X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Farchive%2Fbinaries%2Fmac%2Fsrc%2Ffasta34%2Fllgetaa.c;fp=website%2Farchive%2Fbinaries%2Fmac%2Fsrc%2Ffasta34%2Fllgetaa.c;h=0000000000000000000000000000000000000000;hb=fb21789ba11ae9b9f6abed1b01d4542e54abfe34;hp=fc43ea6436bc69faa09b333bdb97a3c23533b9e6;hpb=7d68cf3489c816b2ed7afb1925a6de2168eccf4a;p=jabaws.git

diff --git a/website/archive/binaries/mac/src/fasta34/llgetaa.c b/website/archive/binaries/mac/src/fasta34/llgetaa.c
deleted file mode 100644
index fc43ea6..0000000
--- a/website/archive/binaries/mac/src/fasta34/llgetaa.c
+++ /dev/null
@@ -1,493 +0,0 @@
-/* copyright (c) 1996, 1997, 1998, 1999 William R. Pearson and the
-   U. of Virginia */
-
-/* $Name: fa_34_26_5 $ - $Id: llgetaa.c,v 1.25 2007/01/08 15:38:46 wrp Exp $ */
-
-/*
-   Feb, 1998 - version for prss 
-
-   March, 2001 - modifications to support comp_thr.c: use libpos to indicate
-   whether the score is shuffled==1 or unshuffled==0.  This simplifies
-   complib.c and makes comp_thr.c possible
-
-   modified version of nxgetaa.c that generates random sequences
-   for a library
-*/
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
-#include "defs.h"
-#include "mm_file.h"
-
-#include "uascii.h"
-#include "structs.h"
-
-#define XTERNAL
-#include "upam.h"
-#undef XTERNAL
-
-#define YES 1
-#define NO 0
-#define MAXLINE 512
-
-#ifndef min
-#define min(x,y) ((x) > (y) ? (y) : (x))
-#endif
-
-int nsfnum;	/* number of superfamily numbers */
-int sfnum[10];	/* superfamily number from types 0 and 5 */
-int nsfnum_n;
-int sfnum_n[10];
-
-static int use_stdin=0;
-static char llibstr0[256];
-static char llibstr1[256];
-static char o_line[256];
-
-#define NO_FORMAT 0
-#define FASTA_FORMAT 1
-#define GCG_FORMAT 2
-static int seq_format=NO_FORMAT;
-static char seq_title[200];
-
-extern int irand(int);
-extern void shuffle(unsigned char *from, unsigned char *to, int n);
-extern void wshuffle(unsigned char *from, unsigned char *to, int n, int wsiz, int *ieven);
-
-int
-getseq(char *filen, int *qascii,
-       unsigned char *seq, int maxs, char *libstr,
-       int n_libstr, long *sq0off)
-{
-  FILE *fptr;
-  char line[512],*bp;
-  int i, j, n;
-  int ic;
-  int sstart, sstop, sset=0;
-  int have_desc = 0;
-  int desc_complete = 0;
-  int llen, l_offset;
-
-  seq_title[0]='\0';
-
-  sstart = sstop = -1;
-#ifndef DOS
-  if ((bp=strchr(filen,':'))!=NULL) {
-#else
-  if ((bp=strchr(filen+3,':'))!=NULL) {
-#endif
-    *bp='\0';
-    if (*(bp+1)=='-') sscanf(bp+2,"%d",&sstop);
-    else sscanf(bp+1,"%d-%d",&sstart,&sstop);
-    sset=1;
-  }
-
-  if (strcmp(filen,"-") && strcmp(filen,"@")) {
-    if ((fptr=fopen(filen,"r"))==NULL) {
-      fprintf(stderr," could not open %s\n",filen);
-      return 0;
-    }
-  }
-  else {
-    fptr = stdin;
-    use_stdin++;
-  }
-
-  if (use_stdin > 1) {
-    have_desc = 1;
