+++ /dev/null
-
-/* copyright (c) 1996, 1997, 1998, 1999 William R. Pearson and the
- U. of Virginia */
-
-/* $Name: fa_34_26_5 $ - $Id: compacc.c,v 1.61 2007/04/26 18:37:18 wrp Exp $ */
-
-/* Concurrent read version */
-
-#include <stdio.h>
-#include <stdlib.h>
-#if defined(UNIX) || defined(WIN32)
-#include <sys/types.h>
-#endif
-
-#include <limits.h>
-#include <float.h>
-
-#include <string.h>
-#include <time.h>
-#include <math.h>
-
-#include "defs.h"
-#include "param.h"
-#include "structs.h"
-
-#ifndef PCOMPLIB
-#include "mw.h"
-#else
-#include "p_mw.h"
-#endif
-
-#define XTERNAL
-#include "uascii.h"
-#include "upam.h"
-#undef XTERNAL
-
-#ifdef PCOMPLIB
-#include "msg.h"
-extern int nnodes;
-#ifdef PVM_SRC
-#include "pvm3.h"
-extern int pinums[],hosttid;
-#endif
-#ifdef MPI_SRC
-#include "mpi.h"
-#endif
-#endif
-
-extern time_t tdone, tstart; /* Timing */
-extern void abort ();
-extern void ptime ();
-
-/* because it is used to pre-allocate space, maxn has various
- constraints. For "simple" comparisons, it is simply the length of
- the longest library sequence. But for translated comparisons, it
- must be 3 or 6X the length of the query sequence.
-
- In addition, however, it can be reduced to make certain that
- sequences are read in smaller chunks. And, maxn affect how large
- overlaps must be when sequences are read in chunks.
-*/
-
-int
-reset_maxn(struct mngmsg *m_msg, int maxn) {
-
- /* reduce maxn if requested */
- if (m_msg->maxn > 0 && m_msg->maxn < maxn) maxn = m_msg->maxn;
-
- if (m_msg->qdnaseq==m_msg->ldnaseq || m_msg->qdnaseq==SEQT_DNA ||
- m_msg->qdnaseq == SEQT_RNA) {/* !TFAST - either FASTA or FASTX*/
-
- if (m_msg->n0> m_msg->max_tot/3) {
- fprintf(stderr," query sequence is too long %d > %d %s\n",
- m_msg->n0,
- m_msg->max_tot/3,
- m_msg->sqnam);
- exit(1);
- }
- m_msg->loff = m_msg->n0;
- m_msg->maxt3 = maxn-m_msg->loff;
- }
- else { /* is TFAST */
- if (m_msg->n0 > MAXTST) {
- fprintf(stderr," query sequence is too long %d %s\n",m_msg->n0,m_msg->sqnam);
- exit(1);
- }
-
- if (m_msg->n0*3 > maxn ) { /* n0*3 for the three frames - this
- will only happen if maxn has been
- set low manually */
-
- if (m_msg->n0*4+2 < m_msg->max_tot) { /* m_msg0*3 + m_msg0 */
- fprintf(stderr,
- " query sequence too long for library segment: %d - resetting to %d\n",
- maxn,m_msg->n0*3);
- maxn = m_msg->maxn = m_msg->n0*3;
- }
- else {
- fprintf(stderr," query sequence too long for translated search: %d * 4 > %d %s\n",
- m_msg->n0,maxn, m_msg->sqnam);
- exit(1);
- }
- }
-
- /* set up some constants for overlaps */
- m_msg->loff = 3*m_msg->n0;
- m_msg->maxt3 = maxn-m_msg->loff-3;
- m_msg->maxt3 -= m_msg->maxt3%3;
- m_msg->maxt3++;
-
- maxn = maxn - 3; maxn -= maxn%3; maxn++;
- }
- return maxn;
-}
-
-
-int
-scanseq(unsigned char *seq, int n, char *str) {
- int tot,i;
- char aaray[128]; /* this must be set > nsq */
-
- for (i=0; i<128; i++) aaray[i]=0;
- for (i=0; (size_t)i < strlen(str); i++) aaray[qascii[str[i]]]=1;
