+++ /dev/null
-/* copyright (c) 1996, 1997, 1998, 1999, 2002 William R. Pearson and the
- U. of Virginia */
-
-/* $Name: fa_34_26_5 $ - $Id: comp_lib.c,v 1.100 2007/04/26 18:36:36 wrp Exp $ */
-
-/*
- * Concurrent read version
- *
- * Feb 20, 1998 modifications for prss3
- *
- * December, 1998 - DNA searches are now down with forward and reverse
- * strands
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
-#include <time.h>
-
-#include <limits.h>
-#include <float.h>
-#include <math.h>
-
-#ifdef UNIX
-#include <unistd.h>
-#include <sys/types.h>
-#include <signal.h>
-#endif
-
-#include "defs.h"
-#include "mm_file.h"
-
-#include "mw.h" /* defines beststr */
-#include "structs.h" /* mngmsg, libstruct */
-#include "param.h" /* pstruct, thr_str, buf_head, rstruct */
-
-#define XTERNAL
-#include "uascii.h"
-
-char *mp_verstr="34.26";
-
-/********************************/
-/* global variable declarations */
-/********************************/
-char gstring2[MAX_STR]; /* string for label */
-char gstring3[MAX_STR];
-char hstring1[MAX_STR];
-
-extern int max_workers;
-
-#ifdef SUPERFAMNUM
-int nsfnum;
-int sfnum[10];
-extern int sfn_cmp(int *q, int *s);
-int nsfnum_n;
-int sfnum_n[10];
-#endif
-
-/********************************/
-/* extern variable declarations */
-/********************************/
-extern char *prog_func; /* function label */
-extern char *verstr, *iprompt0, *iprompt1, *iprompt2, *refstr;
-
-/********************************/
-/*extern function declarations */
-/********************************/
-/* open sequence file (getseq.c) */
-extern int getseq(char *filen, int *sascii,
- unsigned char *seq, int maxs,
- char *libstr, int n_libstr,
- long *sq0ff);
-
-struct lmf_str *openlib(char *, int, int *, int, struct lmf_str *);
-
-void set_shuffle(struct mngmsg m_msg);
-void closelib(struct lmf_str *m_fptr);
-
-void irand(int);
-int nrand(int);
-
-extern int ann_scan(unsigned char *, int, struct mngmsg *, int );
-extern int scanseq(unsigned char *seq, int n, char *str);
-extern void re_ascii(int *qascii, int *sascii);
-extern int recode(unsigned char *seq, int n, int *qascii, int nsq);
-extern void revcomp(unsigned char *seq, int n, int *c_nt);
-
-extern void init_ascii(int is_ext, int *sascii, int is_dna);
-extern void qshuffle(unsigned char *aa0, int n0, int nm0);
-extern void free_pam2p(int **);
-
-/* initialize environment (doinit.c) */
-extern void initenv (int argc, char **argv, struct mngmsg *m_msg,
- struct pstruct *ppst, unsigned char **aa0);
-
-/* print timing information */
-extern void ptime (FILE *, time_t);
-
-#ifdef COMP_MLIB
-#define QGETLIB (q_file_p->getlib)
-#endif
-
-#define GETLIB (m_file_p->getlib)
-
-/* calculation functions */
-extern void
-init_work(unsigned char *aa0, int n0,
- struct pstruct *ppst, void **f_arg );
-#ifndef COMP_THR
-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);
-#endif
-
-extern void
-close_work(unsigned char *aa0, int n0, struct pstruct *ppst, void **f_arg);
-extern void
-get_param (struct pstruct *pstr, char *pstring1, char *pstring2);
-
-#ifdef COMP_THR
-#ifndef PRSS
-void
-save_best(struct buf_head *cur_buf, struct mngmsg, struct pstruct pst,
- FILE *fdata, int *, struct hist_str *, void **);
-#else
-void
-save_best(struct buf_head *cur_buf, struct mngmsg, struct pstruct pst,
- FILE *fdata, int *, struct hist_str *, void **, int *, int *);
-#endif
-#endif
-
-/* statistics functions */
-extern int
-process_hist(struct stat_str *sptr, int nstat,
- struct mngmsg m_msg,
- struct pstruct pst,
- struct hist_str *hist, void **, int);
-extern void addhistz(double, struct hist_str *); /* scaleswn.c */
-void selectbestz(struct beststr **, int, int );
-extern double (*find_zp)(int score, double escore, int length, double comp,void *);
-
-void last_stats(const unsigned char *, int,
- struct stat_str *sptr, int nstats,
- struct beststr **bestp_arr, int nbest,
- struct mngmsg m_msg, struct pstruct pst,
- struct hist_str *histp, void *);
-
-int last_calc( unsigned char **a0, unsigned char *a1, int maxn,
- struct beststr **bestp_arr, int nbest,
- struct mngmsg m_msg, struct pstruct *ppst,
- void **f_str, void *rs_str);
-
-void scale_scores(struct beststr **bestp_arr, int nbest,
- struct db_str,struct pstruct pst, void *);
-
-#ifndef COMP_THR
-extern int shuffle(unsigned char *, unsigned char *, int);
-extern int wshuffle(unsigned char *, unsigned char *, int, int, int *);
-#endif
-
-extern void set_db_size(int, struct db_str *, struct hist_str *);
-
-/* display functions */
-extern void
-showbest (FILE *fp, unsigned char **aa0, unsigned char *aa1,
- int maxn, struct beststr **bestp_arr, int nbest,
- int qlib, struct mngmsg *m_msg,struct pstruct pst,
- struct db_str db, char *gstring2, void **f_str);
-
-extern void
-showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1,
- int maxn, struct beststr **bestp_arr, int nbest,
- int qlib, struct mngmsg m_msg,struct pstruct pst,
- char *gstring2, void **f_str);
-
-/* misc functions */
-void h_init(struct pstruct *, struct mngmsg *, char *); /* doinit.c */
-void last_init(struct mngmsg *, struct pstruct *); /* initfa/sw.c */
-void last_params(unsigned char *, int, struct mngmsg *, struct pstruct *);
-
-void s_abort(char *, char *); /* compacc.c */
-
-/* initfa/sw.c */
-void resetp(struct mngmsg *, struct pstruct *);
-
-void gettitle(char *, char *, int); /* nxgetaa.c */
-void libchoice(char *lname, int, struct mngmsg *); /* lib_sel.c */
-void libselect(char *lname, struct mngmsg *); /* lib_sel.c */
-void query_parm(struct mngmsg *, struct pstruct *); /* initfa/sw.c */
-void selectbestz(struct beststr **, int, int);
-
-/* compacc.c */
-void prhist(FILE *, struct mngmsg, struct pstruct,
- struct hist_str hist, int nstats, struct db_str, char *);
-void printsum(FILE *, struct db_str db);
-int reset_maxn(struct mngmsg *, int); /* set m_msg.maxt, maxn from maxl */
-
-FILE *outfd; /* Output file */
-
-/* this information is global for fsigint() */
-extern time_t s_time(); /* fetches time */
-time_t tstart, tscan, tprev, tdone; /* Timing */
-#ifdef COMP_MLIB
-time_t ttscan, ttdisp;
-#endif
-time_t tdstart, tddone;
-
-static struct db_str qtt = {0l, 0l, 0};
-
-#ifdef COMP_THR
-/***************************************/
-/* thread global variable declarations */
-/***************************************/
-
-/* functions for getting/sending buffers to threads (thr_sub.c) */
-extern void init_thr(int , struct thr_str *, struct mngmsg, struct pstruct *,
- unsigned char *, int);
-extern void start_thr(void);
-extern void get_rbuf(struct buf_head **cur_buf, int max_wor_buf);
-extern void put_rbuf(struct buf_head *cur_buf, int max_work_buf);
-extern void put_rbuf_done(int nthreads, struct buf_head *cur_buf,
- int max_work_buf);
-#undef XTERNAL
-#include "thr.h"
-struct buf_head buf_list[NUM_WORK_BUF];
-#endif
-
-/* these variables must be global for comp_thr.c so that savebest()
- can use them */
-
-static struct beststr
- *best, /* array of best scores */
- *bestp,
- **bestp_arr; /* array of pointers */
-static int nbest; /* number of best scores */
-
-static struct stat_str *stats, *qstats; /* array of scores for statistics */
-
-/* these variables are global so they can be set both by the main()
- program and savebest() in threaded mode.
