+++ /dev/null
-/* copyright (c) 1996, 1997, 1998, 1999 William R. Pearson and the
- U. of Virginia */
-
-/* $Name: fa_34_26_5 $ - $Id: work_thr.c,v 1.23 2007/04/26 18:33:20 wrp Exp $ */
-
-/* work_thr.c - threaded worker */
-
-/* modified 21-Oct-1998 to work with reverse complement for DNA */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <time.h>
-#include <sys/types.h>
-#include <signal.h>
-
-#include "defs.h" /* various constants */
-#include "mw.h" /* defines beststr */
-#include "structs.h"
-#include "param.h" /* pstruct, thr_str, buf_head, rstruct */
-
-/***************************************/
-/* thread global variable declarations */
-/***************************************/
-
-#define XTERNAL
-#include "thr.h"
-#undef XTERNAL
-
-void alloc_pam (int, int, struct pstruct *);
-int **alloc_pam2p(int, int);
-void revcomp(unsigned char *seq, int n, int *c_nt);
-#ifdef WIN32
-void pthread_exit(void *);
-#else
-void THR_EXIT(void *);
-#endif
-
-/* functions getting/sending buffers to threads (thr_sub.c) */
-extern void wait_thr(void);
-extern int get_wbuf(struct buf_head **cur_buf, int max_work_buf);
-extern void put_wbuf(struct buf_head *cur_buf, int max_work_buf);
-
-/* dropxx.c functions */
-extern void init_work (unsigned char *aa0, int n0,
- struct pstruct *ppst, void **f_arg);
-
-extern void do_work (unsigned char *aa0, int n0, unsigned char *aa1, int n1,
- int frame,
- struct pstruct *ppst, void *f_str, int qr_flg,
- struct rstruct *rst);
-
-extern void close_work (unsigned char *, int, struct pstruct *, void **);
-
-extern void irand(int);
-extern int shuffle(unsigned char *, unsigned char *, int);
-extern int wshuffle(unsigned char *, unsigned char *, int, int, int *);
-extern void qshuffle(unsigned char *aa0, int n0, int nm0);
-extern void free_pam2p(int **);
-
-void
-work_thread (struct thr_str *work_info)
-{
- struct buf_head *cur_buf;
- struct buf_str *cur_buf_p;
- struct buf_str *p_rbuf;
- unsigned char *aa1s;
- int cur_cnt;
- int my_worker;
- int i, j, npam, n0, nm0;
- int ix_score, debug_lib, zsflag, zs_win, do_shuffle, ieven=0;
- int frame;
-
- struct rstruct rrst;
- struct pstruct my_pst, *my_ppst;
- unsigned char *aa0[6], *aa0s;
- void *f_str[6], *qf_str;
-
- my_worker = work_info->worker;
-
- wait_thr(); /* wait for start_thread predicate to drop to 0 */
-
- /* do init_work */
-
- /* let each thread have its own copy of the query */
- n0 = work_info->n0;
- nm0 = work_info->nm0;
-
- if ((aa0[0]=(unsigned char *)calloc((size_t)n0+2,sizeof(unsigned char)))
- ==NULL) {
- fprintf(stderr," cannot allocate aa00[%d] for worker %d\n",
- n0, my_worker);
- exit(1);
- }
- *aa0[0]='\0';
- aa0[0]++;
- memcpy(aa0[0],work_info->aa0,n0+1);
-
- /* make certain that all but 0 have their own copy of pst */
- if (my_worker) {
- my_ppst = &my_pst;
- memcpy(my_ppst,work_info->ppst,sizeof(struct pstruct));
-
- alloc_pam(MAXSQ, MAXSQ, my_ppst);
-
- npam = (my_pst.ext_sq_set) ? my_pst.nsqx : my_pst.nsq;
-
- for (i=0; i<=npam; i++) {
- for (j=0; j<=npam; j++) {
- my_pst.pam2[0][i][j] = work_info->ppst->pam2[0][i][j];
- my_pst.pam2[1][i][j] = work_info->ppst->pam2[1][i][j];
- }
- }
-
- if (work_info->ppst->pam_pssm && work_info->ppst->pam2p[0]) {
- my_ppst->pam2p[0] = alloc_pam2p(n0,npam);
- my_ppst->pam2p[1] = alloc_pam2p(n0,npam);
- for (i=0; i<n0; i++) {
- for (j=0; j <= npam; j++) {
- my_pst.pam2p[0][i][j] = work_info->ppst->pam2p[0][i][j];
- my_pst.pam2p[1][i][j] = work_info->ppst->pam2p[1][i][j];
