+++ /dev/null
-
-/* $Name: fa_34_26_5 $ - $Id: nmgetlib.c,v 1.35 2007/01/08 15:38:46 wrp Exp $ */
-
-/* May, June 1987 - modified for rapid read of database
-
- copyright (c) 1987,1988,1989,1992,1995,2000 William R. Pearson
-
- revised (split) version of nmgetaa.c -> renamed nmgetlib.c
-
- This version seeks to be a thread safe, no global, library
- reading program. While adjusting the routines in this file
- should be relatively easy, ncbl2_mlib.c and mysql_lib.c may be
- more difficult.
-
- nmgetlib.c and mmgetaa.c are used together. nmgetlib.c provides
- the same functions as nxgetaa.c if memory mapping is not used,
- mmgetaa.c provides the database reading functions if memory
- mapping is used. The decision to use memory mapping is made on
- a file-by-file basis.
-
- June 2, 1987 - added TFASTA
- March 30, 1988 - combined ffgetaa, fgetgb;
- April 8, 1988 - added PIRLIB format for unix
- Feb 4, 1989 - added universal subroutines for libraries
- December, 1995 - added range option file.name:1-1000
- September, 1999 - added option for mmap()ed files using ".xin" */
-
-
-/*
- February 4, 1988 - this starts a major revision of the getaa
- routines. The goal is to be able to seach the following format
- libraries:
-
- 0 - normal FASTA format
- 1 - full Genbank tape format
- 2 - NBRF/PIR CODATA format
- 3 - EMBL/Swiss-prot format
- 4 - Intelligentics format
- 5 - NBRF/PIR VMS format
- 6 - GCG 2bit format
-
- 11 - NCBI setdb/blastp (1.3.2) AA/NT
- 12 - NCBI setdb/blastp (2.0) AA/NT
- 16 - mySQL queries
-
- see file altlib.h to confirm numbers
-
-*/
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
-
-#include "defs.h"
-#include "structs.h"
-
-#ifndef SFCHAR
-#define SFCHAR ':'
-#endif
-
-#define EOSEQ 0
-
-#include "uascii.h"
-/* #include "upam.h" */
-
-#define LFCHAR '\015' /* for MWC 5.5 */
-
-#include "altlib.h"
-
-
-#include <fcntl.h>
-#ifndef O_RAW
-#ifdef O_BINARY
-#define O_RAW O_BINARY
-#else
-#define O_RAW 0
-#endif /* O_BINARY */
-#endif /* O_RAW */
-
-#ifdef WIN32
-#define RBSTR "rb" /* read file in binary mode */
-#else
-#define RBSTR "r"
-#endif
-
-#include "mm_file.h"
-struct lmf_str *load_mmap(FILE *, char *, int, int, struct lmf_str *);
-struct lmf_str *ncbl2_reopen(struct lmf_str *);
-struct lmf_str *ncbl2_openlib(char *, int);
-
-static struct lmf_str *last_m_fptr=NULL;
-
-#ifdef MYSQL_DB
-struct lmf_str *mysql_openlib(char *, int, int *);
-struct lmf_str *mysql_reopen(struct lmf_str *);
-#endif
-
-#ifdef PGSQL_DB
-struct lmf_str *pgsql_openlib(char *, int, int *);
-struct lmf_str *pgsql_reopen(struct lmf_str *);
-#endif
-
-void closelib(struct lmf_str *m_fptr);
-extern void newname(char *nname, char *oname, char *suff, int maxn);
-
-/* a file name for openlib may include a library type suffix */
-
-struct lmf_str *
-openlib(char *lname, int ldnaseq, int *sascii,
- int outtty, struct lmf_str *om_fptr)
-{
- char rline[10],sname[MAX_FN], iname[MAX_FN], *bp;
- char opt_text[MAX_FN]; /* save text after ':' */
- int wcnt, opnflg;
- int libtype;
- FILE *libi=NULL;
- FILE *libf;
- int use_stdin;
- struct lmf_str *m_fptr=NULL;
-
- /* this is currently unavailable - later it can return a value somewhere */
- /*
- if (lname[0]=='#') {return -9;}
- */
-
- if (om_fptr != NULL && om_fptr->mm_flg) {
- om_fptr->lpos = 0;