-*/
-static int nstats, nqstats, kstats;
-static double zbestcut; /* cut off for best z-score */
-static int bestfull; /* index for selectbest() */
-static int stats_done=0; /* flag for z-value processing */
-void fsigint();
-
-int
-main (int argc, char *argv[])
-{
- unsigned char *aa0[6], *aa0s, *aa1, *aa1ptr, *aa1s;
- int n1, n1s; /* n1s needed for PRSS so that when getlib() returns -1 (because no more
- library sequences, we have a valid n1 for shuffling */
-
- int *n1tot_ptr=NULL, *n1tot_cur;
- int n1tot_cnt=0;
- int n1tot_v, aa1_loff;
-
- long qoffset; /* qoffset is the equivalent of loffset */
- /* m_msg.sq0off is the l_off equivalent */
-
- long loffset, l_off; /* loffset is the coordinate of first residue
- when lcont > 0; l_off is not used in the
- main loop, only in showbest and showalign */
- char lib_label[MAX_FN];
- char pgm_abbr[MAX_SSTR];
- char qlabel[MAX_FN];
-#ifdef COMP_MLIB
- char q_bline[MAX_STR];
- fseek_t qseek;
- int qlib;
- struct lmf_str *q_file_p;
- int sstart, sstop, is;
-#endif
- int id;
- struct lmf_str *m_file_p;
-
- int t_best, t_rbest, t_qrbest; /* best score of two/six frames */
- double t_escore, t_rescore, t_qrescore; /* best evalues of two/six frames */
- int i_score;
-#ifdef PRSS
- int s_score[3];
- int s_n1;
-#endif
-
- struct pstruct pst;
- void *f_str[6], *qf_str; /* different f_str[]'s for different
- translation frames, or forward,reverse */
- int have_f_str=0;
-
-#ifdef COMP_THR
- long ntbuff;
- int max_buf_cnt, ave_seq_len, buf_siz;
- int max_work_buf;
- struct buf_head *cur_buf;
- struct buf_str *cur_buf_p;
- int nseq;
- struct thr_str *work_info;
-#endif
-
- struct mngmsg m_msg; /* Message from host to manager */
- int iln, itt; /* index into library names */
- char rline[MAX_FN];
- char argv_line[MAX_STR];
- int t_quiet;
-
- struct rstruct rst; /* results structure */
- struct rstruct rrst; /* results structure for shuffle*/
- int i;
-
- FILE *fdata=NULL; /* file for full results */
- char libstr[MAX_UID]; /* string for labeling full results */
- char *libstr_p; /* choose between libstr and ltitle */
- int n_libstr; /* length of libstr */
- int jstats;
- int leng; /* leng is length of the descriptive line */
- int maxn; /* size of the library sequence examined */
- int maxl; /* size of library buffer */
- fseek_t lmark; /* seek into library of current sequence */
- int qlcont; /* continued query sequence */
- int lcont, ocont, maxt; /* continued sequence */
- int igncnt=0; /* count for ignoring sequences warning */
- int ieven=0; /* tmp for wshuffle */
- double zscore; /* tmp value */
- char *bp; /* general purpose string ptr */
-
- /* Initialization */
-
-#if defined(UNIX)
- m_msg.quiet= !isatty(1);
-#else
- m_msg.quiet = 0;
-#endif
-
-#ifdef PGM_DOC
- argv_line[0]='#'; argv_line[1]='\0';
- for (i=0; i<argc; i++) {
- strncat(argv_line," ",sizeof(argv_line)-strlen(argv_line)-1);
- if (strchr(argv[i],' ')) {
- strncat(argv_line,"\"",sizeof(argv_line)-strlen(argv_line)-1);
- strncat(argv_line,argv[i],sizeof(argv_line)-strlen(argv_line)-1);
- strncat(argv_line,"\"",sizeof(argv_line)-strlen(argv_line)-1);
- }
- else {
- strncat(argv_line,argv[i],sizeof(argv_line)-strlen(argv_line)-1);
- }
- }
- argv_line[sizeof(argv_line)-1]='\0';
-#endif
-
- /* first initialization routine - nothing is known */
- h_init(&pst, &m_msg, pgm_abbr);
-
- m_msg.db.length = qtt.length = 0l;
- m_msg.db.entries = m_msg.db.carry = qtt.entries = qtt.carry = 0;
- m_msg.pstat_void = NULL;
- m_msg.hist.entries = 0;
-
- for (iln=0; iln<MAX_LF; iln++) m_msg.lb_mfd[iln]=NULL;
-
- f_str[0] = f_str[1] = NULL;
-
- aa0[0] = NULL;
- /* second initialiation - get commmand line arguments */
- initenv (argc, argv, &m_msg, &pst,&aa0[0]);
-
-#ifdef COMP_THR
- /* now have max_workers - allocate work_info[] */
- if (max_workers >= MAX_WORKERS) max_workers = MAX_WORKERS;
- if ((work_info=
- (struct thr_str *)calloc(max_workers,sizeof(struct thr_str)))==NULL) {
- fprintf(stderr, " cannot allocate work_info[%d]\n",max_workers);
- exit(1);
- }
-#else
- max_workers = 1;
-#endif
-
-#ifndef PRSS
- /* label library size limits */
- if (m_msg.n1_low > 0 && m_msg.n1_high < BIGNUM)
- sprintf(lib_label,"library (range: %d-%d)",m_msg.n1_low,m_msg.n1_high);
- else if (m_msg.n1_low > 0)
- sprintf(lib_label,"library (range: >%d)",m_msg.n1_low);
- else if (m_msg.n1_high < BIGNUM)
- sprintf(lib_label,"library (range: <%d)",m_msg.n1_high);
- else
- strncpy(lib_label,"library",sizeof(lib_label));
-#else
- sprintf(lib_label,"shuffled sequence");
-#endif
- lib_label[sizeof(lib_label)-1]='\0';
-
- tstart = tscan = s_time();
- tdstart = time(NULL);
-
- /* Allocate space for the query and library sequences */
- /* pad aa0[] with an extra 32 chars for ALTIVEC padding */
- if (aa0[0]==NULL) {
- if ((aa0[0] = (unsigned char *)malloc((m_msg.max_tot+1+32)*sizeof(unsigned char)))
- == NULL)
- s_abort ("Unable to allocate query sequence", "");
- *aa0[0]=0;
- aa0[0]++;
- }
- aa0[5]=aa0[4]=aa0[3]=aa0[2]=aa0[1]=aa0[0];
-
- /* make room for random sequence -
- also used as storage for COMP_THR library overlaps
- */
- if ((aa1s = (unsigned char *)malloc((m_msg.max_tot+1+32)*sizeof (char))) == NULL) {
- s_abort ("Unable to allocate shuffled library sequence", "");
- }
- *aa1s=0;
- aa1s++;
-
- irand(0);
-
- if (m_msg.markx & MX_HTML) {
-#ifdef HTML_HEAD
- fprintf(stdout,"<html>\n<head>\n<title>%s Results</title>\n</head>\n<body>\n",prog_func);
-#endif
- fprintf(stdout,"<pre>\n");
- }
-
-#ifdef PGM_DOC
- fputs(argv_line,stdout);
- fputc('\n',stdout);
-#endif
-
- fprintf(stdout,"%s\n",iprompt0);
- fprintf(stdout," %s%s\n",verstr,refstr);
- if (m_msg.markx & MX_HTML) fputs("</pre>\n",stdout);
-
- /* Query library */
- if (m_msg.tname[0] == '\0') {
- if (m_msg.quiet == 1)
- s_abort("Query sequence undefined","");
- l1: fputs (iprompt1, stdout);
- fflush (stdout);
- if (fgets (m_msg.tname, MAX_FN, stdin) == NULL)
- s_abort ("Unable to read query library name","");
- m_msg.tname[MAX_FN-1]='\0';
- if ((bp=strchr(m_msg.tname,'\n'))!=NULL) *bp='\0';
- if (m_msg.tname[0] == '\0') goto l1;
- }
-
- /* Fetch first sequence */
- qoffset = 0l;
- qlcont = 0;
-#ifdef COMP_MLIB
- /* Open query library */
- if ((q_file_p= openlib(m_msg.tname, m_msg.qdnaseq,qascii,!m_msg.quiet,NULL))==NULL) {
- s_abort(" cannot open library ",m_msg.tname);
- }
- qlib = 0;
- m_msg.n0 =
- QGETLIB (aa0[0], MAXTST, m_msg.qtitle, sizeof(m_msg.qtitle),
- &qseek, &qlcont,q_file_p,&m_msg.sq0off);
- if ((bp=strchr(m_msg.qtitle,' '))!=NULL) *bp='\0';
- strncpy(qlabel,m_msg.qtitle,sizeof(qlabel));
- if (bp != NULL) *bp = ' ';
- qlabel[sizeof(qlabel)-1]='\0';
-
- /* if annotations are included in sequence, remove them */
- if (m_msg.ann_flg) {
- m_msg.n0 = ann_scan(aa0[0],m_msg.n0,&m_msg,m_msg.qdnaseq);
- }
-
- if (m_msg.term_code && !(m_msg.qdnaseq==SEQT_DNA || m_msg.qdnaseq==SEQT_RNA) &&
- aa0[0][m_msg.n0-1]!='*') {
- aa0[0][m_msg.n0++]='*';
- aa0[0][m_msg.n0]=0;
- }
-
- /* check for subset */
- if (q_file_p->opt_text[0]!='\0') {
- if (q_file_p->opt_text[0]=='-') {
- sstart=0; sscanf(&q_file_p->opt_text[1],"%d",&sstop);
- }
- else {