- for (i=tot=0; i<n; i++) tot += aaray[seq[i]];
- return tot;
-}
-
-/* subs_env takes a string, possibly with ${ENV}, and looks up all the
- potential environment variables and substitutes them into the
- string */
-
-void subs_env(char *dest, char *src, int dest_size) {
- char *last_src, *bp, *bp1;
-
- last_src = src;
-
- if ((bp = strchr(src,'$'))==NULL) {
- strncpy(dest, src, dest_size);
- dest[dest_size-1] = '\0';
- }
- else {
- *dest = '\0';
- while (strlen(dest) < dest_size-1 && bp != NULL ) {
- /* copy stuff before ${*/
- *bp = '\0';
- strncpy(dest, last_src, dest_size);
- *bp = '$';
-
- /* copy ENV */
- if (*(bp+1) != '{') {
- strncat(dest, "$", dest_size - strlen(dest) -1);
- dest[dest_size-1] = '\0';
- bp += 1;
- }
- else { /* have ${ENV} - put it in */
- if ((bp1 = strchr(bp+2,'}'))==NULL) {
- fprintf(stderr, "Unterminated ENV: %s\n",src);
- break;
- }
- else {
- *bp1 = '\0';
- if (getenv(bp+2)!=NULL) {
- strncat(dest, getenv(bp+2), dest_size - strlen(dest) - 1);
- dest[dest_size-1] = '\0';
- *bp1 = '}';
- }
- bp = bp1+1; /* bump bp even if getenv == NULL */
- }
- }
- last_src = bp;
-
- /* now get the next ${ENV} if present */
- bp = strchr(last_src,'$');
- }
- /* now copy the last stuff */
- strncat(dest, last_src, dest_size - strlen(dest) - 1);
- dest[dest_size-1]='\0';
- }
-}
-
-
-void selectbest(bptr,k,n) /* k is rank in array */
- struct beststr **bptr;
- int k,n;
-{
- int v, i, j, l, r;
- struct beststr *tmptr;
-
- l=0; r=n-1;
-
- while ( r > l ) {
- v = bptr[r]->score[0];
- i = l-1;
- j = r;
- do {
- while (bptr[++i]->score[0] > v) ;
- while (bptr[--j]->score[0] < v) ;
- tmptr = bptr[i]; bptr[i]=bptr[j]; bptr[j]=tmptr;
- } while (j > i);
- bptr[j]=bptr[i]; bptr[i]=bptr[r]; bptr[r]=tmptr;
- if (i>=k) r = i-1;
- if (i<=k) l = i+1;
- }
-}
-
-void selectbestz(bptr,k,n) /* k is rank in array */
- struct beststr **bptr;
- int k,n;
-{
- int i, j, l, r;
- struct beststr *tmptr;
- double v;
-
- l=0; r=n-1;
-
- while ( r > l ) {
- v = bptr[r]->zscore;
- i = l-1;
- j = r;
- do {
- while (bptr[++i]->zscore > v) ;
- while (bptr[--j]->zscore < v) ;
- tmptr = bptr[i]; bptr[i]=bptr[j]; bptr[j]=tmptr;
- } while (j > i);
- bptr[j]=bptr[i]; bptr[i]=bptr[r]; bptr[r]=tmptr;
- if (i>=k) r = i-1;
- if (i<=k) l = i+1;
- }
-}
-
-/* improved shellsort with high-performance increments */
-/*
-shellsort(itemType a[], int l, int r)
-{ int i, j, k, h; itemType v;
- int incs[16] = { 1391376, 463792, 198768, 86961, 33936,
- 13776, 4592, 1968, 861, 336,
- 112, 48, 21, 7, 3, 1 };
- for ( k = 0; k < 16; k++)
- for (h = incs[k], i = l+h; i <= r; i++)
- {
- v = a[i]; j = i;
- while (j > h && a[j-h] > v)
- { a[j] = a[j-h]; j -= h; }
- a[j] = v;
- }
-}
-*/
-
-/* ?improved? version of sortbestz using optimal increments and fewer
- exchanges */
-void sortbestz(struct beststr **bptr, int nbest)
-{
- int gap, i, j, k;
- struct beststr *tmp;
- double v;
- int incs[16] = { 1391376, 463792, 198768, 86961, 33936,
