Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / fasta34 / last_tat.c

diff --git a/website/archive/binaries/mac/src/fasta34/last_tat.c b/website/archive/binaries/mac/src/fasta34/last_tat.c
new file mode 100644 (file)
index 0000000..0d0724a
--- /dev/null
+++ b/website/archive/binaries/mac/src/fasta34/last_tat.c
@@ -0,0 +1,162 @@
+
+/* copyright (c) 1996, 1997, 1998, 1999 William R. Pearson and the
+   U. of Virginia */
+
+/* $Name: fa_34_26_5 $ - $Id: last_tat.c,v 1.8 2006/04/12 18:00:02 wrp Exp $ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "defs.h"
+#include "mm_file.h"
+
+#include "structs.h"
+#include "param.h"
+
+#ifndef PCOMPLIB
+#include "mw.h"
+#else
+#include "msg.h"
+#include "p_mw.h"
+
+void do_stage2(struct beststr **bptr, int nbest, struct mngmsg m_msg0,
+              int s_func, struct qmng_str *qm_msp);
+#endif
+
+
+extern int (*ranlib) (char *str, int cnt,
+              fseek_t libpos, char *libstr,
+              struct lmf_str *lm_fd);
+
+#define RANLIB (m_fptr->ranlib)
+
+#define MAX_BLINE 200
+
+int
+re_getlib(unsigned char *, int, int, int, int, int, long *, long *, 
+         struct lmf_str *m_fptr);
+
+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
+do_opt (unsigned char *aa0, int n0, unsigned char *aa1, int n1,
+       int frame, struct pstruct *pst, void *f_str,
+       struct rstruct *rst);
+
+struct lmf_str *re_openlib(struct lmf_str *, int outtty);
+
+void sortbestz (struct beststr **bptr, int nbest);
+
+double zs_to_E(double zs,int n1, int isdna, long entries, struct db_str db);
+
+double scale_one_score(int ipos, double escore, struct db_str db, void *rs_str);
+
+void sortbests (struct beststr **bptr, int nbest)
+{
+    int gap, i, j;
+    struct beststr *tmp;
+
+    for (gap = nbest/2; gap > 0; gap /= 2)
+       for (i = gap; i < nbest; i++)
+           for (j = i - gap; j >= 0; j-= gap) {
+             if (bptr[j]->score[0] >= bptr[j + gap]->score[0]) break;
+             tmp = bptr[j];
+             bptr[j] = bptr[j + gap];
+             bptr[j + gap] = tmp;
+           }
+}
+
+int
+last_calc(
+#ifndef PCOMPLIB
+         unsigned char **aa0, unsigned char *aa1, int maxn,
+#endif   
+         struct beststr **bptr, int nbest, 
+         struct mngmsg m_msg, struct pstruct *ppst
+#ifdef PCOMPLIB
+         , struct qmng_str *qm_msp
+#else
+         , void **f_str
+#endif
+         , void *rstat_str)
+{
+  int nopt, ib;
+  struct beststr *bbp;
+  long loffset, l_off;
+  int n0, n1;
+  struct rstruct rst;
+  struct lmf_str *m_fptr;
+  char bline[60];
+  int tat_samp, tat_inc, loop_cnt, i;
+  double min_escore, ess;
+
+  n0 = m_msg.n0;
+
+  sortbestz(bptr,nbest);
+
+  tat_inc = 500;
+/*
+  if (zs_to_E(bptr[0]->zscore,bptr[0]->n1,0,ppst->zdb_size,m_msg.db)/ 
+      zs_to_E(bptr[nbest-1]->zscore,bptr[nbest-1]->n1,0,ppst->zdb_size,m_msg.db)
+       < 1e-20) { tat_inc /= 4 ;}
+*/
+
+/* || (zs_to_E(bptr[0]->zscore,bptr[0]->n1,0,ppst->zdb_size,m_msg.db)< 1e-5); */
+
+  ib = tat_samp = 0;
+  for (loop_cnt = 0; loop_cnt < 5; loop_cnt++) {
+    tat_samp += tat_inc;
+    nopt = min(nbest,tat_samp);
+    min_escore = 1000000.0;
+#ifndef PCOMPLIB
+    for ( ; ib<nopt; ib++) {
+      bbp = bptr[ib];
+
+      if (bbp->score[0] < 0) break;
+
+      if ((m_fptr=re_openlib(bbp->m_file_p,!m_msg.quiet))==NULL) {
+       fprintf(stderr,"*** cannot re-open %s\n",bbp->m_file_p->lb_name);
+       exit(1);
+      }
+      RANLIB(bline,sizeof(bline),bbp->lseek,bbp->libstr,m_fptr);
+
+      n1 = re_getlib(aa1,maxn,m_msg.maxt3,m_msg.loff,bbp->cont,m_msg.term_code,
+                    &loffset,&l_off,bbp->m_file_p);
+
+      do_opt(aa0[bbp->frame],m_msg.n0,aa1,n1,bbp->frame,ppst,
+            f_str[bbp->frame],&rst);
+      bbp->score[0]=rst.score[0];
+      bbp->score[1]=rst.score[1];
+      bbp->score[2]=rst.score[2];
+      bbp->escore=rst.escore;
+      bbp->segnum = rst.segnum;
+      bbp->seglen = rst.seglen;
+
+      if ((ess=scale_one_score(ib, bbp->escore, m_msg.db, rstat_str)) < 
+       min_escore) { min_escore = ess;}
+      /*
+      fprintf(stderr,"%d: %4d %2d %3d %.4g %.4g\n",
+             ib, bbp->score[0], bbp->segnum,bbp->seglen,bbp->escore, ess);
+      */
+    }
+#else
+    do_stage2(&bptr[ib], nopt-ib, m_msg, DO_CALC_FLG, qm_msp);
+
+    for ( ; ib < nopt; ib++) {
+      if ((ess=scale_one_score(ib, bptr[ib]->escore, m_msg.db, rstat_str)) < 
+       min_escore) { min_escore = ess;}
+      /*
+      fprintf(stderr, "%d: %4d %2d %3d %.4g %.4g\n",
+             ib,bptr[ib]->score[0],bptr[ib]->segnum,bptr[ib]->seglen,bptr[ib]->escore,ess);
+      */
+    }
+#endif
+
+
+    if (min_escore > m_msg.e_cut) return ib;
+  }
+  return ib;
+}