pairwise.h File Reference

#include <stdlib.h>

Include dependency graph for pairwise.h:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Data Structures
struct	fasta
Functions
void	fatal_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)

---

Function Documentation

void check_length (  struct fasta **  array  )

Definition at line 160 of file pairwise.c. References fatal_error(). Referenced by main(). { int i, length; if (array[0] != NULL) length = strlen(array[0]->seq); else { fprintf(stderr, "check_length() not passed an array of fasta structs\n"); return; } for (i = 0; array[i] != NULL; i++) { if (length != strlen(array[i]->seq)) { fatal_error("Not all of the sequences are the same length\n"); } } }

Here is the call graph for this function:

int diff (  char  a, char  b )

Definition at line 92 of file pairwise.c. Referenced by pairwise(). { if (a == b && a == '-') return 0; if (a == b) return 1; return 0; }

void fatal_error (  char *  message  )

Definition at line 53 of file pairwise.c. Referenced by check_length(). { printf(message); exit(EXIT_FAILURE); }

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(). { float result; int start, end, numres, i, id = 0; /* If the sequences don't overlap then the seq ID is 0 */ if (a->end < b->start || a->start > b->end) return 0; start = MIN( a->start, b->start ); end = MAX( a->end, b->end ); numres = MAX( a->numres, b->numres ); for (i = start; i < end; i++) id += diff(a->seq[i], b->seq[i]); result = 100 * (float) id / (float) numres; return result; }

Here is the call graph for this function:

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(). { int i; int len = strlen(a->seq); a->numres = 0; for (i = 0; i <= len; i++) { if (a->seq[i] != '-') { a->start = i; break; } } for (i = len; i > 0; i--) { if (a->seq[i] != '-') { a->end = i; break; } } for (i = a->start; i < a->end; i++) { if (a->seq[i] != '-') { a->numres++; } } }

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(). { int i, j, k, c, filesize = 1; char *file; struct fasta **array; array = (struct fasta **) xmalloc(ARRAY * sizeof(struct fasta *)); file = (char *) xmalloc(sizeof(char)); /* Allocate initial space for the file */ file = xrealloc(file, sizeof(char) * filesize); file[filesize] = '\0'; /* Read in the file */ while ((c = getc(fh)) != EOF) { if (filesize % FILEBUF) file = xrealloc(file, sizeof(char) * (FILEBUF + filesize)); file[filesize] = c; filesize++; } /* Parse the FASTA file into an array of structures */ for (i = 0, j = 0, k = 0; i < filesize; i++) { if (file[i] == '>') { if (j % ARRAY == 0) array = (struct fasta **) xrealloc(array, sizeof(struct fasta *) * (j + ARRAY)); array[j] = (struct fasta *) xmalloc(sizeof(struct fasta)); array[j]->id = (char *) xmalloc(sizeof(char)); array[j]->seq = (char *) xmalloc(sizeof(char)); array[j]->numres = 0; i++; while (file[i] != '\0' && file[i] != '\n') { if (k % ARRAY == 0) array[j]->id = (char *) xrealloc(array[j]->id, sizeof(char) * (ARRAY + k)); array[j]->id[k] = file[i]; k++; i++; } array[j]->id = (char *) xrealloc(array[j]->id, sizeof(char) * (ARRAY + k)); array[j]->id[k] = '\0'; k = 0; while (file[i] != '\0' && file[i] != '>') { if (file[i] == '\n') { i++; continue; } if (k % ARRAY == 0) array[j]->seq = (char *) xrealloc(array[j]->seq, sizeof(char) * (ARRAY + k)); array[j]->seq[k] = file[i]; k++; i++; } array[j]->seq = (char *) xrealloc(array[j]->seq, sizeof(char) * (ARRAY + k)); array[j]->seq[k] = '\0'; k = 0; i--; j++; } } free(file); array = (struct fasta **) xrealloc(array, sizeof(struct fasta *) * j); array[j] = NULL; /* find the start and end points for the alignments */ for (i = 0; array[i] != NULL; i++) { populate(array[i]); } return array; }

Here is the call graph for this function:

FILE* xfopen (  const char *  path, const char *  mode )

Definition at line 65 of file pairwise.c. References fatal_sys_error(). Referenced by main(). { FILE *fh; fh = fopen(path, mode); if (fh == NULL) fatal_sys_error("fopen returned NULL"); return fh; }

Here is the call graph for this function:

void* xmalloc (  size_t  size  )

Definition at line 74 of file pairwise.c. References fatal_sys_error(). Referenced by read_fasta(). { void *ptr; ptr = (void *) malloc(size); if (ptr == NULL) fatal_sys_error("malloc returned NULL"); return ptr; }

Here is the call graph for this function:

void* xrealloc (  void *  ptr, size_t  size )

Definition at line 83 of file pairwise.c. References fatal_sys_error(). Referenced by read_fasta(). { ptr = (void *) realloc(ptr, size); if (ptr == NULL && size != 0) fatal_sys_error("realloc returned NULL"); return ptr; }

Here is the call graph for this function:

---