- 13776, 4592, 1968, 861, 336,
- 112, 48, 21, 7, 3, 1 };
-
- for ( k = 0; k < 16; k++) {
- gap = incs[k];
- for (i=gap; i < nbest; i++) {
- tmp = bptr[i];
- j = i;
- v = bptr[i]->zscore;
- while ( j >= gap && bptr[j-gap]->zscore < v) {
- bptr[j] = bptr[j - gap];
- j -= gap;
- }
- bptr[j] = tmp;
- }
- }
-}
-
-
-void sortbeste(struct beststr **bptr, int nbest)
-{
- int gap, i, j, k;
- struct beststr *tmp;
- double v;
- int incs[16] = { 1391376, 463792, 198768, 86961, 33936,
- 13776, 4592, 1968, 861, 336,
- 112, 48, 21, 7, 3, 1 };
-
- for ( k = 0; k < 16; k++) {
- gap = incs[k];
- for (i=gap; i < nbest; i++) {
- j = i;
- tmp = bptr[i];
- v = tmp->escore;
- while ( j >= gap && bptr[j-gap]->escore > v) {
- bptr[j] = bptr[j - gap];
- j -= gap;
- }
- bptr[j] = tmp;
- }
- }
-
- /* sometimes there are many high scores with E()==0.0, sort
- those by z() score */
-
- j = 0;
- while (j < nbest && bptr[j]->escore <= 2.0*DBL_MIN ) {j++;}
- if (j > 1) sortbestz(bptr,j);
-}
-
-extern double zs_to_Ec(double zs, long entries);
-
-/*
-extern double ks_dev;
-extern int ks_df; */
-extern char hstring1[];
-
-void
-prhist(FILE *fd, struct mngmsg m_msg,
- struct pstruct pst,
- struct hist_str hist,
- int nstats,
- struct db_str ntt,
- char *gstring2)
-{
- int i,j,hl,hll, el, ell, ev;
- char hline[80], pch, *bp;
- int mh1, mht;
- int maxval, maxvalt, dotsiz, ddotsiz,doinset;
- double cur_e, prev_e, f_int;
- double max_dev, x_tmp;
- double db_tt;
- int n_chi_sq, cum_hl=0, max_i;
-
-
- fprintf(fd,"\n");
-
- if (pst.zsflag_f < 0) {
- fprintf(fd, "%7ld residues in %5ld sequences\n", ntt.length,ntt.entries);
- fprintf(fd,"\n%s\n",gstring2);
- return;
- }
-
- if (nstats > 20) {
- max_dev = 0.0;
- mh1 = hist.maxh-1;
- mht = (3*hist.maxh-3)/4 - 1;
-
- if (!m_msg.nohist && mh1 > 0) {
- for (i=0,maxval=0,maxvalt=0; i<hist.maxh; i++) {
- if (hist.hist_a[i] > maxval) maxval = hist.hist_a[i];
- if (i >= mht && hist.hist_a[i]>maxvalt) maxvalt = hist.hist_a[i];
- }
- n_chi_sq = 0;
- cum_hl = -hist.hist_a[0];
- dotsiz = (maxval-1)/60+1;
- ddotsiz = (maxvalt-1)/50+1;
- doinset = (ddotsiz < dotsiz && dotsiz > 2);
-
- if (pst.zsflag_f>=0)
- fprintf(fd," opt E()\n");
- else
- fprintf(fd," opt\n");
-
- prev_e = zs_to_Ec((double)(hist.min_hist-hist.histint/2),hist.entries);
- for (i=0; i<=mh1; i++) {
- pch = (i==mh1) ? '>' : ' ';
- pch = (i==0) ? '<' : pch;
- hll = hl = hist.hist_a[i];
- if (pst.zsflag_f>=0) {
- cum_hl += hl;
- f_int = (double)(i*hist.histint+hist.min_hist)+(double)hist.histint/2.0;
- cur_e = zs_to_Ec(f_int,hist.entries);
- ev = el = ell = (int)(cur_e - prev_e + 0.5);
- if (hl > 0 && i > 5 && i < (90-hist.min_hist)/hist.histint) {
- x_tmp = fabs(cum_hl - cur_e);
- if ( x_tmp > max_dev) {
- max_dev = x_tmp;
- max_i = i;
- }
- n_chi_sq++;
- }
- if ((el=(el+dotsiz-1)/dotsiz) > 60) el = 60;
- if ((ell=(ell+ddotsiz-1)/ddotsiz) > 40) ell = 40;
- fprintf(fd,"%c%3d %5d %5d:",
