +

pairwise.c File Reference

#include <stdio.h>
+#include <stdlib.h>
+#include <errno.h>
+#include <string.h>
+#include "pairwise.h"
+ +

+Include dependency graph for pairwise.c:

+ + + + +

+Go to the source code of this file. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Defines
#define ARRAY   50
#define FILEBUF   1000
#define MAX(A, B)   ((A) > (B) ? (A) : (B))
#define MIN(A, B)   ((A) < (B) ? (A) : (B))
#define MALLOC(PTR, SIZE)   do { PTR = malloc(SIZE); if (PTR == NULL) fatal_sys_error("malloc returned NULL"); } while (0)
#define REALLOC(PTR, SIZE)   do { PTR = realloc(PTR, SIZE); if (PTR == NULL && SIZE != 0) fatal_sys_error("realloc returned NULL"); } while (0)

Functions
void fatal_error (char *message)
void fatal_sys_error (char *message)
FILE * xfopen (const char *path, const char *mode)
void * xmalloc (size_t size)
void * xrealloc (void *ptr, size_t size)
int diff (char a, char b)
float pairwise (struct fasta *a, struct fasta *b)
void populate (struct fasta *a)
void check_length (struct fasta **array)
fasta ** read_fasta (FILE *fh)
int main (int argc, char **argv)
+

Define Documentation

+ + + + +
+ + +
#define ARRAY 50 +
+
+ + + + + +
+ + + +
+ +
+Definition at line 29 of file pairwise.c. +
+Referenced by read_fasta().
+

+ + + + +
+ + +
#define FILEBUF 1000 +
+
+ + + + + +
+ + + +
+ +
+Definition at line 30 of file pairwise.c. +
+Referenced by read_fasta().
+

+ + + + +
+ + + + + + + + + + +
#define MALLOC ( PTR,
SIZE ) do { PTR = malloc(SIZE); if (PTR == NULL) fatal_sys_error("malloc returned NULL"); } while (0) +
+
+ + + + + +
+ + + +
+ +
+Definition at line 45 of file pairwise.c.
+

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+ + + + + + + + + + +
#define MAX ( A,
B ) ((A) > (B) ? (A) : (B)) +
+
+ + + + + +
+ + + +
+ +
+Definition at line 35 of file pairwise.c. +
+Referenced by pairwise().
+

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+ + + + + + + + + + +
#define MIN ( A,
B ) ((A) < (B) ? (A) : (B)) +
+
+ + + + + +
+ + + +
+ +
+Definition at line 39 of file pairwise.c. +
+Referenced by pairwise().
+

+ + + + +
+ + + + + + + + + + +
#define REALLOC ( PTR,
SIZE ) do { PTR = realloc(PTR, SIZE); if (PTR == NULL && SIZE != 0) fatal_sys_error("realloc returned NULL"); } while (0) +
+
+ + + + + +
+ + + +
+ +
+Definition at line 49 of file pairwise.c.
+

Function Documentation

+ + + + +
+ + + + + + + + + + +
void check_length ( struct fasta ** array )
+
+ + + + + +
+ + + +
+ +
+Definition at line 160 of file pairwise.c. +
+References fatal_error(). +
+Referenced by main(). +
+
00160 { +00161 int i, length; +00162 +00163 if (array[0] != NULL) +00164 length = strlen(array[0]->seq); +00165 else { +00166 fprintf(stderr, "check_length() not passed an array of fasta structs\n"); +00167 return; +00168 } +00169 +00170 for (i = 0; array[i] != NULL; i++) { +00171 if (length != strlen(array[i]->seq)) { +00172 fatal_error("Not all of the sequences are the same length\n"); +00173 } +00174 } +00175 } +

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int diff ( char a,
char b
)
+
+ + + + + +
+ + + +
+ +
+Definition at line 92 of file pairwise.c. +
+Referenced by pairwise(). +
+
00092 { +00093 if (a == b && a == '-') +00094 return 0; +00095 if (a == b) +00096 return 1; +00097 return 0; +00098 } +

+

+ + + + +
+ + + + + + + + + + +
void fatal_error ( char * message )
+
+ + + + + +
+ + + +
+ +
+Definition at line 53 of file pairwise.c. +
+Referenced by check_length(). +
+
00053 { +00054 printf(message); +00055 exit(EXIT_FAILURE); +00056 } +

+

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+ + + + + + + + + + +
void fatal_sys_error ( char * message )
+
+ + + + + +
+ + + +
+ +
+Definition at line 59 of file pairwise.c. +
+Referenced by xfopen(), xmalloc(), and xrealloc(). +
+
00059 { +00060 perror(message); +00061 exit(EXIT_FAILURE); +00062 } +