-    if ((bp=strchr(o_line,'\001'))!=NULL) *bp='\0';
-    strncpy(llibstr1,o_line,sizeof(llibstr1));
-    strncpy(libstr,o_line,n_libstr);
-    libstr[n_libstr-1]='\0';
-    l_offset = 0;
-  }
-
-  if (sset==1) {
-    filen[strlen(filen)]=':';
-    if (*sq0off==1 || sstart>1) *sq0off = sstart;
-  }
-
-  desc_complete = 0;
-  n=0;
-  while(fgets(line,sizeof(line),fptr)!=NULL) {
-    if (line[0]=='>') {
-      if (have_desc) {
-	strncpy(o_line,line,sizeof(o_line));
-	goto last;
-      }
-      l_offset = 0;
-      seq_format = FASTA_FORMAT;
-#ifdef STAR_X
-      qascii['*'] = qascii['X'];
-#endif
-      sfnum[0] = nsfnum = 0;
-
-      if ((bp=(char *)strchr(line,'\n'))!=NULL) {
-	*bp='\0';				/* have newline */
-	desc_complete = 1;
-      }
-
-      if ((bp=strchr(line+1,'\001'))!=NULL) *bp='\0';
-      strncpy(seq_title,line+1,sizeof(seq_title));
-      strncpy(llibstr0,line+1,sizeof(llibstr0));
-      if (n_libstr <= 20) {
-	if ((bp=(char *)strchr(line,' '))!=NULL) *bp='\0';
-      }
-      strncpy(libstr,line+1,n_libstr);
-      libstr[n_libstr-1]='\0';
-
-      if (!desc_complete) {
-	while (fgets(line, sizeof(line), fptr) != NULL) {
-	  if (strchr(line,'\n') != NULL) {
-	    line[0]='>';
-	    break;
-	  }
-	}
-	desc_complete = 1;
-      }
-    }
-    else if (seq_format==NO_FORMAT) {
-      seq_format = GCG_FORMAT;
-      qascii['*'] = qascii['X'];
-      l_offset = 10;
-      llen = strlen(line);
-      while (strncmp(&line[llen-3],"..\n",(size_t)3) != 0) {
-	if (fgets(line,sizeof(line),fptr)==NULL) return 0;
-	llen = strlen(line);
-      }
-      if (n_libstr <= 20) {
-	if ((bp=(char *)strchr(line,' '))!=NULL) *bp='\0';
-	else if ((bp=(char *)strchr(line,'\n'))!=NULL) *bp='\0';
-      }
-      strncpy(libstr,line,n_libstr);
-      libstr[n_libstr-1]='\0';
-      if (fgets(line,sizeof(line),fptr)==NULL) return 0;
-    }
-
-    if (seq_format==GCG_FORMAT && strlen(line)<l_offset) continue;
-
-    if (line[0]!='>'&& line[0]!=';') {
-      for (i=l_offset; (n<maxs)&&
-	     ((ic=qascii[line[i]&AAMASK])<EL); i++)
-	if (ic<NA) seq[n++]= ic;
-      if (ic == ES) break;
-    }
-    else {
-      if (have_desc) {
-	strncpy(o_line,line,sizeof(o_line));
-	goto last;
-      }
-      else {
-	have_desc = 1;
-      }
-    }
-  }
-
- last:
-  if (n==maxs) {
-    fprintf(stderr," sequence may be truncated %d %d\n",n,maxs);
-    fflush(stderr);
-  }
-  if ((bp=strchr(libstr,'\n'))!=NULL) *bp = '\0';
-  if ((bp=strchr(libstr,'\r'))!=NULL) *bp = '\0';
-  seq[n]= EOSEQ;
-
-  if (fptr!=stdin) fclose(fptr);
-
-  if (sset) {
-    if (sstart <= 0) sstart = 1;
-    if (sstop <= 0) sstop = n;
-    sstart--;
-    sstop--;
-    for (i=0, j=sstart; j<=sstop; i++,j++)
-      seq[i] = seq[j];
-    n = sstop - sstart +1;
-    seq[n]=EOSEQ;
-  }
-
-  return n;
-}
-
-int
-gettitle(filen,title,len)
-  char *filen, *title; int len;
-{
-  FILE *fptr;
-  char line[512];