- sscanf(&q_file_p->opt_text[0],"%d-%d",&sstart,&sstop);
- sstart--;
- if (sstop <= 0 ) sstop = BIGNUM;
- }
- for (id=0,is=sstart; is<min(m_msg.n0,sstop); ) aa0[0][id++]=aa0[0][is++];
- aa0[0][id]=0;
- m_msg.n0 = min(m_msg.n0,sstop)-sstart;
- if (m_msg.sq0off==1) m_msg.sq0off = sstart+1;
- }
-
-#if defined(SW_ALTIVEC) || defined(SW_SSE2)
- /* for ALTIVEC, must pad with 15 NULL's */
- for (id=0; id<SEQ_PAD; id++) {aa0[0][m_msg.n0+id]=0;}
-#endif
-
- if (qlcont) {
- qoffset += m_msg.n0 - m_msg.sq0off;
- }
- else {
- qoffset = 0l;
- }
-
-#else
- m_msg.n0 = getseq (m_msg.tname, qascii, aa0[0], m_msg.max_tot,
- m_msg.qtitle, sizeof(m_msg.qtitle),
- &m_msg.sq0off);
- strncpy(qlabel,m_msg.tname,sizeof(qlabel));
- qlabel[sizeof(qlabel)-1]='\0';
-
- /* if annotations are included in sequence, remove them */
- if (m_msg.ann_flg) {
- m_msg.n0 = ann_scan(aa0[0],m_msg.n0,&m_msg,m_msg.qdnaseq);
- }
-#endif
-
- if (m_msg.n0 > MAXTST) {
- fprintf(stderr," sequence truncated to %d\n %s\n",MAXTST,m_msg.sqnam);
- fprintf(stdout," sequence truncated to %d\n %s\n",MAXTST,m_msg.sqnam);
- aa0[0][MAXTST]='\0';
- m_msg.n0=MAXTST;
- }
-
- if (m_msg.qdnaseq == SEQT_UNK) {
-
- /* do automatic sequence recognition,but only for sequences > 20 residues */
- if (m_msg.n0 > 20 &&
- (float)scanseq(aa0[0],m_msg.n0,"ACGTUNacgtun")/(float)m_msg.n0 >0.85) {
- pascii = nascii;
- m_msg.qdnaseq = SEQT_DNA;
- }
- else { /* its protein */
- pascii = aascii;
- m_msg.qdnaseq = SEQT_PROT;
- }
- /* modify qascii to use encoded version
- cannot use memcpy() because it loses annotations
- */
- re_ascii(qascii,pascii);
- init_ascii(pst.ext_sq_set,qascii,m_msg.qdnaseq);
- m_msg.n0 = recode(aa0[0],m_msg.n0,qascii, pst.nsqx);
- }
-
- if (m_msg.n0 <= 0)
- s_abort ("Query sequence length <= 0: ", m_msg.tname);
-
-#ifdef SUPERFAMNUM
- m_msg.nqsfnum = nsfnum;
- for (i=0; i <= nsfnum & i<10; i++) m_msg.qsfnum[i] = sfnum[i];
- m_msg.nqsfnum_n = nsfnum_n;
- for (i=0; i <= nsfnum_n & i<10; i++) m_msg.qsfnum_n[i] = sfnum_n[i];
-#endif
-
- resetp (&m_msg, &pst);
-
-#ifndef COMP_MLIB
- gettitle(m_msg.tname,m_msg.qtitle,sizeof(m_msg.qtitle));
- if (m_msg.tname[0]=='-' || m_msg.tname[0]=='@') {
- strncmp(m_msg.tname,m_msg.qtitle,sizeof(m_msg.tname));
- if ((bp=strchr(m_msg.tname,' '))!=NULL) *bp='\0';
- }
-#endif
-
- /* get library file names */
-
-#ifndef PRSS
- if (strlen (m_msg.lname) == 0) {
- if (m_msg.quiet == 1) s_abort("Library name undefined","");
- libchoice(m_msg.lname,sizeof(m_msg.lname),&m_msg);
- }
-
- libselect(m_msg.lname, &m_msg);
-#else
- if (strlen (m_msg.lname) == 0) {
- if (m_msg.quiet == 1) s_abort("Shuffle sequence undefined","");
-l2: fputs(iprompt2,stdout);
- fflush(stdout);
- if (fgets (m_msg.lname, MAX_FN, stdin) == NULL)
- s_abort ("Unable to read shuffle file name","");
- m_msg.lname[MAX_FN-1]='\0';
- if ((bp=strchr(m_msg.lname,'\n'))!=NULL) *bp='\0';
- if (m_msg.lname[0] == '\0') goto l2;
- }
- m_msg.lbnames[0]= m_msg.lname;
- m_msg.nln = 1;
- m_msg.nshow = 0;
-#endif
-
- /* Get additional parameters here */
- if (!m_msg.quiet) query_parm (&m_msg, &pst);
-
- last_init(&m_msg, &pst);
-
- /* Allocate space for saved scores */
- if ((best =
- (struct beststr *)calloc((MAXBEST+1),sizeof(struct beststr)))==NULL)
- s_abort ("Cannot allocate best struct","");
- if ((bestp_arr =
- (struct beststr **)malloc((MAXBEST+1)*sizeof(struct beststr *)))==NULL)
- s_abort ("Cannot allocate bestp_arr","");
-
- /* Initialize bestp_arr */
- for (nbest = 0; nbest < MAXBEST+1; nbest++)
- bestp_arr[nbest] = &best[nbest];
- best++; bestp_arr++;
- best[-1].score[0]=best[-1].score[1]=best[-1].score[2]= INT_MAX;
- best[-1].zscore=FLT_MAX; /* for Z-scores, bigger is best */
- best[-1].escore=FLT_MIN; /* for E()-values, lower is best */
-
- if ((stats =
- (struct stat_str *)calloc(MAXSTATS,sizeof(struct stat_str)))==NULL)
- s_abort ("Cannot allocate stats struct","");
-
-#ifdef UNIX
- /* set up signals now that input is done */
- signal(SIGHUP,SIG_IGN);
-#endif
-
-#ifdef COMP_THR
- /* Set up buffers for reading the library:
-
- We will start by using a 2 Mbyte buffer for each worker. For
- proteins, that means 5,000 sequences of length 400 (average).
- For DNA, that means 2,000 sequences of length 1000. At the
- moment, those are good averages.
- */
-
- if (m_msg.ldnaseq== SEQT_DNA) {
- max_buf_cnt = MAX_NT_BUF;
- ave_seq_len = AVE_NT_LEN;
- }
- else {
- max_buf_cnt = MAX_AA_BUF;
- ave_seq_len = AVE_AA_LEN;
- }
-
- /* however - buffer sizes should be a function of the number of
- workers so that all the workers are kept busy. Assuming a 10,000
- entry library is the smallest we want to schedule, then
- */
-
- if (max_buf_cnt > 10000/max_workers)
- max_buf_cnt = 10000/(2*max_workers);
-
- max_buf_cnt /= m_msg.thr_fact;
-
- /* finally, max_work_buf should be mod 6 for tfasta */
- max_buf_cnt -= (max_buf_cnt % 6);
-
- max_work_buf = 2*max_workers;
-
- /* allocate space for library buffers and results */
-
- buf_siz=max_buf_cnt*ave_seq_len;
- if (buf_siz < m_msg.max_tot) buf_siz = m_msg.max_tot;
- for (i=0; i<max_work_buf; i++) {
- if ((buf_list[i].buf =(struct buf_str *)calloc((size_t)(max_buf_cnt+1),
- sizeof(struct buf_str)))
- ==NULL) {
- fprintf(stderr," cannot allocate buffer struct %d %d\n",i,max_buf_cnt+1);
- exit(1);
- }
- buf_list[i].buf_cnt=0;
- buf_list[i].have_results=0;
- if ((buf_list[i].start =
- (unsigned char *)calloc((size_t)(buf_siz),sizeof(unsigned char)))
- ==NULL) {
- fprintf(stderr," cannot allocate buffer %d\n",i);
- exit(1);
- }
-
- /* make certain there is a '\0' at the beginning */
- buf_list[i].start++;
-
- reader_buf[i] = &buf_list[i];
- }
-
- /* initialization of global variables for threads/buffers */
-
- num_worker_bufs = 0;
- num_reader_bufs = max_work_buf;
- reader_done = 0;
- worker_buf_workp = 0;
- worker_buf_readp = 0;
- reader_buf_workp = 0;
- reader_buf_readp = 0;
-
- start_thread = 1; /* keeps threads from starting */
-#endif
-
- /* Label the output */
- if ((bp = (char *) strchr (m_msg.lname, ' ')) != NULL) *bp = '\0';
- if (m_msg.ltitle[0] == '\0') {
- strncpy(m_msg.ltitle,m_msg.lname,sizeof(m_msg.ltitle));
- m_msg.ltitle[sizeof(m_msg.ltitle)-1]='\0';
- }
-
-#ifdef COMP_MLIB
- printf("Query library %s vs %s library\n", m_msg.tname,m_msg.lname);
- if (m_msg.nln > 0) printf("searching %s library\n\n",m_msg.lbnames[0]);
-#endif
-
-#ifdef COMP_MLIB
- while(1) {
- m_msg.db.length = 0l;
- m_msg.db.entries = m_msg.db.carry = 0;
- qlib++;
- stats_done = 0;
-#endif
-
- maxl = m_msg.max_tot - m_msg.n0 -2; /* maxn = max library sequence space */
-
- maxn = reset_maxn(&m_msg,maxl);
- pst.maxlen = maxn;
-
- outfd = stdout;
- nbest = 0;
- zbestcut = -FLT_MAX;
- nstats = 0;
-
- /* get the last parameters */
- last_params(aa0[0],m_msg.n0, &m_msg, &pst);
-
- /*
- if our function returns approximate E()-scores, we do not need to
- work with raw scores and later calculate z-scores. When
- approx. E()-scores are calculated, we still need various
- statistics structures, but we can get them immediately. In this
- case, find_zp() must produce a z_score (large positive is good)
- from an e_score.