+

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int main ( int argc,
char ** argv
)
+
+ + + + + +
+ + + +
+ +
+Definition at line 253 of file pairwise.c. +
+References check_length(), pairwise(), read_fasta(), and xfopen(). +
+
00253 { +00254 FILE *fh; +00255 struct fasta **array; +00256 int i = 0, j; +00257 +00258 /* Read in the FASTA file */ +00259 if (argc == 2) +00260 fh = xfopen(argv[1], "r"); +00261 else +00262 fh = stdin; +00263 +00264 array = read_fasta(fh); +00265 fclose(fh); +00266 +00267 check_length(array); +00268 +00269 /* start the OC output */ +00270 while (array[i] != NULL) +00271 i++; +00272 +00273 fprintf(stdout, "%i\n", i); +00274 +00275 for (i = 0; array[i] != NULL; i++) +00276 fprintf(stdout, "%s\n", array[i]->id); +00277 +00278 /* do the pairwise comparison */ +00279 for (i = 0; array[i] != NULL; i++) { +00280 for (j = i + 1; array[j] != NULL; j++) { +00281 printf("%f\n", pairwise(array[i], array[j])); +00282 } +00283 } +00284 +00285 return EXIT_SUCCESS; +00286 } +

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float pairwise ( struct fasta * a,
struct fasta * b
)
+
+ + + + + +
+ + + +
+ +
+Definition at line 106 of file pairwise.c. +
+References diff(), fasta::end, MAX, MIN, fasta::numres, fasta::seq, and fasta::start. +
+Referenced by main(). +
+
00106 { +00107 float result; +00108 int start, end, numres, i, id = 0; +00109 +00110 /* If the sequences don't overlap then the seq ID is 0 */ +00111 if (a->end < b->start || a->start > b->end) +00112 return 0; +00113 +00114 start = MIN( a->start, b->start ); +00115 end = MAX( a->end, b->end ); +00116 numres = MAX( a->numres, b->numres ); +00117 +00118 for (i = start; i < end; i++) +00119 id += diff(a->seq[i], b->seq[i]); +00120 +00121 result = 100 * (float) id / (float) numres; +00122 +00123 return result; +00124 } +

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+ + + + + + + + + + +
void populate ( struct fasta * a )
+
+ + + + + +
+ + + +
+ +
+Definition at line 133 of file pairwise.c. +
+References fasta::end, fasta::numres, fasta::seq, and fasta::start. +
+Referenced by read_fasta(). +
+
00133 { +00134 int i; +00135 int len = strlen(a->seq); +00136 +00137 a->numres = 0; +00138 +00139 for (i = 0; i <= len; i++) { +00140 if (a->seq[i] != '-') { +00141 a->start = i; +00142 break; +00143 } +00144 } +00145 for (i = len; i > 0; i--) { +00146 if (a->seq[i] != '-') { +00147 a->end = i; +00148 break; +00149 } +00150 } +00151 for (i = a->start; i < a->end; i++) { +00152 if (a->seq[i] != '-') { +00153 a->numres++; +00154 } +00155 } +00156 } +