-  char *bp;
-  int ll,sset;
-#ifdef WIN32
-  char *strpbrk();
-#endif
-  sset = 0;
-
-  if (use_stdin) {
-    if (use_stdin == 1) {
-      /*      use_stdin++; */
-      strncpy(title,llibstr0,len);
-    }
-    else {
-      strncpy(title,llibstr1,len);
-    }
-    if ((bp=strchr(title,'\001'))!=NULL) *bp='\0';
-    return strlen(title);
-  }
-
-  if ((bp=strchr(filen,':'))!=NULL) { *bp='\0'; sset=1;}
-	  
-  if ((fptr=fopen(filen,"r"))==NULL) {
-    fprintf(stderr," file %s was not found\n",filen);
-    fflush(stderr);
-    return 0;
-  }
-
-  if (sset==1) filen[strlen(filen)]=':';
-
-  while(fgets(line,sizeof(line),fptr)!=0) {
-    if (line[0]=='>'|| line[0]==';') goto found;
-  }
-  fclose(fptr);
-  title[0]='\0';
-  return 0;
-
- found:
-  if ((bp=strchr(line,'\001'))!=NULL) *bp = 0;
-#ifdef WIN32
-  bp = strpbrk(line,"\n\r");
-#else
-  bp = strchr(line,'\n');
-#endif
-  if (bp!=NULL) *bp = 0;
-  strncpy(title,line,len);
-  title[len-1]='\0';
-  fclose(fptr);
-  return strlen(title);
-}	
-
-FILE *libf=NULL;
-
-long lpos;
-char lline[MAXLINE];
-int lfflag=0;	/* flag for CRLF in EMBL CDROM files */
-#define LFCHAR '\015'  /* for MWC 5.5 */
-
-int agetlib(); void aranlib();	/* pearson fasta format */
-
-/*	the following is from fgetgb.c */
-
-/* a file name for openlib may now include a library type suffix */
-/* only opens fasta format files */
-
-static char libn_save[MAX_FN];
-static int ldna_save=0;
-static int do_shuffle;
-static int shuff_cnt=10;
-static int w_flag = 0;
-#ifdef DEBUG
-static FILE *dfile=NULL;
-#endif
-static unsigned char *aa_save;
-static int n1_save;
-static int i_even;
-
-/* lmf_str * is used here for compatibility with the "normal" openlib,
-   but is largely unnecessary */
-
-void 
-set_shuffle(struct mngmsg m_msg) {
-  char dfname[MAX_FN];
-
-  if (m_msg.shuff_wid > 0) w_flag = m_msg.shuff_wid;
-  if (m_msg.shuff_max > shuff_cnt) shuff_cnt = m_msg.shuff_max;
-
-#ifdef DEBUG
-  if (m_msg.dfile[0]!='\0') {
-    strncpy(dfname,m_msg.dfile,sizeof(dfname));
-    strncat(dfname,"_rlib",sizeof(dfname));
-    dfile = fopen(dfname,"w");
-  }
-#endif
-}
-
-struct lmf_str *
-openlib(char *lname, int ldnaseq, int *sascii, int quiet, struct lmf_str *m_fd)
-{
-  char rline[10],libn[MAX_FN], *bp;
-  int wcnt, ll, opnflg;
-  int libtype;
-  struct lmf_str *m_fptr;
-
-  wcnt = 0;
-  libtype = 0;
-
-  strncpy(libn_save,lname,sizeof(libn_save));
-
-  /* now allocate a buffer for the opened text file */
-  if ((m_fptr = calloc(1,sizeof(struct lmf_str)))==NULL) {
-    fprintf(stderr," cannot allocate lmf_str (%ld) for %s\n",
-	    sizeof(struct lmf_str),lname);
-    return NULL;
-  }
-
-  strncpy(m_fptr->lb_name,lname,MAX_FN);
-  m_fptr->lb_name[MAX_FN-1]='\0';
-
-  m_fptr->sascii = sascii;
-  m_fptr->getlib = agetlib;
-  m_fptr->ranlib = aranlib;
-  m_fptr->mm_flg = 0;
-
-  do_shuffle = 0;
