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#include <stdlib.h>
#include <errno.h>
#include <stdio.h>
#include <unistd.h>
#include <string.h>
#include "misc.h"
#include "dna_utils.h"
char *seq_left_end ( char seq[], int seq_length, int start, int window_length,
int inc) {
int num_elements, middle_start, half_window, left_start, right_end;
char *edge_seq;
int i, j;
/* work in array element nos.
middle_start first element that caller will remove from left edge
left_start is first element we need to fill with dash or seq
right_end is last element we need to fill with seq
*/
middle_start = start;
half_window = window_length/2;
left_start = middle_start - inc * ( half_window / inc );
right_end = middle_start + window_length - 1;
num_elements = window_length + inc * ( half_window / inc );
/* quick sanity checks */
if ( right_end > seq_length ) return NULL;
if ( start < 0 ) return NULL;
if ( ( NULL == ( edge_seq = ( char* ) xmalloc ( sizeof (char) * (num_elements+1))))) return NULL;
/* if required fill start with dashes */
edge_seq[num_elements] = '\0';
for ( i = 0, j = left_start; j < 0; i++, j++ ) {
edge_seq[i] = '-';
}
/* fill rest with real sequence */
for ( ; j <= right_end; i++, j++ ) {
edge_seq[i] = seq[j];
}
return edge_seq;
}
char *seq_right_end ( char seq[], int seq_length, int end, int window_length,
int inc ) {
int num_elements, left_start, right_end;
char *edge_seq;
int i, j, jend;
/* work in array element nos.
return the last base which the middle game used
- so its score can be removed from the left edge
*/
/* quick sanity checks */
if ( end >= seq_length ) return NULL;
if ( window_length > seq_length ) return NULL;
left_start = end - window_length + 1;
right_end = end + window_length/2;
if ( inc == 3 ) right_end += 1;
num_elements = right_end - left_start + 1;
if ( ( NULL == ( edge_seq = ( char* ) xmalloc ( sizeof (char) * (num_elements+1))))) return NULL;
/* fill start with real sequence */
edge_seq[num_elements] = '\0';
jend = MAX(end+1,seq_length);
for ( i = 0, j = left_start; (j < jend)&&( i<num_elements); i++, j++ ) {
edge_seq[i] = seq[j];
}
/* if required fill rest with dashes */
for ( ; j <= right_end; i++, j++ ) {
edge_seq[i] = '-';
}
return edge_seq;
}
void get_base_comp ( char seq[], int seq_length, double base_comp[5] ) {
int i;
for ( i = 0; i < 5; i++ ) {
base_comp[i] = 0.0;
}
for ( i = 0; i < seq_length; i++ ) {
base_comp[ char_lookup [ (unsigned int)seq[i] ] ] += 1.0;
}
}
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