- pch,(i<mh1)?(i)*hist.histint+hist.min_hist :
- mh1*hist.histint+hist.min_hist,hl,ev);
- }
- else fprintf(fd,"%c%3d %5d :",
- pch,(i<mh1)?(i)*hist.histint+hist.min_hist :
- mh1*hist.histint+hist.min_hist,hl);
-
- if ((hl=(hl+dotsiz-1)/dotsiz) > 60) hl = 60;
- if ((hll=(hll+ddotsiz-1)/ddotsiz) > 40) hll = 40;
- for (j=0; j<hl; j++) hline[j]='=';
- if (pst.zsflag_f>=0) {
- if (el <= hl ) {
- if (el > 0) hline[el-1]='*';
- hline[hl]='\0';
- }
- else {
- for (j = hl; j < el; j++) hline[j]=' ';
- hline[el-1]='*';
- hline[hl=el]='\0';
- }
- }
- else hline[hl] = 0;
- if (i==1) {
- for (j=hl; j<10; j++) hline[j]=' ';
- sprintf(&hline[10]," one = represents %d library sequences",dotsiz);
- }
- if (doinset && i == mht-2) {
- for (j = hl; j < 10; j++) hline[j]=' ';
- sprintf(&hline[10]," inset = represents %d library sequences",ddotsiz);
- }
- if (i >= mht&& doinset ) {
- for (j = hl; j < 10; j++) hline[j]=' ';
- hline[10]=':';
- for (j = 11; j<11+hll; j++) hline[j]='=';
- hline[11+hll]='\0';
- if (pst.zsflag_f>=0) {
- if (ell <= hll) hline[10+ell]='*';
- else {
- for (j = 11+hll; j < 10+ell; j++) hline[j]=' ';
- hline[10+ell] = '*';
- hline[11+ell] = '\0';
- }
- }
- }
-
- fprintf(fd,"%s\n",hline);
- prev_e = cur_e;
- }
- }
- }
-
- if (ntt.carry==0) {
- fprintf(fd, "%7ld residues in %5ld sequences\n", ntt.length, ntt.entries);
- }
- else {
- db_tt = (double)ntt.carry*(double)LONG_MAX + (double)ntt.length;
- fprintf(fd, "%.0f residues in %5ld library sequences\n", db_tt, ntt.entries);
- }
-
- if (pst.zsflag_f>=0) {
- if (MAXSTATS < hist.entries)
-#ifdef SAMP_STATS
- fprintf(fd," statistics sampled from %d to %ld sequences\n",
- MAXSTATS,hist.entries);
-#else
- fprintf(fd," statistics extrapolated from %d to %ld sequences\n",
- MAXSTATS,hist.entries);
-#endif
- /* summ_stats(stat_info); */
- fprintf(fd," %s\n",hist.stat_info);
- if (!m_msg.nohist && cum_hl > 0)
- fprintf(fd," Kolmogorov-Smirnov statistic: %6.4f (N=%d) at %3d\n",
- max_dev/(float)cum_hl, n_chi_sq,max_i*hist.histint+hist.min_hist);
- if (m_msg.markx & MX_M10FORM) {
- while ((bp=strchr(hist.stat_info,'\n'))!=NULL) *bp=' ';
- if (cum_hl <= 0) cum_hl = -1;
- sprintf(hstring1,"; mp_extrap: %d %ld\n; mp_stats: %s\n; mp_KS: %6.4f (N=%d) at %3d\n",
- MAXSTATS,hist.entries,hist.stat_info,max_dev/(float)cum_hl, n_chi_sq,max_i*hist.histint+hist.min_hist);
- }
- }
- fprintf(fd,"\n%s\n",gstring2);
- fflush(fd);
-}
-
-extern char prog_name[], *verstr;
-
-void s_abort (char *p, char *p1)
-{
- int i;
-
- fprintf (stderr, "\n***[%s] %s%s***\n", prog_name, p, p1);
-#ifdef PCOMPLIB
-#ifdef PVM_SRC
- for (i=FIRSTNODE; i< nnodes; i++) pvm_kill(pinums[i]);
- pvm_exit();
-#endif
-#ifdef MPI_SRC
- MPI_Abort(MPI_COMM_WORLD,1);
- MPI_Finalize();
-#endif
-#endif
- exit (1);
-}
-
-#ifndef MPI_SRC
-void w_abort (char *p, char *p1)
-{
- fprintf (stderr, "\n***[%s] %s%s***\n\n", prog_name, p, p1);
- exit (1);
-}
-#endif
-
-#ifndef PCOMPLIB
-/* copies from from to to shuffling */
-
