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#include <stdio.h>
#include <ctype.h>
#include <string.h>
#include "os.h"
#include "align.h"
#include "align_lib_old.h"
FastInt W128[128][128] = {{0},{0}};
char base_val[128] = {0};
static FastInt (*align_arr[])() = {align_ss,
align_sv,
/*balign_sv*/NULL,
align_ss2};
static void (*display_arr[])() = {display_ss,
display_sv,
display_sv,
display_ss2};
static void (*expand_arr[])() = {expand,
expand_6,
expand_6,
expand};
/*
* Initialise 128x128 weight matrix from our score matrix
*/
void init_align_mat(int **matrix,
char *order, int unknown,
FastInt W128[][128]) {
int i, j, i_end;
unsigned char ci, cj;
for (i = 0; i < 128; i++) {
for (j = 0; j < 128; j++) {
W128[i][j] = unknown;
}
}
i_end = strlen(order);
for (i = 0; i < i_end; i++) {
ci = order[i];
for (j = 0; j < i_end; j++) {
cj = order[j];
W128[ ci ][ cj ] = matrix[i][j];
W128[tolower(ci)][ cj ] = matrix[i][j];
W128[ ci ][tolower(cj)] = matrix[i][j];
W128[tolower(ci)][tolower(cj)] = matrix[i][j];
}
}
for (i=0; i<128; i++)
base_val[i] = 5;
base_val['A'] = 0;
base_val['a'] = 0;
base_val['C'] = 1;
base_val['c'] = 1;
base_val['G'] = 2;
base_val['g'] = 2;
base_val['T'] = 3;
base_val['t'] = 3;
base_val['U'] = 3;
base_val['u'] = 3;
base_val['*'] = 4;
/* base_val['-'] = 5; the default */
}
void init_W128(int **matrix,
char *order, int unknown) {
init_align_mat(matrix, order, unknown, W128);
}
/*
* Generic alignment interface:
*
* Job 0 = Sequence against sequence global aligment
* Job 1 = Sequence against vector global aligment
* Job 2 = vector against vector global aligment (unimplemented)
* Job 3 = Job 0 except with end gaps no penalised (to replace 0 eventually)
*
* Passing low_band == 0 && high_band == 0 implies using the full, rather than
* band, algorithm.
* Currently the band algorithm does not work so well always use the full.
*
* Passing rseq1 and rseq2 as non NULL implies storing the new aligned
* sequences in rseq1 and rseq2.
*
* Protein alignment only works for sequence against sequence.
*
* Return values:
* -1 for error
* >0 for success (value returned is score)
*/
int calignm(void *seq1, void *seq2, int len1, int len2,
void *rseq1, void *rseq2, int *rlen1, int *rlen2,
int low_band, int high_band, int gap_open, int gap_extend,
int job, int is_protein, align_int *res, FastInt W[][128]) {
/* int full = low_band == 0 && high_band == 0; */
int retval = -1;
FastInt *results;
int ajob = job & ALIGN_J_MASK;
if (ajob < 0 || ajob > 3) {
verror(ERR_FATAL, "align", "unknown job %d", ajob);
return -1;
}
if (res == NULL) {
if (NULL == (results = (FastInt *)malloc((len1+len2) *
sizeof(FastInt)))) {
verror(ERR_FATAL, "align", "not enough memory");
return -1;
}
} else {
results = (FastInt *)res;
}
retval = align_arr[ajob](seq1, seq2, (FastInt)len1, (FastInt)len2,
(FastInt)low_band, (FastInt)high_band, W,
(FastInt)gap_open, (FastInt)gap_extend,
(FastInt *)results,
/* End gaps */
(job & ALIGN_GAP_S1) ? 1 : 0,
(job & ALIGN_GAP_S2) ? 1 : 0,
(job & ALIGN_GAP_E1) ? 1 : 0,
(job & ALIGN_GAP_E2) ? 1 : 0
);
/* non vectors */
if (rseq1 && rseq2) {
if (retval != -1) {
expand_arr[ajob](seq1, seq2, len1, len2,
rseq1, rseq2, rlen1, rlen2,
results, job & ALIGN_J_PADS);
}
}
if (res == NULL)
free (results);
return retval;
}
/*
* As above, but hardcoded to use W128
*/
int calign(void *seq1, void *seq2, int len1, int len2,
void *rseq1, void *rseq2, int *rlen1, int *rlen2,
int low_band, int high_band, int gap_open, int gap_extend,
int job, int is_protein, align_int *res) {
return calignm(seq1, seq2, len1, len2, rseq1, rseq2, rlen1, rlen2,
low_band, high_band, gap_open, gap_extend,
job, is_protein, res, W128);
}
/*
* Generic alignment display interface
*
* Job 0 = Sequence against sequence display
* Job 1 = Sequence against vector display
* Job 2 = vector against vector display (unimplemented)
* Job 3 = Job 0 except with end gaps no penalised (to replace 0 eventually)
*
*/
void cdisplay(void *seq1, void *seq2, int len1, int len2, int job,
align_int *results, int pos1, int pos2) {
display_arr[job & ALIGN_J_MASK](seq1, seq2, len1, len2,
results, pos1, pos2);
}
/*
* Generic alignment expansion interface
*
* Job 0 = Sequence against sequence expand
* Job 1 = Sequence against vector expand
* Job 2 = vector against vector expand (unimplemented)
*
* seq1 and seq2 are the original sequences. Expanded sequences will be
* returned in rseq1 and rseq2 (it is expected that the caller allocate
* memory for these buffers) and the lengths in rlen1 and rlen2.
*
*/
void cexpand(void *seq1, void *seq2, int len1, int len2,
void *rseq1, void *rseq2, int *rlen1, int *rlen2,
int job, align_int *results) {
expand_arr[job & ALIGN_J_MASK](seq1, seq2, len1, len2,
rseq1, rseq2, rlen1, rlen2,
results, job & ALIGN_J_PADS);
}
/*
* FORTRAN interfaces
*/
int_f align_(void *seq1, int_f *len1, void *seq2, int_f *len2,
void *rseq1, int_f *rlen1, void *rseq2, int_f *rlen2,
int_f *low_band, int_f *high_band,
int_f *gap_open, int_f *gap_extend,
int_f *job, int_f *is_protein,
int_fl seq1_l, int_fl seq2_l, int_fl rseq1_l, int_fl rseq2_l) {
return calign(seq1, seq2, *len1, *len2, rseq1, rseq2, rlen1, rlen2,
*low_band, *high_band, *gap_open, *gap_extend,
*job, *is_protein, NULL);
}
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