+

+ + + + +
+ + + + + + + + + + +
struct fasta** read_fasta ( FILE * fh )
+
+ + + + + +
+ + + +
+ +
+Definition at line 179 of file pairwise.c. +
+References ARRAY, FILEBUF, fasta::id, fasta::numres, populate(), read_fasta(), fasta::seq, xmalloc(), and xrealloc(). +
+Referenced by main(), and read_fasta(). +
+
00179 { +00180 int i, j, k, c, filesize = 1; +00181 char *file; +00182 struct fasta **array; +00183 +00184 array = (struct fasta **) xmalloc(ARRAY * sizeof(struct fasta *)); +00185 file = (char *) xmalloc(sizeof(char)); +00186 +00187 /* Allocate initial space for the file */ +00188 file = xrealloc(file, sizeof(char) * filesize); +00189 file[filesize] = '\0'; +00190 +00191 /* Read in the file */ +00192 while ((c = getc(fh)) != EOF) { +00193 if (filesize % FILEBUF) +00194 file = xrealloc(file, sizeof(char) * (FILEBUF + filesize)); +00195 +00196 file[filesize] = c; +00197 filesize++; +00198 } +00199 +00200 /* Parse the FASTA file into an array of structures */ +00201 for (i = 0, j = 0, k = 0; i < filesize; i++) { +00202 if (file[i] == '>') { +00203 if (j % ARRAY == 0) +00204 array = (struct fasta **) xrealloc(array, sizeof(struct fasta *) * (j + ARRAY)); +00205 +00206 array[j] = (struct fasta *) xmalloc(sizeof(struct fasta)); +00207 array[j]->id = (char *) xmalloc(sizeof(char)); +00208 array[j]->seq = (char *) xmalloc(sizeof(char)); +00209 array[j]->numres = 0; +00210 +00211 i++; +00212 while (file[i] != '\0' && file[i] != '\n') { +00213 if (k % ARRAY == 0) +00214 array[j]->id = (char *) xrealloc(array[j]->id, sizeof(char) * (ARRAY + k)); +00215 array[j]->id[k] = file[i]; +00216 k++; i++; +00217 } +00218 array[j]->id = (char *) xrealloc(array[j]->id, sizeof(char) * (ARRAY + k)); +00219 array[j]->id[k] = '\0'; +00220 k = 0; +00221 +00222 while (file[i] != '\0' && file[i] != '>') { +00223 if (file[i] == '\n') { +00224 i++; +00225 continue; +00226 } +00227 if (k % ARRAY == 0) +00228 array[j]->seq = (char *) xrealloc(array[j]->seq, sizeof(char) * (ARRAY + k)); +00229 array[j]->seq[k] = file[i]; +00230 k++; i++; +00231 } +00232 array[j]->seq = (char *) xrealloc(array[j]->seq, sizeof(char) * (ARRAY + k)); +00233 array[j]->seq[k] = '\0'; +00234 k = 0; +00235 i--; +00236 j++; +00237 } +00238 } +00239 +00240 free(file); +00241 array = (struct fasta **) xrealloc(array, sizeof(struct fasta *) * j); +00242 array[j] = NULL; +00243 +00244 /* find the start and end points for the alignments */ +00245 for (i = 0; array[i] != NULL; i++) { +00246 populate(array[i]); +00247 } +00248 +00249 return array; +00250 } +

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FILE* xfopen ( const char * path,
const char * mode
)
+
+ + + + + +
+ + + +
+ +
+Definition at line 65 of file pairwise.c. +
+References fatal_sys_error(). +
+Referenced by main(). +
+
00065 { +00066 FILE *fh; +00067 fh = fopen(path, mode); +00068 if (fh == NULL) +00069 fatal_sys_error("fopen returned NULL"); +00070 return fh; +00071 } +

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void* xmalloc ( size_t size )
+
+ + + + + +
+ + + +
+ +
+Definition at line 74 of file pairwise.c. +
+References fatal_sys_error(). +
+Referenced by read_fasta(). +
+
00074 { +00075 void *ptr; +00076 ptr = (void *) malloc(size); +00077 if (ptr == NULL) +00078 fatal_sys_error("malloc returned NULL"); +00079 return ptr; +00080 } +

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void* xrealloc ( void * ptr,
size_t size
)
+
+ + + + + +
+ + + +
+ +
+Definition at line 83 of file pairwise.c. +
+References fatal_sys_error(). +
+Referenced by read_fasta(). +
+
00083 { +00084 ptr = (void *) realloc(ptr, size); +00085 if (ptr == NULL && size != 0) +00086 fatal_sys_error("realloc returned NULL"); +00087 return ptr; +00088 } +

+ +

+Here is the call graph for this function:

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Generated on Thu Jul 24 12:17:51 2003 for pairwise by + +

+1.3.2

+ +


Defines
#define	ARRAY 50
#define	FILEBUF 1000
#define	MAX(A, B) ((A) > (B) ? (A) : (B))
#define	MIN(A, B) ((A) < (B) ? (A) : (B))
#define	MALLOC(PTR, SIZE) do { PTR = malloc(SIZE); if (PTR == NULL) fatal_sys_error("malloc returned NULL"); } while (0)
#define	REALLOC(PTR, SIZE) do { PTR = realloc(PTR, SIZE); if (PTR == NULL && SIZE != 0) fatal_sys_error("realloc returned NULL"); } while (0)
Functions
void	fatal_error (char *message)
void	fatal_sys_error (char *message)
FILE *	xfopen (const char path, const char mode)
void *	xmalloc (size_t size)
void *	xrealloc (void *ptr, size_t size)
int	diff (char a, char b)
float	pairwise (struct fasta a, struct fasta b)
void	populate (struct fasta *a)
void	check_length (struct fasta **array)
fasta **	read_fasta (FILE *fh)
int	main (int argc, char **argv)