-extern int nrand(int);
-
-void
-shuffle(unsigned char *from, unsigned char *to, int n)
-{
- int i,j; unsigned char tmp;
-
- if (from != to) memcpy((void *)to,(void *)from,n);
-
- for (i=n; i>0; i--) {
- j = nrand(i);
- tmp = to[j];
- to[j] = to[i-1];
- to[i-1] = tmp;
- }
- to[n] = 0;
-}
-
-/* copies from from to from shuffling, ieven changed for threads */
-void
-wshuffle(unsigned char *from, unsigned char *to, int n, int wsiz, int *ieven)
-{
- int i,j, k, mm;
- unsigned char tmp, *top;
-
- memcpy((void *)to,(void *)from,n);
-
- mm = n%wsiz;
-
- if (*ieven) {
- for (k=0; k<(n-wsiz); k += wsiz) {
- top = &to[k];
- for (i=wsiz; i>0; i--) {
- j = nrand(i);
- tmp = top[j];
- top[j] = top[i-1];
- top[i-1] = tmp;
- }
- }
- top = &to[n-mm];
- for (i=mm; i>0; i--) {
- j = nrand(i);
- tmp = top[j];
- top[j] = top[i-1];
- top[i-1] = tmp;
- }
- *ieven = 0;
- }
- else {
- for (k=n; k>=wsiz; k -= wsiz) {
- top = &to[k-wsiz];
- for (i=wsiz; i>0; i--) {
- j = nrand(i);
- tmp = top[j];
- top[j] = top[i-1];
- top[i-1] = tmp;
- }
- }
- top = &to[0];
- for (i=mm; i>0; i--) {
- j = nrand(i);
- tmp = top[j];
- top[j] = top[i-1];
- top[i-1] = tmp;
- }
- *ieven = 1;
- }
- to[n] = 0;
-}
-
-#endif
-
-int
-sfn_cmp(int *q, int *s)
-{
- if (*q == *s) return *q;
- while (*q && *s) {
- if (*q == *s) return *q;
- else if (*q < *s) q++;
- else if (*q > *s) s++;
- }
- return 0;
-}
-
-#ifndef MPI_SRC
-
-#define ESS 49
-
-void
-revcomp(unsigned char *seq, int n, int *c_nt)
-{
- unsigned char tmp;
- int i, ni;
-
- for (i=0, ni = n-1; i< n/2; i++,ni--) {
- tmp = c_nt[seq[i]];
- seq[i] = c_nt[seq[ni]];
- seq[ni] = tmp;
- }
- if ((n%2)==1) {
- i = n/2;
- seq[i] = c_nt[seq[i]];
- }
- seq[n]=0;
-}
-#endif
-
-#ifdef PCOMPLIB
-
-/* init_stage2 sets up the data structures necessary to send a subset
- of sequences to the nodes, and then collects the results
-*/
-
-/* wstage2[] FIRSTNODE .. nnodes has the next sequence to be do_opt()/do_walign()ed */
-/* wstage2p[] is a list of sequence numbers/frames, to be sent to workers */
-/* wstage2b[] is a list of bptr's that shares the index with wstage2p[] */
-
-static int wstage2[MAXWRKR +1]; /* count of second stage scores */
-static struct stage2_str *wstage2p[MAXWRKR+1]; /* list of second stage sequences */
-static int wstage2i[MAXWRKR+1]; /* index into second stage sequences */
-static struct beststr *bbptr,
- **wstage2b[MAXWRKR+1]; /* reverse pointers to bestr */
-
-void
-do_stage2(struct beststr **bptr, int nbest, struct mngmsg m_msg0,
- int s_func, struct qmng_str *qm_msp) {
-
- int i, is, ib, iw, nres;
- int node, snode, node_done;
- int bufid, numt, tid;
- char errstr[120];
- struct comstr2 bestr2[BFR2+1]; /* temporary structure array */
- char *seqc_buff, *seqc;
- int seqc_buff_len, aln_code_n;
-#ifdef MPI_SRC
- MPI_Status mpi_status;
-#endif
-
- /* initialize the counter for each worker to 0 */
- for (iw = FIRSTNODE; iw < nnodes; iw++) wstage2[iw] = 0;
-