- */
-
- if (m_msg.escore_flg) {
- pst.zsflag_f = process_hist(stats,nstats,m_msg,pst,
- &m_msg.hist,&m_msg.pstat_void,0);
- stats_done=1;
- }
-
-#ifndef COMP_THR
- if (m_msg.qshuffle) {
- if ((aa0s=(unsigned char *)calloc(m_msg.n0+2,sizeof(char)))==NULL) {
- fprintf(stderr,"cannot allocate aa0s[%d]\n",m_msg.n0+2);
- exit(1);
- }
- *aa0s='\0';
- aa0s++;
- memcpy(aa0s,aa0[0],m_msg.n0);
- qshuffle(aa0s,m_msg.n0,m_msg.nm0);
- }
-
- /* previous versions of FASTA have stored the reverse complement in
- the same array as the forward query sequence. This version
- changes that, by allocating separate space for the reverse complement,
- and thus reducing the demand for a large MAXLIB/MAXTRN for long queries
- */
- if (m_msg.qframe == 2) {
- if ((aa0[1]=(unsigned char *)calloc(m_msg.n0+2,sizeof(char)))==NULL) {
- fprintf(stderr,"cannot allocate aa0[1][%d]\n",m_msg.n0+2);
- exit(1);
- }
- *aa0[1] = '\0';
- aa0[1]++;
- memcpy(aa0[1],aa0[0],m_msg.n0+1);
- revcomp(aa0[1],m_msg.n0,&pst.c_nt[0]);
- }
- /* set aa1 for serial - threaded points aa1 to buffer */
-
- aa1 = aa0[0] + m_msg.n0+1; /* modified now that aa0[1] is done separately */
- *aa1++='\0';
-#else
- init_thr(max_workers, work_info, m_msg, &pst, aa0[0], max_work_buf);
-#endif
-
- if (m_msg.qshuffle && qstats==NULL) {
- if ((qstats =
- (struct stat_str *)calloc(m_msg.shuff_max+1,sizeof(struct stat_str)))==NULL)
- s_abort ("Cannot allocate qstats struct","");
- }
- nqstats = 0;
-
- if (m_msg.markx & MX_HTML) fputs("<pre>\n",stdout);
-#ifndef PRSS
- /* rline[] is a tmp string */
- if (m_msg.qdnaseq == SEQT_DNA || m_msg.qdnaseq == SEQT_RNA) {
- strncpy(rline,(m_msg.qframe==1)? " (forward-only)" : "\0",sizeof(rline));
- rline[sizeof(rline)-1]='\0';
- }
- else rline[0]='\0';
-
- leng = (int)strlen(m_msg.qtitle);
- if (leng > 50) leng -= 10;
-
- sprintf (&m_msg.qtitle[leng], " %d %s", m_msg.n0, m_msg.sqnam);
- m_msg.seqnm = 0;
-
-
-#ifdef COMP_MLIB
- printf("%3d>>>%s - %d %s%s\n vs %.60s %s\n", qlib,
- m_msg.qtitle, m_msg.n0, m_msg.sqnam,
- (m_msg.revcomp ? " (reverse complement)" : rline),
- m_msg.ltitle,lib_label);
-#else
- printf("%.50s: %d %s%s\n %s\n vs %.60s %s\n",
- qlabel, m_msg.n0, m_msg.sqnam,
- (m_msg.revcomp ? " (reverse complement)" : rline),
- m_msg.qtitle,m_msg.ltitle,lib_label);
-#endif
- libstr_p = &libstr[0];
- n_libstr=sizeof(libstr);
-#else /* PRSS */
- libstr_p = &m_msg.ltitle[0];
- n_libstr= sizeof(m_msg.ltitle);
- set_shuffle(m_msg); /* set count/width parameters in llgetaa.c */
-#endif
-
- fflush (outfd);
-
- tprev = s_time();
-
- if (m_msg.dfile[0] && (fdata=fopen(m_msg.dfile,"w"))!=NULL)
- fprintf(fdata,"%3d\t%-50s\n",m_msg.n0,m_msg.qtitle);
-
- qtt.length += m_msg.n0;
- qtt.entries++;
-
-#ifdef COMP_THR
- start_thr();
-
- /* now open the library and start reading */
- /* get a buffer and fill it up */
- get_rbuf(&cur_buf,max_work_buf);
-
- cur_buf->buf_cnt = 0;
- cur_buf->have_results = 0;
- cur_buf->buf[0].aa1b = cur_buf->start;
- ntbuff = 0;
- nseq = 0;
-#else /* ! COMP_THR */
- /* initialize the comparison function, returning f_str */
- init_work (aa0[0], m_msg.n0, &pst, &f_str[0]);
- have_f_str=1;
-
- f_str[5] = f_str[4] = f_str[3] = f_str[2] = f_str[1] = f_str[0];
- if (m_msg.qframe == 2) {
- init_work ( aa0[1], m_msg.n0, &pst, &f_str[1]);
- }
- if (m_msg.qshuffle) {
- init_work ( aa0s, m_msg.n0, &pst, &qf_str);
- }
-#endif /* COMP_THR */
-
- /* open the library - start the search */
-
- for (iln = 0; iln < m_msg.nln; iln++) {
- if ((m_msg.lb_mfd[iln] = m_file_p=
- openlib(m_msg.lbnames[iln], m_msg.ldnaseq, lascii, !m_msg.quiet, m_msg.lb_mfd[iln]))
- ==NULL) {
- fprintf(stderr," cannot open library %s\n",m_msg.lbnames[iln]);
- continue;
- }
-#if !defined(PRSS) && !defined(COMP_MLIB)
- else
- printf ("searching %s %s\n",m_msg.lbnames[iln],lib_label);
-#endif
-
- loffset = 0l;
- lcont = 0;
- ocont = 0;
- n1tot_v = n1tot_cnt = 0;
- n1tot_cur = n1tot_ptr = NULL;
-
- /* get next buffer to read into */
- maxt = maxn;
-
-#ifndef COMP_THR
- aa1ptr = aa1;
-#else
- /* read sequence directly into buffer */
- aa1ptr = aa1 = cur_buf->buf[nseq].aa1b;
-#endif
-
- while ((n1=GETLIB(aa1ptr,maxt,libstr_p,n_libstr,&lmark,&lcont,m_file_p,&l_off))>=0) {
-
- if (n_libstr <= MAX_UID) {
- if ((bp=strchr(libstr_p,' '))!=NULL) *bp='\0';
- }
-
- if (m_msg.term_code && !lcont &&
- m_msg.ldnaseq==SEQT_PROT && aa1ptr[n1-1]!=m_msg.term_code) {
- aa1ptr[n1++]=m_msg.term_code;
- aa1ptr[n1]=0;
- }
-
-#if defined(SW_ALTIVEC) || defined(SW_SSE2)
- /* for ALTIVEC, must pad with 15 NULL's */
- for (id=0; id<SEQ_PAD; id++) {aa1ptr[n1+id]=0;}
-#endif
-
-#ifdef DEBUG
- if (aa1[-1]!='\0' || aa1ptr[n1]!='\0') {
- fprintf(stderr,"%s: aa1[%d] missing NULL boundaries: %d %d\n",libstr_p,n1,aa1[-1],aa1ptr[n1]);
- }
-#endif
-
- /* check for a continued sequence and provide a pointer to
- the n1_tot array if lcont || ocont */
- n1tot_v += n1;
- if (lcont && !ocont) { /* get a new pointer */
- if (n1tot_cnt <= 0) {
- if ((n1tot_ptr=calloc(1000,sizeof(int)))==NULL) {
- fprintf(stderr," cannot allocate n1tot_ptr\n");
- exit(1);
- }
- else {n1tot_cnt=1000;}
- }
- n1tot_cnt--;
- n1tot_cur = n1tot_ptr++;
- }
-
- if (n1tot_v < m_msg.n1_low || n1tot_v > m_msg.n1_high) {
- goto loop2;
- }
-
- m_msg.db.entries++;
- m_msg.db.length += n1;
- if (m_msg.db.length > LONG_MAX) {
- m_msg.db.length -= LONG_MAX; m_msg.db.carry++;
- }
-
-#ifdef DEBUG
- /* This finds most reasons for core dumps */
- if (pst.debug_lib)
- for (i=0; i<n1; i++)
- if (aa1[i]>=pst.nsqx)
- {fprintf(stderr,
- "%s residue[%d/%d] %d range (%d) lcont/ocont: %d/%d\n%s\n",
- libstr,i,n1,aa1[i],pst.nsqx,lcont,ocont,aa1ptr+i);
- aa1[i]=0;
- n1=i-1;
- break;
- }
-#endif
-
- /* don't count long sequences more than once */
- if (aa1!=aa1ptr) {n1 += m_msg.loff; m_msg.db.entries--;}
-
-#ifdef PROGRESS
- if (!m_msg.quiet)
- if (m_msg.db.entries % 200 == 199) {
- fputc('.',stderr);
- if (m_msg.db.entries % 10000 == 9999) fputc('\n',stderr);
