+++ /dev/null
-/* 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;
-}
-
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