- return om_fptr;
- }
-
- wcnt = 0; /* number of times to ask for file name */
-
- /* check to see if there is a file option ":1-100" */
-#ifndef WIN32
- if ((bp=strchr(lname,':'))!=NULL && *(bp+1)!='\0') {
-#else
- if ((bp=strchr(lname+3,':'))!=NULL && *(bp+1)!='\0') {
-#endif
- strncpy(opt_text,bp+1,sizeof(opt_text));
- opt_text[sizeof(opt_text)-1]='\0';
- *bp = '\0';
- }
- else opt_text[0]='\0';
-
- if (lname[0] == '-' || lname[0] == '@') {
- use_stdin = 1;
- }
- else use_stdin=0;
-
- strncpy(sname,lname,sizeof(sname));
- sname[sizeof(sname)-1]='\0';
- /* check for library type */
- if ((bp=strchr(sname,' '))!=NULL) {
- *bp='\0';
- sscanf(bp+1,"%d",&libtype);
- if (libtype<0 || libtype >= LASTLIB) {
- fprintf(stderr," invalid library type: %d (>%d)- resetting\n%s\n",
- libtype,LASTLIB,lname);
- libtype=0;
- }
- }
- else libtype=0;
-
- if (use_stdin && libtype !=0) {
- fprintf(stderr," @/- STDIN libraries must be in FASTA format\n");
- return NULL;
- }
-
- /* check to see if file can be open()ed? */
-
- l1:
- if (libtype<=LASTTXT) {
- if (!use_stdin) {
- opnflg=((libf=fopen(sname,RBSTR))!=NULL);
- }
- else {
- libf=stdin;
- strncpy(sname,"STDIN",sizeof(sname));
- sname[sizeof(sname)-1]='\0';
- opnflg=1;
- }
- }
-#ifdef NCBIBL13
- else if (libtype==NCBIBL13) opnflg=(ncbl_openlib(sname,ldnaseq)!= -1);
-#endif
-#ifdef NCBIBL20
- else if (libtype==NCBIBL20) {
- opnflg=((m_fptr=ncbl2_openlib(sname,ldnaseq))!=NULL);
- }
-#endif
-
-#ifdef MYSQL_DB
- /* a mySQL filename contains mySQL commands, not sequences */
- else if (libtype==MYSQL_LIB) {
- opnflg=((m_fptr=mysql_openlib(sname,ldnaseq,sascii))!=NULL);
- }
-#endif
-#ifdef PGSQL_DB
- /* a mySQL filename contains mySQL commands, not sequences */
- else if (libtype==PGSQL_LIB) {
- opnflg=((m_fptr=pgsql_openlib(sname,ldnaseq,sascii))!=NULL);
- }
-#endif
-
- if (!opnflg) { /* here if open failed */
- if (outtty) {
- fprintf(stderr," cannot open %s library\n",sname);
- fprintf(stderr," enter new file name or <RET> to quit ");
- fflush(stderr);
- if (fgets(sname,sizeof(sname),stdin)==NULL) return NULL;
- if ((bp=strchr(sname,'\n'))!=0) *bp='\0';
- if (strlen(sname)==0) return NULL;
- if (++wcnt > 10) return NULL;
- strncpy(lname,sname,sizeof(lname)-1);
- lname[sizeof(lname)-1]='\0';
- goto l1;
- }
- else return NULL;
- } /* !openflg */
-
- if (libtype <= LASTTXT) {
- /* 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),sname);
- return NULL;
- }
- if ((m_fptr->lline = calloc(MAX_STR,sizeof(char)))==NULL) {
- fprintf(stderr," cannot allocate lline (%d) for %s\n",
- MAX_STR,sname);
- return NULL;
- }
-
- strncpy(m_fptr->lb_name,sname,MAX_FN);
- m_fptr->lb_name[MAX_FN-1]='\0';
- strncpy(m_fptr->opt_text,opt_text,MAX_FN);
- m_fptr->opt_text[MAX_FN-1]='\0';
- m_fptr->sascii = sascii;
-
- m_fptr->libf = libf;
- m_fptr->lb_type = libtype;
- m_fptr->getlib = getliba[libtype];
- m_fptr->ranlib = ranliba[libtype];
- m_fptr->mm_flg = 0;
- m_fptr->tot_len = 0;
- m_fptr->max_len = 0;
- m_fptr->lib_aa = (ldnaseq==0);
- }
- last_m_fptr = m_fptr;
-
-#ifdef USE_MMAP
- /* check for possible mmap()ed files */
- if (!use_stdin && (libtype <= LASTTXT) && (getlibam[libtype]!=NULL)) {
- /* this is a file we can mmap() */
- /* look for .xin file */
- newname(iname,sname,"xin",sizeof(iname));