- else if (m_msg.db.entries % 1000 == 999) fputc(' ',stderr);
-
- }
-#endif
-
- if (n1<=1) {
- /* if (igncnt++ <10)
- fprintf(stderr,"Ignoring: %s\n",libstr);
- */
- goto loop2;
- }
-
-#ifdef PRSS
- if (lmark==0) {
- n1s = n1;
- memcpy(aa1s,aa1,n1s);
- m_msg.db.entries=0;
- m_msg.db.length=0;
- }
-#endif
-
- /* if COMP_THR - fill and empty buffers */
-#ifdef COMP_THR
- ntbuff += n1+1;
-
- for (itt=m_msg.revcomp; itt<=m_msg.nitt1; itt++) {
-
- cur_buf->buf_cnt++;
- cur_buf_p = &(cur_buf->buf[nseq++]);
- cur_buf_p->n1 = n1;
- cur_buf_p->n1tot_p = n1tot_cur;
- cur_buf_p->lseek = lmark;
- cur_buf_p->cont = ocont+1;
- cur_buf_p->m_file_p = (void *)m_file_p;
- cur_buf_p->frame = itt;
- memcpy(cur_buf_p->libstr,libstr,MAX_UID);
-#ifdef SUPERFAMNUM
- cur_buf_p->nsfnum = nsfnum;
- if ((cur_buf_p->sfnum[0]=sfnum[0])>0 &&
- (cur_buf_p->sfnum[1]=sfnum[1])>0 &&
- (cur_buf_p->sfnum[2]=sfnum[2])>0 &&
- (cur_buf_p->sfnum[3]=sfnum[3])>0 &&
- (cur_buf_p->sfnum[4]=sfnum[4])>0 &&
- (cur_buf_p->sfnum[5]=sfnum[5])>0 &&
- (cur_buf_p->sfnum[6]=sfnum[6])>0 &&
- (cur_buf_p->sfnum[7]=sfnum[7])>0 &&
- (cur_buf_p->sfnum[8]=sfnum[8])>0 &&
- (cur_buf_p->sfnum[9]=sfnum[9])>0) ;
-#endif
-
- /* this assumes that max_buf_cnt is guaranteed %6=0 so that
- additional pointers to the same buffer can be used
- nseq now points to next buffer
- */
-
- cur_buf->buf[nseq].aa1b = cur_buf->buf[nseq-1].aa1b;
- } /* for (itt .. */
-
- /* make a copy of the overlap (threaded only) */
- if (lcont) {
- memcpy(aa1s,&aa1[n1-m_msg.loff],m_msg.loff);
- }
-
- /* if the buffer is filled */
- if (nseq >= max_buf_cnt || ntbuff >= buf_siz - maxn) {
-
- /* provide filled buffer to workers */
- put_rbuf(cur_buf,max_work_buf);
-
- /* get an empty buffer to fill */
- get_rbuf(&cur_buf,max_work_buf);
-
- /* "empty" buffers have results that must be processed */
- if (cur_buf->buf_cnt && cur_buf->have_results) {
- save_best(cur_buf,m_msg,pst,fdata,m_msg.qsfnum,&m_msg.hist,
- &m_msg.pstat_void
-#ifdef PRSS
- ,s_score,&s_n1
-#endif
- );
-
- }
-
- /* now the buffer is truly empty, fill it up */
- cur_buf->buf_cnt = 0;
- cur_buf->have_results = 0;
- /* point the first aa1 ptr to the buffer start */
- aa1=cur_buf->buf[0].aa1b = cur_buf->start;
- ntbuff = 0;
- nseq=0;
- }
- else { /* room left in current buffer, increment ptrs */
- aa1=cur_buf->buf[nseq].aa1b = cur_buf->buf[nseq-1].aa1b+n1+1;
- }
-#else /* if !COMP_THR - do a bunch of searches */
-
- /* t_best and t_rbest are used to save the best score or shuffled
- score from all the frames */
-
- t_best = t_rbest = t_qrbest = -1;
- t_escore = t_rescore = t_qrescore = FLT_MAX;
- for (itt=m_msg.revcomp; itt<=m_msg.nitt1; itt++) {
-
- rst.score[0] = rst.score[1] = rst.score[2] = 0;
- do_work (aa0[itt], m_msg.n0,aa1,n1,itt,&pst,f_str[itt],0,&rst);
-
- if (rst.score[pst.score_ix] > t_best) {
- t_best = rst.score[pst.score_ix];
- }
-
- if (fdata) {
- fprintf(fdata,
- "%-12s %5d %6d %d %.5f %.5f %4d %4d %4d %g %d %d %8lld\n",
- libstr,
-#ifdef SUPERFAMNUM
- sfn_cmp(m_msg.qsfnum,sfnum),
-#else
- 0,
-#endif
- n1,itt,
- rst.comp,rst.H,
- rst.score[0],rst.score[1],rst.score[2],
- rst.escore, rst.segnum, rst.seglen, lmark);
- fflush(fdata);
- }
-
-#ifdef PRSS
- if (lmark==0) {
- s_score[0] = rst.score[0];
- s_score[1] = rst.score[1];
- s_score[2] = rst.score[2];
-
- s_n1 = n1;
- aa1_loff = l_off;
- }
- t_best = t_rbest = rst.score[pst.score_ix];
- t_escore = t_rescore = rst.escore;
-#else
- if (m_msg.qshuffle) {
- do_work (aa0s, m_msg.n0,aa1,n1,itt,&pst,qf_str,1,&rrst);
-
- if (rrst.score[pst.score_ix] > t_qrbest)
- t_qrbest = rrst.score[pst.score_ix];
- if (rrst.escore < t_qrescore)
- t_qrescore = rrst.escore;
-
- if (itt==m_msg.nitt1 && nqstats < m_msg.shuff_max) {
- qstats[nqstats].n1 = n1; /* save the best score */
- qstats[nqstats].comp = rst.comp;
- qstats[nqstats].H = rst.H;
- qstats[nqstats].escore = t_qrescore;
- qstats[nqstats++].score = t_qrbest;
- t_qrbest = -1; /* reset t_qrbest, t_qrescore */
- t_qrescore = FLT_MAX;
- }
- }
-
- if (pst.zsflag >= 10) {
- if (pst.zs_win > 0) wshuffle(aa1,aa1s,n1,pst.zs_win,&ieven);
- else shuffle(aa1,aa1s,n1);
- do_work (aa0[itt], m_msg.n0, aa1s, n1,itt,&pst,f_str[itt],0,&rrst);
- if (rrst.score[pst.score_ix] > t_rbest) {
- t_rbest = rrst.score[pst.score_ix];
- t_rescore = rrst.escore;
- }
- }
-#endif
- i_score = rst.score[pst.score_ix];
-
-/* this section saves scores for statistics calculations. For
- comparisons that can be from one of 2 or 6 frames, it should only
- be run once, for the best of the 2 or 6 scores. t_rbest,t_rescore
- have the best of the 2 or 6 scores from the frames. For proteins,
- this is run for every score.
-
-*/
-#ifdef PRSS /* don't save the first score (unshuffled) with PRSS */
- if (lmark > 0) {
-#endif
-
- if (itt == m_msg.nitt1) {
- if (nstats < MAXSTATS) {
- stats[nstats].n1 = n1; /* save the best score */
- stats[nstats].comp = rst.comp;
- stats[nstats].H = rst.H;
- if (pst.zsflag >=10) {
- t_best = t_rbest;
- t_escore = t_rescore;
- }
- stats[nstats].escore = t_escore;
- stats[nstats++].score = t_best;
- t_best = t_rbest = -1; /* reset t_rbest, t_best */
- t_escore = t_rescore = FLT_MAX;
- }
- else if (pst.zsflag >= 0) {
- if (!stats_done) {
- pst.zsflag_f = process_hist(stats,nstats,m_msg,pst,
- &m_msg.hist,&m_msg.pstat_void,0);
- stats_done = 1;
- kstats = nstats;
- for (i=0; i<MAXBEST; i++) {
- bestp_arr[i]->zscore =
- (*find_zp)(bestp_arr[i]->score[pst.score_ix],
- bestp_arr[i]->escore, bestp_arr[i]->n1,
- bestp_arr[i]->comp, m_msg.pstat_void);
- }
- zbestcut = bestp_arr[nbest-1]->zscore;
- }
-
-#ifdef SAMP_STATS
-/* older versions saved the first MAXSTATS scores, and ignored the
- rest in the statistics. With SAMP_STATS, scores after MAX_STATS
- are sampled at random, and included in the sample set and the
- statistics parameters are re-derived at the end of the run using
- the sampled scores.
-
- It would be faster not to do the nrand(); if(jstats < MAXSTATS)
- less often.