- /* for each result, bump the counter for the worker that has
- the sequence */
- for (ib = 0; ib < nbest; ib++ ) { wstage2[bptr[ib]->wrkr]++; }
-
- /* now allocate enough space to send each worker a
- list of its sequences stage2_str {seqnm, frame} */
- for (iw = FIRSTNODE; iw < nnodes; iw++) {
- if (wstage2[iw]>0) {
- if ((wstage2p[iw]=
- (struct stage2_str *)
- calloc(wstage2[iw],sizeof(struct stage2_str)))==NULL) {
- sprintf(errstr," cannot allocate sequence listp %d %d",
- iw,wstage2[iw]);
- s_abort(errstr,"");
- }
-
- /* allocate space to remember the bptr's for each result */
- if ((wstage2b[iw]=(struct beststr **)
- calloc(wstage2[iw],sizeof(struct beststr *)))==NULL) {
- sprintf(errstr," cannot allocate sequence listb %d %d",
- iw,wstage2[iw]);
- s_abort(errstr,"");
- }
- wstage2i[iw]=0;
- }
- else {
- wstage2p[iw] = NULL;
- wstage2b[iw] = NULL;
- }
- }
-
- /* for each result, set wstage2p[worker][result_index_in_worker] */
- for (is = 0; is < nbest; is++) {
- iw=bptr[is]->wrkr;
- wstage2p[iw][wstage2i[iw]].seqnm = bptr[is]->seqnm;
- wstage2p[iw][wstage2i[iw]].frame = bptr[is]->frame;
- wstage2b[iw][wstage2i[iw]] = bptr[is];
- wstage2i[iw]++;
- }
-
-
- /* at this point, wstage2i[iw] should equal wstage2[iw] */
- node_done = 0;
- for (node = FIRSTNODE; node < nnodes; node++) {
-
- /* fprintf(stderr,"node: %d stage2: %d\n",node,wstage2[node]); */
-
- /* if a worker has no results, move on */
- if (wstage2[node]<=0) { node_done++; continue;}
-
- qm_msp->slist = wstage2[node]; /* set number of results to return */
- qm_msp->s_func = s_func; /* set s_funct for do_opt/do_walign */
-#ifdef PVM_SRC
- pvm_initsend(PvmDataRaw);
- pvm_pkbyte((char *)qm_msp,sizeof(struct qmng_str),1);
- pvm_send(pinums[node],MSEQTYPE); /* send qm_msp */
- pvm_initsend(PvmDataRaw); /* send the list of seqnm/frame */
- pvm_pkbyte((char *)wstage2p[node],wstage2[node]*sizeof(struct stage2_str),1);
- pvm_send(pinums[node],LISTTYPE);
-#endif
-#ifdef MPI_SRC
- MPI_Send(qm_msp,sizeof(struct qmng_str),MPI_BYTE,node,MSEQTYPE,
- MPI_COMM_WORLD);
- MPI_Send((char *)wstage2p[node],wstage2[node]*
- sizeof(struct stage2_str),MPI_BYTE,node,LISTTYPE,
- MPI_COMM_WORLD);
-#endif
- }
-
- /* all the workers have their list of sequences */
- /* reset the index of results to obtain */
- for (iw = 0; iw < nnodes; iw++) wstage2i[iw]=0;
-
- while (node_done < nnodes-FIRSTNODE) {
-#ifdef PVM_SRC
- bufid = pvm_recv(-1,LISTRTYPE); /* wait for results */
- pvm_bufinfo(bufid,NULL,NULL,&tid);
- /* get a chunk of comstr2 results */
- pvm_upkbyte((char *)&bestr2[0],sizeof(struct comstr2)*(BFR2+1),1);
- snode = (iw=tidtonode(tid));
- pvm_freebuf(bufid);
-#endif
-#ifdef MPI_SRC
- MPI_Recv((char *)&bestr2[0],sizeof(struct comstr2)*(BFR2+1),
- MPI_BYTE,MPI_ANY_SOURCE,LISTRTYPE,MPI_COMM_WORLD,
- &mpi_status);
- snode = mpi_status.MPI_SOURCE;
- iw = snode;
-#endif
-
- seqc_buff = NULL;
- if (s_func == DO_OPT_FLG && m_msg0.show_code==SHOW_CODE_ALIGN) {
-#ifdef PVM_SRC