- if ((libi=fopen(iname,"r"))!=NULL) { /* have a *.xin file, use mmap */
- if (load_mmap(libi,sname,libtype,ldnaseq,m_fptr)!=NULL) {
- fclose(libi); /* close index file */
- m_fptr->lb_type = libtype;
- m_fptr->getlib = getlibam[libtype];
- m_fptr->ranlib = ranlibam[libtype];
- m_fptr->mm_flg = 1;
- return m_fptr;
- }
- fclose(libi); /* memory mapping failed, but still must close file */
- }
- }
-#endif
-
- if (libtype <= LASTTXT) {
- m_fptr->lpos = 0;
- if (fgets(m_fptr->lline,MAX_STR,libf)==NULL) return NULL;
- }
- return m_fptr;
-}
-
-void
-closelib(struct lmf_str *m_fptr) {
-
-
-#ifdef MMAP
- if (m_fptr->mm_flag) {
-/* don't close memory mapped files
- close_mmap(m_fptr);
-*/
- return;
- }
-#endif
-
- if (m_fptr->libf!=NULL && m_fptr->libf != stdin) {
- fclose(m_fptr->libf);
- m_fptr->libf = NULL;
- }
-
-#ifdef NCBIBL13
- if (m_fptr->lb_type == NCBIBL13) ncbl_closelib(m_fptr);
-#endif
-#ifdef NCBIBL20
- if (m_fptr->lb_type == NCBIBL20) ncbl2_closelib(m_fptr);
-#endif
-#ifdef MYSQL_DB
- if (m_fptr->lb_type == MYSQL_LIB) mysql_closelib(m_fptr);
-#endif
-}
-
-struct lmf_str *
-re_openlib(struct lmf_str *om_fptr, int outtty)
-{
- int opnflg;
-
- /* if the file mmap()ed and has been opened - use it and return */
- if (om_fptr->mm_flg) {
- return om_fptr;
- }
-#ifdef MYSQL_DB
- /* if this is a mysql database - use it and return */
- else if (om_fptr->lb_type == MYSQL_LIB) {
- return om_fptr;
- }
-#endif
-
- /* data is available, but file is closed or not memory mapped, open it */
- /* no longer check to memory map - because we could not do it before */
-
- opnflg = 1;
- if (om_fptr->lb_type<=LASTTXT && om_fptr->libf==NULL)
- opnflg=((om_fptr->libf=fopen(om_fptr->lb_name,RBSTR))!=NULL);
-#ifdef NCBIBL13
- else if (om_fptr->lb_type==NCBIBL13)
- opnflg=(ncbl_openlib(om_fptr->lb_name,!om_fptr->lib_aa)!= -1);
-#endif
-#ifdef NCBIBL20
- else if (om_fptr->lb_type==NCBIBL20) {
- opnflg=((om_fptr=ncbl2_openlib(om_fptr->lb_name,!om_fptr->lib_aa))!=NULL);
- }
-#endif
-#ifdef MYSQL_DB
- /* a mySQL filename contains mySQL commands, not sequences */
- else if (om_fptr->lb_type==MYSQL_LIB)
- opnflg=(mysql_reopen(om_fptr)!=NULL);
-#endif
-
- if (!opnflg) {
- fprintf(stderr,"*** could not re_open %s\n",om_fptr->lb_name);
- return NULL;
- }
-
- /* use the old buffer for the opened text file */
- om_fptr->mm_flg = 0;
- last_m_fptr = om_fptr;
-
- return om_fptr;
-}
-
-#ifdef SUPERFAMNUM
-static char tline[512];
-extern int nsfnum; /* number of superfamily numbers */
-extern int sfnum[10]; /* superfamily number from types 0 and 5 */
-extern int nsfnum_n;
-extern int sfnum_n[10];
-#endif
-
-void sf_sort(int *, int);
-
-int
-agetlib(unsigned char *seq, int maxs,
- char *libstr, int n_libstr,
- fseek_t *libpos,
- int *lcont,
- struct lmf_str *lm_fd,
- long *l_off)
-{
- int i;
- register unsigned char *cp, *seqp;
- register int *ap;
- unsigned char *seqm, *seqm1;
- /* int ic, l_start, l_stop, l_limit, rn; */
- char *bp, *bp1, *bpa, *tp;
-
- seqp = seq;
- seqm = &seq[maxs-9];
- seqm1 = seqm-1;
-
- ap = lm_fd->sascii;
-
- if (*lcont==0) {
- *l_off = 1;
- while (lm_fd->lline[0]!='>' && lm_fd->lline[0]!=';') {
- if (lm_fd->libf != stdin) lm_fd->lpos = FTELL(lm_fd->libf);
- if (fgets(lm_fd->lline,MAX_STR,lm_fd->libf)==NULL) return (-1);
- }
-#ifdef SUPERFAMNUM