-*/
- if (!m_msg.escore_flg) { /* only for zscores */
- jstats = nrand(++kstats); /* no mod % 0 */
- if (jstats < MAXSTATS) {
- stats[jstats].n1 = n1; /* save the best score */
- stats[jstats].comp = rst.comp;
- stats[jstats].H = rst.H;
- if (pst.zsflag >=10) t_best = t_rbest;
- stats[jstats].score = t_best;
- }
- }
-#endif
- } /* ( nstats >= MAXSTATS) && zsflag >= 0 */
- } /* itt1 == nitt1 */
-#ifdef PRSS
- }
-#endif
-
- /* this section completes work on the current score */
- if (stats_done) { /* stats_done > 0 => nstats >= MAXSTATS */
- zscore=(*find_zp)(i_score, rst.escore, n1, rst.comp,
- m_msg.pstat_void);
-
- if (itt == m_msg.nitt1) {
- if (pst.zsflag >= 10) t_best = t_rbest;
-
- addhistz((*find_zp)(t_best, t_escore, n1, rst.comp,
- m_msg.pstat_void),
- &m_msg.hist);
- t_best = t_rbest = -1;
- }
- }
- else zscore = (double) i_score;
-
-#ifndef PRSS
- if (zscore > zbestcut ) {
- if (nbest >= MAXBEST) {
- bestfull = nbest-MAXBEST/4;
- selectbestz(bestp_arr,bestfull-1,nbest);
- zbestcut = bestp_arr[bestfull-1]->zscore;
- nbest = bestfull;
- }
-
- bestp = bestp_arr[nbest++];
- bestp->score[0] = rst.score[0];
- bestp->score[1] = rst.score[1];
- bestp->score[2] = rst.score[2];
- bestp->comp = rst.comp;
- bestp->H = rst.H;
- bestp->zscore = zscore;
- bestp->escore = rst.escore;
- bestp->segnum = rst.segnum;
- bestp->seglen = rst.seglen;
- bestp->lseek = lmark;
- bestp->cont = ocont+1;
- bestp->m_file_p = m_file_p;
- bestp->n1 = n1;
- bestp->n1tot_p=n1tot_cur;
- bestp->frame = itt;
- memcpy(bestp->libstr,libstr,MAX_UID);
-#ifdef SUPERFAMNUM
- bestp->nsfnum = nsfnum;
- if ((bestp->sfnum[0]=sfnum[0])>0 &&
- (bestp->sfnum[1]=sfnum[1])>0 &&
- (bestp->sfnum[2]=sfnum[2])>0 &&
- (bestp->sfnum[3]=sfnum[3])>0 &&
- (bestp->sfnum[4]=sfnum[4])>0 &&
- (bestp->sfnum[5]=sfnum[5])>0 &&
- (bestp->sfnum[6]=sfnum[6])>0 &&
- (bestp->sfnum[7]=sfnum[7])>0 &&
- (bestp->sfnum[8]=sfnum[8])>0 &&
- (bestp->sfnum[9]=sfnum[9])>0) ;
-#endif
- }
-#else /* PRSS */
- if (lmark == 0) {
- bestp = bestp_arr[nbest++];
- bestp->score[0] = rst.score[0];
- bestp->score[1] = rst.score[1];
- bestp->score[2] = rst.score[2];
- bestp->comp = rst.comp;
- bestp->H = rst.H;
- bestp->zscore = zscore;
- bestp->escore = rst.escore;
- bestp->segnum = rst.segnum;
- bestp->seglen = rst.seglen;
- bestp->lseek = lmark;
- bestp->cont = 0;
- bestp->m_file_p = m_file_p;
- bestp->n1 = n1;
- bestp->n1tot_p=n1tot_cur;
- bestp->frame = itt;
- memcpy(bestp->libstr,libstr,MAX_UID);
- bestp->nsfnum = 0;
- }
-#endif
- }
-#endif
-
- loop2:
- if (lcont) {
- maxt = m_msg.maxt3;
-#ifndef COMP_THR
- memcpy(aa1,&aa1[n1-m_msg.loff],m_msg.loff);
-#else
- memcpy(aa1,aa1s,m_msg.loff);
-#endif
- aa1ptr= &aa1[m_msg.loff];
- loffset += n1 - m_msg.loff;
- ocont = lcont;
- }
- else {
- maxt = maxn;
- aa1ptr=aa1;
- if (ocont) *n1tot_cur = n1tot_v;
- ocont = 0;
- loffset = 0l;
- n1tot_v = 0;
- n1tot_cur = NULL;
- }
- } /* end while((n1=getlib())) */
- } /* end iln=1..nln */
-
- /* all done */
-
-#ifdef COMP_THR
- /* check last buffers for any results */
- put_rbuf_done(max_workers,cur_buf,max_work_buf);
-
- for (i=0; i < num_reader_bufs; i++) {
- reader_buf_readp = (reader_buf_readp+1)%(max_work_buf);
- if (reader_buf[reader_buf_readp]->buf_cnt > 0 &&
- reader_buf[reader_buf_readp]->have_results) {
- save_best(reader_buf[reader_buf_readp],m_msg,pst,fdata,m_msg.qsfnum,
- &m_msg.hist, &m_msg.pstat_void
-#ifdef PRSS
- ,s_score,&s_n1
-#endif
- );
- }
- }
-#endif
-
-#ifdef PROGRESS
- if (!m_msg.quiet)
- if (m_msg.db.entries >= 200) {fprintf(stderr," Done!\n");}
-#endif
-
- m_msg.nbr_seq = m_msg.db.entries;
- get_param(&pst, gstring2,gstring3);
-
-/* *************************** */
-/* analyze the last results */
-/* *************************** */
-
-#ifndef PRSS
-#ifndef SAMP_STATS
- if (!stats_done && nstats > 0) {
-#endif
- pst.zsflag_f = process_hist(stats,nstats,m_msg,pst,&m_msg.hist,
- &m_msg.pstat_void,stats_done);
- if (m_msg.pstat_void != NULL) {
- stats_done = 1;
- for (i = 0; i < nbest; i++) {
- bestp_arr[i]->zscore =
- (*find_zp)(bestp_arr[i]->score[pst.score_ix],
- bestp_arr[i]->escore, bestp_arr[i]->n1,
- bestp_arr[i]->comp, m_msg.pstat_void);
- }
-#ifndef SAMP_STATS
- }
- else pst.zsflag = -1;
-#endif
- }
-#else /* PRSS */
- if (pst.zsflag < 10) pst.zsflag += 10;
- pst.zsflag_f = process_hist(stats,nstats,m_msg,pst,
- &m_msg.hist, &m_msg.pstat_void,0);
- stats_done = 1;
- for (i = 0; i < nbest; i++) {
- bestp_arr[i]->zscore = (*find_zp)(bestp_arr[i]->score[pst.score_ix],
- bestp_arr[i]->escore, bestp_arr[i]->n1,
- bestp_arr[i]->comp, m_msg.pstat_void);
- }
-#endif
-
- if (pst.zdb_size <= 1) pst.zdb_size = m_msg.db.entries;
-
-#ifdef COMP_THR
- /* before I call last_calc/showbest/showalign, I need init_work() to
- get an f_str. This duplicates some code above, which is used in
- the non-threaded version
- */
-
- if (!have_f_str) {
- init_work(aa0[0],m_msg.n0,&pst,&f_str[0]);
- have_f_str = 1;
- f_str[5] = f_str[4] = f_str[3] = f_str[2] = f_str[1] = f_str[0];
-
- if (m_msg.qframe == 2) {
- if ((aa0[1]=(unsigned char *)calloc((size_t)m_msg.n0+2,
- sizeof(unsigned char)))==NULL) {
- fprintf(stderr," cannot allocate aa0[1][%d] for alignments\n",
- m_msg.n0+2);
- }
- *aa0[1]='\0';
- aa0[1]++;
- memcpy(aa0[1],aa0[0],m_msg.n0+1);
- revcomp(aa0[1],m_msg.n0,&pst.c_nt[0]);
- init_work(aa0[1],m_msg.n0,&pst,&f_str[1]);
- }
-
- /* I also need a "real" aa1 */
- aa1 = buf_list[0].start;
-#ifdef PRSS
- /* for PRSS - I need the original second (non-shuffled) sequence */
- memcpy(aa1,aa1s,n1s+1);
-#endif
- }
-#endif
-
-/* now we have one set of scaled scores for in bestp_arr -
- for FASTS/F, we need to do some additional processing */
-
- if (!m_msg.qshuffle) {
- last_stats(aa0[0], m_msg.n0, stats,nstats, bestp_arr,nbest,
- m_msg, pst, &m_msg.hist, &m_msg.pstat_void);
- }
- else {
- last_stats(aa0[0], m_msg.n0,
- qstats,nqstats, bestp_arr,nbest, m_msg, pst,
- &m_msg.hist, &m_msg.pstat_void);
- }
-
- /* here is a contradiction: if pst.zsflag < 0, then m_msg.pstat_void
- should be NULL; if it is not, then process_hist() has been called */
- if (pst.zsflag < 0 && m_msg.pstat_void != NULL) pst.zsflag = 1;
-
- if (m_msg.last_calc_flg) {
- /* last_calc may need coefficients from last_stats() */
- nbest = last_calc(aa0, aa1, maxn, bestp_arr, nbest, m_msg, &pst,
- f_str, m_msg.pstat_void);
- }
-
- scale_scores(bestp_arr,nbest,m_msg.db,pst,m_msg.pstat_void);
-
- get_param(&pst, gstring2,gstring3);
-
-#ifdef PRSS
- /* gettitle(m_msg.lname,m_msg.ltitle,sizeof(m_msg.ltitle)); */
- printf("%.50s - %s %d %s%s\n vs %.60s - %s shuffled sequence\n",
- m_msg.tname, m_msg.qtitle,m_msg.n0, m_msg.sqnam,
- (m_msg.revcomp ? " (reverse complement)" : "\0"),
- m_msg.lname,m_msg.ltitle);
-#endif
-
- prhist (stdout, m_msg, pst, m_msg.hist, nstats, m_msg.db, gstring2);