- }
- }
- }
- }
- else my_ppst=work_info->ppst;
-
- /* note that aa[5,4,3,2] are never used, but are provided so that frame
- can range from 0 .. 5; likewise for f_str[5..2] */
-
- aa0[5] = aa0[4] = aa0[3] = aa0[2] = aa0[1] = aa0[0];
- init_work (aa0[0], n0, my_ppst, &f_str[0]);
-
- f_str[5] = f_str[4] = f_str[3] = f_str[2] = f_str[1] = f_str[0];
-
- if (work_info->qframe == 2) {
- if ((aa0[1]=(unsigned char *)calloc((size_t)n0+2,sizeof(unsigned char)))==NULL) {
- fprintf(stderr," cannot allocate aa01[%d] for worker %d\n",
- n0, my_worker);
- }
- *aa0[1]='\0';
- aa0[1]++;
- memcpy(aa0[1],work_info->aa0,n0+1);
- revcomp(aa0[1],n0,my_ppst->c_nt);
- init_work (aa0[1], n0, my_ppst, &f_str[1]);
- }
-
- if (work_info->qshuffle) {
- if ((aa0s=(unsigned char *)calloc(n0+2,sizeof(char)))==NULL) {
- fprintf(stderr,"cannot allocate aa0s[%d]\n",n0+2);
- exit(1);
- }
- *aa0s='\0';
- aa0s++;
- memcpy(aa0s,aa0[0],n0);
- qshuffle(aa0s,n0,nm0);
- init_work (aa0s, n0, my_ppst, &qf_str);
- }
-
- ix_score = my_ppst->score_ix;
- debug_lib = my_ppst->debug_lib;
- zsflag = my_ppst->zsflag;
- zs_win = my_ppst->zs_win;
-
- if (zsflag >= 10) {
- if((aa1s=calloc(work_info->max_tot+1,sizeof(char))) == NULL) {
- fprintf(stderr,"unable to allocate shuffled library sequence\n");
- }
- else {
- *aa1s=0;
- aa1s++;
- do_shuffle =1;
- irand(0);
- }
- }
- else {do_shuffle = 0;}
-
- /* main work loop */
- while (get_wbuf(&cur_buf,work_info->max_work_buf)) {
-
- cur_cnt = cur_buf->buf_cnt;
- if (cur_cnt == -1) break;
- cur_buf_p = cur_buf->buf;
-
- while (cur_cnt--) { /* count down the number of sequences */
- p_rbuf = cur_buf_p++; /* step through each sequence */
- p_rbuf->rst.score[0] = p_rbuf->rst.score[1] = p_rbuf->rst.score[2] = 0;
- frame = p_rbuf->frame;
-
-#ifdef DEBUG
- if (debug_lib) {
- if (frame >= 2) fprintf(stderr,"* frame: %d\n",frame);
- for (i=0; i<p_rbuf->n1; i++)
- if (p_rbuf->aa1b[i]>=my_ppst->nsqx) {
- fprintf(stderr,
- "%s residue[%d/%d] %d range (%d)\n",
- p_rbuf->libstr,i,p_rbuf->n1,p_rbuf->aa1b[i],my_ppst->nsqx);
- p_rbuf->aa1b[i]=0;
- p_rbuf->n1=i-1;
- break;
- }
- }
-#endif
-
- do_work (aa0[frame], n0, p_rbuf->aa1b, p_rbuf->n1, frame,
- my_ppst, f_str[frame], 0, &p_rbuf->rst);
-
- if (work_info->qshuffle) {
- do_work(aa0s,n0,p_rbuf->aa1b, p_rbuf->n1, frame,
- my_ppst, qf_str, 1, &rrst);
- p_rbuf->qr_score = rrst.score[ix_score];
- p_rbuf->qr_escore = rrst.escore;
- }
-
- if (do_shuffle) {
- if (zs_win > 0) wshuffle(p_rbuf->aa1b,aa1s,p_rbuf->n1,zs_win,&ieven);
- else shuffle(p_rbuf->aa1b,aa1s,p_rbuf->n1);
-
- do_work (aa0[frame], n0, aa1s, p_rbuf->n1, frame,
- my_ppst, f_str[frame], 0, &rrst);
- p_rbuf->r_score = rrst.score[ix_score];
- p_rbuf->r_escore = rrst.escore;
- }
- }
-
- cur_buf->have_results = 1;
-
- put_wbuf(cur_buf,work_info->max_work_buf);
-
- } /* end main while */
-
- close_work(aa0[0], n0, my_ppst, &f_str[0]);
- free(aa0[0]-1);
- if (work_info->qframe == 2) {
- close_work(aa0[1], n0, my_ppst, &f_str[1]);
- free(aa0[1]-1);
- }
-
- if (do_shuffle) free(aa1s-1);
-
- if (my_worker) {
- free(my_pst.pam2[1][0]);
- free(my_pst.pam2[0][0]);
- free(my_pst.pam2[1]);
- free(my_pst.pam2[0]);
-
- if (my_pst.pam_pssm) {
- free_pam2p(my_pst.pam2p[0]);
- free_pam2p(my_pst.pam2p[1]);
- }
- }
-
-#ifdef WIN32
- pthread_exit(&work_info->status);
-#else
- THR_EXIT(&work_info->status);
-#endif
-
-} /* end work_thread */
-
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