Delete unneeded directory

[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
deleted file mode 100644 (file)
index 0d0724a..0000000
--- a/website/archive/binaries/mac/src/fasta34/last_tat.c
+++ /dev/null
@@ -1,162 +0,0 @@
-
-/* 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;
-}