-
- tscan = s_time();
- printf (" Scan time: ");
- ptime(stdout,tscan-tprev);
- printf ("\n");
-#ifdef COMP_MLIB
- ttscan += tscan-tprev;
-#endif
-
- l3:
- if (!m_msg.quiet) {
- printf("Enter filename for results [%s]: ", m_msg.outfile);
- fflush(stdout);
- }
-
- rline[0]='\0';
- if (!m_msg.quiet && fgets(rline,sizeof(rline),stdin)==NULL) goto end_l;
- if ((bp=strchr(rline,'\n'))!=NULL) *bp = '\0';
- if (rline[0]!='\0') strncpy(m_msg.outfile,rline,sizeof(m_msg.outfile));
- if (m_msg.outfile[0]!='\0') {
- if ((outfd=fopen(m_msg.outfile,"w"))==NULL) {
- fprintf(stderr," could not open %s\n",m_msg.outfile);
- if (!m_msg.quiet) goto l3;
- else goto l4;
- }
-
-#ifdef PGM_DOC
- fputs(argv_line,outfd);
- fputc('\n',outfd);
-#endif
- fputs(iprompt0,outfd);
- fprintf(outfd," %s%s\n",verstr,refstr);
-
- fprintf(outfd," %s%s, %d %s\n vs %s %s\n",
- qlabel, (m_msg.revcomp ? "-" : "\0"), m_msg.n0,
- m_msg.sqnam, m_msg.ltitle, lib_label);
-
- prhist(outfd,m_msg,pst,m_msg.hist, nstats, m_msg.db, gstring2);
- }
-
- l4:
- if (m_msg.markx & MX_HTML) {
- fputs("</pre>\n<p>\n<hr>\n<p>\n",outfd);
- }
-
- /* code from p2_complib.c to pre-calculate -m 9 alignment info -
- requires -q with -m 9 */
-
- if (m_msg.quiet || m_msg.markx & MX_M9SUMM) {
-
- /* to determine how many sequences to re-align (either for
- do_opt() or calc_id() we need to modify m_msg.mshow to get
- the correct number of alignments */
-
- if (m_msg.mshow_flg != 1 && pst.zsflag >= 0) {
- for (i=0; i<nbest && bestp_arr[i]->escore< m_msg.e_cut; i++) {}
- m_msg.mshow = i;
- }
-
-#ifndef PRSS
- if (m_msg.mshow <= 0) { /* no results to display */
- fprintf(outfd,"!! No sequences with E() < %f\n",m_msg.e_cut);
- m_msg.nshow = 0;
- goto end_l;
- }
-#endif
- }
-
-#ifdef PRSS
- memcpy(aa1,aa1s,n1s);
- maxn = n1s;
- nbest = 1;
-#endif
-
- showbest (stdout, aa0, aa1, maxn, bestp_arr, nbest, qtt.entries, &m_msg, pst,
- m_msg.db, gstring2, f_str);
-
- if (outfd != stdout) {
- t_quiet = m_msg.quiet;
- m_msg.quiet = -1; /* should guarantee 1..nbest shown */
- showbest (outfd, aa0, aa1, maxn, bestp_arr, nbest, qtt.entries, &m_msg, pst,
- m_msg.db, gstring2, f_str);
- m_msg.quiet = t_quiet;
- }
-
- if (m_msg.nshow > 0) {
- rline[0]='N';
- if (!m_msg.quiet){
- printf(" Display alignments also? (y/n) [n] "); fflush(stdout);
- if (fgets(rline,sizeof(rline),stdin)==NULL) goto end_l;
- }
- else rline[0]='Y';
-
- if (toupper((int)rline[0])=='Y') {
- if (!m_msg.quiet) {
- printf(" number of alignments [%d]? ",m_msg.nshow);
- fflush(stdout);
- if (fgets(rline,sizeof(rline),stdin)==NULL) goto end_l;
- if (rline[0]!=0) sscanf(rline,"%d",&m_msg.nshow);
- m_msg.ashow=m_msg.nshow;
- }
-
- if (m_msg.markx & (MX_AMAP+ MX_HTML + MX_M9SUMM)) {
- fprintf(outfd,"\n>>>%s%s, %d %s vs %s library\n",
- qlabel,(m_msg.revcomp ? "_rev":"\0"), m_msg.n0,
- m_msg.sqnam,m_msg.lname);
- }
-
- if (m_msg.markx & MX_M10FORM) {
- fprintf(outfd,"\n>>>%s%s, %d %s vs %s library\n",
- qlabel,(m_msg.revcomp ? "-":"\0"), m_msg.n0, m_msg.sqnam,
- m_msg.lname);
- fprintf(outfd,"; pg_name: %s\n",argv[0]);
- fprintf(outfd,"; pg_ver: %s\n",mp_verstr);
- fprintf(outfd,"; pg_argv:");
- for (i=0; i<argc; i++)
- fprintf(outfd," %s",argv[i]);
- fputc('\n',outfd);
- fputs(gstring3,outfd);
- fputs(hstring1,outfd);
- }
-
-#ifndef PRSS
- showalign (outfd, aa0, aa1, maxn, bestp_arr, nbest, qtt.entries,
- m_msg, pst, gstring2, f_str);
-#else
- if (pst.sw_flag > 0 || (!m_msg.quiet && m_msg.nshow>0)) {
- showalign (outfd, aa0, aa1, maxn, bestp_arr, nbest, qtt.entries,
- m_msg, pst, gstring2, f_str);
- }
-#endif
-
- fflush(outfd);
- }
- }
-
- end_l:
-#if defined(COMP_THR) && defined(COMP_MLIB)
- for (i=0; i<max_work_buf; i++) {
- buf_list[i].buf_cnt=0;
- buf_list[i].have_results=0;
- }
-
- num_worker_bufs = 0;
- num_reader_bufs = max_work_buf;
- reader_done = 0;
- worker_buf_workp = 0;
- worker_buf_readp = 0;
- reader_buf_workp = 0;
- reader_buf_readp = 0;
-
- start_thread = 1; /* stop thread from starting again */
-#endif
-
- /* clean up alignment encodings */
- for (i=0; i < m_msg.nshow; i++) {
- if (bestp_arr[i]->have_ares) {
- free(bestp_arr[i]->a_res.res);
- bestp_arr[i]->a_res.res = NULL;
- bestp_arr[i]->have_ares = 0;
- }
- }
-
- if (m_msg.qframe == 2) free(aa0[1]-1);
-
- if (have_f_str) {
- if (f_str[1]!=f_str[0]) {
- close_work (aa0[1], m_msg.n0, &pst, &f_str[1]);
- }
- close_work (aa0[0], m_msg.n0, &pst, &f_str[0]);
- have_f_str = 0;
-#ifndef COMP_THR
- if (m_msg.qshuffle) close_work (aa0s, m_msg.n0, &pst, &qf_str);
-#endif
- if (pst.pam_pssm) {
- free_pam2p(pst.pam2p[0]);
- free_pam2p(pst.pam2p[1]);
- }
- }
-
- for (iln=0; iln < m_msg.nln; iln++) {
- if (m_msg.lb_mfd[iln]!=NULL) closelib(m_msg.lb_mfd[iln]);
- }
-
- tddone = time(NULL);
- tdone = s_time();
- fflush(outfd);
-
- if (fdata) {
- fprintf(fdata,"/** %s **/\n",gstring2);
- fprintf(fdata,"%3ld%-50s\n",qtt.entries-1,m_msg.qtitle);
- fflush(fdata);
- }
-
-#ifdef COMP_MLIB
- ttdisp += tdone-tscan;
-
- maxn = m_msg.max_tot;
- m_msg.n0 =
- QGETLIB (aa0[0], MAXTST, m_msg.qtitle, sizeof(m_msg.qtitle),
- &qseek, &qlcont,q_file_p,&m_msg.sq0off);
- if (m_msg.n0 <= 0) break;
- if ((bp=strchr(m_msg.qtitle,' '))!=NULL) *bp='\0';
- strncpy(qlabel, m_msg.qtitle,sizeof(qlabel));
- if (bp != NULL) *bp=' ';
- qlabel[sizeof(qlabel)-1]='\0';
-
- if (m_msg.ann_flg) {
- m_msg.n0 = ann_scan(aa0[0],m_msg.n0,&m_msg,m_msg.qdnaseq);
- }
-
- if (m_msg.term_code && m_msg.qdnaseq==SEQT_PROT &&
- aa0[0][m_msg.n0-1]!=m_msg.term_code) {
- aa0[0][m_msg.n0++]=m_msg.term_code;
- aa0[0][m_msg.n0]=0;
- }
-
-#if defined(SW_ALTIVEC) || defined(SW_SSE2)
- /* for ALTIVEC, must pad with 15 NULL's */
- for (id=0; id<SEQ_PAD; id++) {aa0[0][m_msg.n0+id]=0;}
-#endif
-
-#ifdef SUPERFAMNUM
- m_msg.nqsfnum = nsfnum;
- for (i=0; i <= nsfnum & i<10; i++) m_msg.qsfnum[i] = sfnum[i];
- m_msg.nqsfnum_n = nsfnum_n;
- for (i=0; i <= nsfnum_n & i<10; i++) m_msg.qsfnum_n[i] = sfnum_n[i];
-#endif
- }
-#endif
- if (m_msg.markx & MX_M10FORM)
- fprintf(outfd,">>><<<\n");
-
- tdone = s_time();
- if ( m_msg.markx & MX_HTML) fputs("<p><pre>\n",outfd);
- printsum(outfd, m_msg.db);
- if ( m_msg.markx & MX_HTML) fputs("</pre>\n",outfd);
-#ifdef HTML_HEAD
- if (m_msg.markx & MX_HTML) fprintf(outfd,"</body>\n</html>\n");
-#endif
- if (outfd!=stdout) printsum(stdout,m_msg.db);
-
- exit(0);
-} /* End of main program */
-
-void
-printsum(FILE *fd, struct db_str ntt)
-{
- double db_tt;
- char tstr1[26], tstr2[26];
-
- strncpy(tstr1,ctime(&tdstart),sizeof(tstr1));
- strncpy(tstr2,ctime(&tddone),sizeof(tstr1));
- tstr1[24]=tstr2[24]='\0';
-
- /* Print timing to output file as well */
- fprintf(fd, "\n\n%ld residues in %ld query sequences\n", qtt.length, qtt.entries);
- if (ntt.carry == 0)
- fprintf(fd, "%ld residues in %ld library sequences\n", ntt.length, ntt.entries);