- bufid = pvm_recv(tid,CODERTYPE);
- pvm_upkint(&seqc_buff_len,1,1); /* get the code string length */
-#endif
-#ifdef MPI_SRC
- MPI_Recv((char *)&seqc_buff_len,1,MPI_INT, snode,
- CODERTYPE,MPI_COMM_WORLD, &mpi_status);
-#endif
-
- seqc=seqc_buff = NULL;
- if (seqc_buff_len > 0) { /* allocate space for it */
- if ((seqc=seqc_buff=calloc(seqc_buff_len,sizeof(char)))==NULL) {
- fprintf(stderr,"Cannot allocate seqc_buff: %d\n",seqc_buff_len);
- seqc_buff_len=0;
- }
- else {
-#ifdef PVM_SRC
- pvm_upkbyte(seqc_buff,seqc_buff_len*sizeof(char),1);
-#endif
-#ifdef MPI_SRC
- MPI_Recv((char *)seqc_buff,seqc_buff_len*sizeof(char),
- MPI_BYTE,snode,CODERTYPE,MPI_COMM_WORLD, &mpi_status);
-#endif
- }
- }
-#ifdef PVM_SRC
- pvm_freebuf(bufid);
-#endif
- }
-
- /* get number of results in this message */
- nres = bestr2[BFR2].seqnm & ~FINISHED;
- /* check to see if finished */
- if (bestr2[BFR2].seqnm&FINISHED) {node_done++;}
-
- seqc = seqc_buff;
-
- /* count through results from a specific worker */
- for (i=0,is=wstage2i[iw]; i < nres; i++,is++) {
-
- /* get the (saved) bptr for this result */
- bbptr=wstage2b[iw][is];
- /* consistency check seqnm's must agree */
- if (wstage2p[iw][is].seqnm == bbptr->seqnm) {
- if (s_func == DO_CALC_FLG && m_msg0.last_calc_flg) {
- bbptr->score[0] = bestr2[i].score[0];
- bbptr->score[1] = bestr2[i].score[1];
- bbptr->score[2] = bestr2[i].score[2];
- bbptr->escore = bestr2[i].escore;
- bbptr->segnum = bestr2[i].segnum;
- bbptr->seglen = bestr2[i].seglen;
- }
- else if (m_msg0.stages > 1) {
- bbptr->score[0] = bestr2[i].score[0];
- bbptr->score[1] = bestr2[i].score[1];
- bbptr->score[2] = bestr2[i].score[2];
- }
-
- if (s_func == DO_OPT_FLG && m_msg0.markx & MX_M9SUMM) {
- /* get score, alignment information, percents */
- bbptr->sw_score = bestr2[i].sw_score;
- memcpy(bbptr->aln_d,&bestr2[i].aln_d,sizeof(struct a_struct));
- bbptr->percent = bestr2[i].percent;
- bbptr->gpercent = bestr2[i].gpercent;
-
- if (m_msg0.show_code == 2) { /* if show code */
- /* length of encoding */
- aln_code_n = bbptr->aln_code_n = bestr2[i].aln_code_n;
- if (aln_code_n > 0) {
- if ((bbptr->aln_code =
- (char *)calloc(aln_code_n+1,sizeof(char)))==NULL) {
- fprintf(stderr,"cannot allocate seq_code[%d:%d]: %d\n",
- bbptr->wrkr,bbptr->seqnm,aln_code_n);
- seqc += aln_code_n+1;
- bbptr->aln_code_n = 0;
- }
- else {
- strncpy(bbptr->aln_code,seqc,aln_code_n);
- bbptr->aln_code[aln_code_n]='\0';
- seqc += aln_code_n+1;
- }
- }
- else {
- fprintf(stderr," aln_code_n <=0: %d\n",aln_code_n);
- }
- }
- }
- }
- else fprintf(stderr,"phase error in phase II return %d %d", iw,i);
- }
- if (seqc_buff != NULL) {
- free(seqc_buff);
- seqc_buff = NULL;
- }
- wstage2i[iw] += nres;
- }
-
- for (iw=FIRSTNODE; iw < nnodes; iw++) {
- if ((void *)wstage2p[iw]!=NULL) free((void *)wstage2p[iw]);
- if ((void *)wstage2b[iw]!=NULL) free((void *)wstage2b[iw]);
- }
-}
-
-#endif
git://source.jalview.org / jabaws.git / blobdiff