-  irand(0);		/* initialize the random number generator */
-
-  return m_fptr;
-}
-
-void
-closelib()
-{
-  if (libf!=NULL) {
-    fclose(libf);
-    libf = NULL;
-  }
-#ifdef DEBUG
-  if (dfile) fclose(dfile);
-#endif
-}
-
-static int ieven=0;
-static char *desc_save;
-
-int
-agetlib(unsigned char *seq, 
-	int maxs,
-	char *libstr,
-	int n_libstr,
-	fseek_t *libpos,
-	int *lcont, 
-	struct lmf_str *lf_fd,
-	long *l_off)
-{
-  long sq1_off;
-  char lib_desc[120];
-  int i;
-
-  *l_off = 1;
-
-  if (!do_shuffle) {
-    do_shuffle = 1;
-    
-    if ((n1_save = getseq(libn_save,lf_fd->sascii,
-			  seq,maxs,lib_desc,sizeof(lib_desc),&sq1_off)) < 1)
-      return n1_save;
-
-    strncpy(libstr,lib_desc,n_libstr);
-    libstr[n_libstr-1]='\0';
-
-    if ((aa_save = (unsigned char *)calloc(n1_save+1,sizeof(unsigned char)))==
-	NULL) fprintf(stderr," cannot allocate %d for saved sequence\n",
-		       n1_save);
-    memcpy((void *)aa_save,(void *)seq,n1_save);
-
-    if ((desc_save =
-	 (char *)calloc(strlen(lib_desc)+1,sizeof(char)))== NULL) {
-      fprintf(stderr," cannot allocate saved desciption [%d]\n",
-	      strlen(lib_desc)+1);
-    }
-    else {
-      strncpy (desc_save,lib_desc,strlen(lib_desc));
-      desc_save[strlen(lib_desc)]=='\0';
-    }
-
-    *libpos = 0;
-    return n1_save;
-  }
-  else {	/* return a shuffled sequence - here we need a window size; */
-    strncpy(libstr,desc_save,n_libstr);
-    libstr[n_libstr-1]='\0';
-
-    if (shuff_cnt-- <= 0 ) return -1;
-    if (w_flag > 0) wshuffle(aa_save,seq,n1_save,w_flag,&ieven);
-    else shuffle(aa_save,seq,n1_save);
-    seq[n1_save] = EOSEQ;
-#ifdef DEBUG
-    if (dfile!=NULL) {
-      fprintf(dfile,">%d\n",shuff_cnt);
-      for (i=0; i<n1_save; i++) {
-	if (aa[seq[i]]>0) fputc(aa[seq[i]],dfile);
-	else {fprintf(stderr,"error aa0[%d]: %d %d\n",
-		      i,seq[i],aa[seq[i]]);}
-	if (i%60 == 59) fputc('\n',dfile);
-      }
-      fputc('\n',dfile);
-    }
-#endif
-    *libpos = 1;
-    return n1_save;
-  }
-}
-
-void
-aranlib(char *str,
-	int cnt,
-	fseek_t seek,
-	char *libstr,
-	struct lmf_str *lm_fd)
-{
-  char *bp;
-  int ll;
-
-  if (use_stdin == 2) {
-    if (llibstr1[0]=='>' || llibstr1[0]==';') {
-      strncpy(str,llibstr1+1,cnt);
-    }
-    else {
-      strncpy(str,llibstr1,cnt);
-    }
-  }
-  else {
-    strncpy(str,desc_save,cnt);
-  }
-  str[cnt-1]='\0';
-  if ((bp = strchr(str,'\001'))!=NULL) *bp='\0';
-  else if ((bp = strchr(str,'\n'))!=NULL) *bp='\0';
-  else str[cnt-1]='\0';
-}
-
-/*
-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]];
-  }
-}
-*/
-
-struct lmf_str *
-re_openlib(struct lmf_str *om_fptr, int outtty)
-{
-  return om_fptr;
-}
-
-int re_getlib(unsigned char *aa1, int n1, int maxt3, int loff, int cont,
-	      int term_code, long *loffset, long *l_off,
-	      struct lmf_str *m_file_p)
-{
-  *loffset = 0;
-  *l_off = 1;
-  return n1;
-}
-