- else {
- db_tt = (double)ntt.carry*(double)LONG_MAX + (double)ntt.length;
- fprintf(fd, "%.0f residues in %ld library sequences\n", db_tt, ntt.entries);
- }
-
-#ifndef COMP_THR
- fprintf(fd," Scomplib [%s]\n start: %s done: %s\n",mp_verstr,tstr1,tstr2);
-#else
- fprintf(fd," Tcomplib [%s] (%d proc)\n start: %s done: %s\n", mp_verstr,
- max_workers,tstr1,tstr2);
-#endif
-#ifndef COMP_MLIB
- fprintf(fd," Scan time: ");
- ptime(fd, tscan - tprev);
- fprintf (fd," Display time: ");
- ptime (fd, tdone - tscan);
-#else
- fprintf(fd," Total Scan time: ");
- ptime(fd, ttscan);
- fprintf (fd," Total Display time: ");
- ptime (fd, ttdisp);
-#endif
- fprintf (fd,"\n");
- fprintf (fd, "\nFunction used was %s [%s]\n", prog_func,verstr);
-}
-
-void fsigint()
-{
- struct db_str db;
-
- db.entries = db.length = db.carry = 0;
- tdone = s_time();
- tddone = time(NULL);
-
- printf(" /*** interrupted ***/\n");
- if (outfd!=stdout) fprintf(outfd,"/*** interrupted ***/\n");
- fprintf(stderr,"/*** interrupted ***/\n");
-
- printsum(stdout,db);
- if (outfd!=stdout) printsum(outfd,db);
-
- exit(1);
-}
-
-#ifdef COMP_THR
-void save_best(struct buf_head *cur_buf, struct mngmsg m_msg, struct pstruct pst,
- FILE *fdata, int *qsfnum, struct hist_str *histp,
- void **pstat_voidp
-#ifdef PRSS
- , int *s_score, int *s_n1
-
-#endif
- )
-{
- double zscore;
- int i_score;
- struct buf_str *p_rbuf, *cur_buf_p;
- int i, t_best, t_rbest, t_qrbest, tm_best, t_n1, sc_ix;
- double e_score, tm_escore, t_rescore, t_qrescore;
- int jstats;
-
- sc_ix = pst.score_ix;
-
- cur_buf_p = cur_buf->buf;
-
- t_best = t_rbest = t_qrbest = -1;
- tm_escore = t_rescore = t_qrescore = FLT_MAX;
-
- while (cur_buf->buf_cnt--) { /* count down the number of results */
- p_rbuf = cur_buf_p++; /* step through the results buffer */
-
- i_score = p_rbuf->rst.score[sc_ix];
- e_score = p_rbuf->rst.escore;
-
- /* need to look for frame 0 if TFASTA, then save stats at frame 6 */
- if (fdata) {
- fprintf(fdata,
- "%-12s %5d %6d %d %.5f %.5f %4d %4d %4d %g %d %d %8ld\n",
- p_rbuf->libstr,
-#ifdef SUPERFAMNUM
- sfn_cmp(qsfnum,p_rbuf->sfnum),
-#else
- 0,
-#endif
- p_rbuf->n1,p_rbuf->frame,p_rbuf->rst.comp,p_rbuf->rst.H,
- p_rbuf->rst.score[0],p_rbuf->rst.score[1],p_rbuf->rst.score[2],
- p_rbuf->rst.escore, p_rbuf->rst.segnum, p_rbuf->rst.seglen, p_rbuf->lseek);
- }
-
-#ifdef PRSS
- if (p_rbuf->lseek==0) {
- s_score[0] = p_rbuf->rst.score[0];
- s_score[1] = p_rbuf->rst.score[1];
- s_score[2] = p_rbuf->rst.score[2];
- *s_n1 = p_rbuf->n1;
-
- bestp = bestp_arr[nbest++];
- bestp->score[0] = s_score[0];
- bestp->score[1] = s_score[1];
- bestp->score[2] = s_score[2];
- bestp->n1 = *s_n1;
- bestp->escore = p_rbuf->rst.escore;
- bestp->segnum = p_rbuf->rst.segnum;
- bestp->seglen = p_rbuf->rst.seglen;
- bestp->zscore = zscore;
- bestp->lseek = p_rbuf->lseek;
- bestp->m_file_p = p_rbuf->m_file_p;
- memcpy(bestp->libstr,p_rbuf->libstr,MAX_UID);
- bestp->n1tot_p = p_rbuf->n1tot_p;
- bestp->frame = p_rbuf->frame;
-
- continue;
- }
-#endif
-
- t_n1 = p_rbuf->n1;
- if (i_score > t_best) tm_best = t_best = i_score;
- if (e_score < tm_escore) tm_escore = e_score;
-
- if (m_msg.qshuffle) {
- if (p_rbuf->qr_score > t_qrbest)
- t_qrbest = p_rbuf->qr_score;
- if (p_rbuf->qr_escore < t_qrescore)
- t_qrescore = p_rbuf->qr_escore;
-
- if (p_rbuf->frame == m_msg.nitt1 && nqstats < m_msg.shuff_max) {
- qstats[nqstats].n1 = p_rbuf->n1; /* save the best score */
- qstats[nqstats].comp = p_rbuf->rst.comp;
- qstats[nqstats].H = p_rbuf->rst.H;
- qstats[nqstats].escore = t_qrescore;
- qstats[nqstats++].score = t_qrbest;
- t_qrbest = -1; /* reset t_qrbest, t_qrescore */
- t_qrescore = FLT_MAX;
- }
- }
-
- if (pst.zsflag >= 10 && p_rbuf->r_score > t_rbest) {
- t_rbest = p_rbuf->r_score;
- t_rescore = p_rbuf->r_escore;
- }
-
- /* statistics done for best score of set */
-
-
- if (p_rbuf->frame == m_msg.nitt1) {
- if (nstats < MAXSTATS ) {
- stats[nstats].n1 = t_n1;
- stats[nstats].comp = p_rbuf->rst.comp;
- stats[nstats].H = p_rbuf->rst.H;
- if (pst.zsflag >= 10) {
- tm_best = t_rbest;
- tm_escore = t_rescore;
- t_rbest = -1;
- t_rescore = FLT_MAX;
- }
- stats[nstats].escore = tm_escore;
- stats[nstats++].score = tm_best;
- t_best = -1;
- tm_escore = FLT_MAX;
- }
- else if (pst.zsflag > 0) {
- if (!stats_done) {
- pst.zsflag_f = process_hist(stats,nstats,m_msg,pst,
- histp, pstat_voidp,0);
- kstats = nstats;
- stats_done = 1;
- for (i=0; i<MAXBEST; i++) {
- bestp_arr[i]->zscore =
- (*find_zp)(bestp_arr[i]->score[pst.score_ix],
- bestp_arr[i]->escore, bestp_arr[i]->n1,
- bestp_arr[i]->comp, *pstat_voidp);
- }
- }
-#ifdef SAMP_STATS
- else {
- if (!m_msg.escore_flg) {
- jstats = nrand(++kstats);
- if (jstats < MAXSTATS) {
- stats[jstats].n1 = t_n1;
- stats[jstats].comp = p_rbuf->rst.comp;
- stats[jstats].H = p_rbuf->rst.H;
- if (pst.zsflag >= 10) {
- tm_best = t_rbest;
- }
- stats[jstats].score = tm_best;
- }
- }
- }
-#endif
- }
- }
-
- /* best saved for every score */
- if (stats_done) {
-
- zscore=(*find_zp)(i_score, e_score, p_rbuf->n1,(double)p_rbuf->rst.comp,
- *pstat_voidp);
-
- if (p_rbuf->frame == m_msg.nitt1) {
- addhistz((*find_zp)(t_best, tm_escore, p_rbuf->n1, (double) p_rbuf->rst.comp,
- *pstat_voidp), histp);
- t_best = t_rbest = -1;
- tm_escore = t_rescore = FLT_MAX;
- }
- }
- else zscore = (double) i_score;
-
-#ifndef PRSS
- if (zscore > zbestcut) {
- if (nbest >= MAXBEST) {
- bestfull = nbest-MAXBEST/4;
- selectbestz(bestp_arr,bestfull-1,nbest);
- zbestcut = bestp_arr[bestfull-1]->zscore;
- nbest = bestfull;
- }
- bestp = bestp_arr[nbest++];
- bestp->score[0] = p_rbuf->rst.score[0];
- bestp->score[1] = p_rbuf->rst.score[1];
- bestp->score[2] = p_rbuf->rst.score[2];
- bestp->comp = (double) p_rbuf->rst.comp;
- bestp->H = (double) p_rbuf->rst.H;
- bestp->escore = p_rbuf->rst.escore;
- bestp->segnum = p_rbuf->rst.segnum;
- bestp->seglen = p_rbuf->rst.seglen;
- bestp->zscore = zscore;
- bestp->lseek = p_rbuf->lseek;
- memcpy(bestp->libstr,p_rbuf->libstr,MAX_UID);
- bestp->cont = p_rbuf->cont; /* not cont+1 because incremented already */
- bestp->m_file_p = p_rbuf->m_file_p;
- bestp->n1 = p_rbuf->n1;
- bestp->n1tot_p = p_rbuf->n1tot_p;
- bestp->frame = p_rbuf->frame;
- bestp->nsfnum = p_rbuf->nsfnum;
-#ifdef SUPERFAMNUM
- if ((bestp->sfnum[0] = p_rbuf->sfnum[0])>0 &&
- (bestp->sfnum[1] = p_rbuf->sfnum[1])>0 &&
- (bestp->sfnum[2] = p_rbuf->sfnum[2])>0 &&
- (bestp->sfnum[3] = p_rbuf->sfnum[3])>0 &&
- (bestp->sfnum[4] = p_rbuf->sfnum[4])>0 &&
- (bestp->sfnum[5] = p_rbuf->sfnum[5])>0 &&
- (bestp->sfnum[6] = p_rbuf->sfnum[6])>0 &&
- (bestp->sfnum[7] = p_rbuf->sfnum[7])>0 &&
- (bestp->sfnum[8] = p_rbuf->sfnum[8])>0 &&
- (bestp->sfnum[9] = p_rbuf->sfnum[9])>0) ;
-#endif
- }
-#endif
- }
-}
-#endif
git://source.jalview.org / jabaws.git / blobdiff