- strncpy(tline,lm_fd->lline+1,sizeof(tline));
- tline[sizeof(tline)-1]='\0';
- sfnum[0]=nsfnum=0;
- if ((bp=strchr(tline,' ')) && (bp=strchr(bp+1,SFCHAR))) {
- if ((bpa = strchr(bp+1,'\001'))!=NULL) *bpa = '\0';
- if ((bp1=strchr(bp+1,SFCHAR))==NULL) {
-/* fprintf(stderr," second %c missing: %s\n",SFCHAR,libstr); */
- }
- else {
- *bp1 = '\0';
- i = 0;
- if ((tp = strtok(bp+1," \t"))!=NULL) {
- sfnum[i++] = atoi(tp);
- while ((tp = strtok((char *)NULL," \t")) != (char *)NULL) {
- if (isdigit(*tp)) sfnum[i++] = atoi(tp);
- if (i>=9) break;
- }
- }
- sfnum[nsfnum=i]= 0;
- if (nsfnum>1) sf_sort(sfnum,nsfnum);
- else {
- if (nsfnum<1) fprintf(stderr," found | but no sfnum: %s\n",libstr);
- }
- }
- }
- else {
- sfnum[0] = nsfnum = 0;
- }
-#endif
-
- if ((bp=strchr(lm_fd->lline,'@'))!=NULL && !strncmp(bp+1,"C:",2)) {
- sscanf(bp+3,"%ld",l_off);
- }
-
- strncpy(libstr,lm_fd->lline+1,n_libstr-1);
- libstr[n_libstr-1]='\0';
- if ((bp=strchr(libstr,'\r'))!=NULL) *bp='\0';
- if ((bp=strchr(libstr,'\n'))!=NULL) *bp='\0';
- if (n_libstr > MAX_UID) {
- tp = libstr;
- while (*tp++) if (*tp == '\001' || *tp== '\t') *tp = ' ';
- }
-
- *libpos = lm_fd->lpos;
-
- /* make certain we have the end of the line */
- while (strchr((char *)lm_fd->lline,'\n')==NULL) {
- if (strlen(lm_fd->lline)<MAX_STR/2)
- fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR/2,lm_fd->libf);
- else
- fgets(&lm_fd->lline[MAX_STR/2],MAX_STR/2,lm_fd->libf);
- }
- lm_fd->lline[MAX_STR-1]='\0';
- }
-
- lm_fd->lline[0]='\0';
- while (seqp<seqm1 && fgets((char *)seqp,(size_t)(seqm-seqp),lm_fd->libf)!=NULL) {
- if (*seqp=='>') goto new;
- if (*seqp==';') {
- if (strchr((char *)seqp,'\n')==NULL) goto cont;
- continue;
- }
-
- /* removed - used for @P:1-n
- if (l_limit) {
- for (cp=seqp; seqp<seqm1 && rn < l_stop && (ic=ap[*cp++])<EL; )
- if (ic < NA && ++rn > l_start) *seqp++ = (unsigned char)ic;
- if (rn > l_stop) goto finish;
- }
- else {
- */
- for (cp=seqp; seqp<seqm1; ) {
- if ((*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA) continue;
- if (*(--seqp)>NA) break;
- }
- if (*seqp==ES) goto done;
- if (lm_fd->libf != stdin) lm_fd->lpos = FTELL(lm_fd->libf);
- }
- goto done;
- new:
- strncpy(lm_fd->lline,(char *)seqp,MAX_STR);
- lm_fd->lline[MAX_STR-1]='\0';
- /* be certain to get complete line, if possible */
- if (strchr(lm_fd->lline,'\n')==NULL)
- fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR-strlen(lm_fd->lline),lm_fd->libf);
- lm_fd->lline[MAX_STR-1]='\0';
- if (strchr(lm_fd->lline,'\n')==NULL && strchr((char *)seqp,'\n')!=NULL)
- lm_fd->lline[strlen(lm_fd->lline)-1]='\n';
- goto done;
-
- /* removed - used for @P:1-n
-finish:
- while (lm_fd->lline[0]!='>' &&
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf)!=NULL) {
- if (lm_fd->libf != stdin) lm_fd->lpos = FTELL(lm_fd->libf);
- }
- goto done;
-*/
- cont:
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- seqm1 = seqp;
- done:
- if (seqp>=seqm1) (*lcont)++;
- else {
- *lcont=0;
- }
-
- *seqp = EOSEQ;
- /* if ((int)(seqp-seq)==0) return 1; */
- return (int)(seqp-seq);
-}
-
-void
-aranlib(char *str, int cnt, fseek_t seek, char *libstr, struct lmf_str *lm_fd)
-{
- char *bp;
-
- if (lm_fd->libf != stdin) {
- FSEEK(lm_fd->libf, seek, 0);
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
-
- if (lm_fd->lline[0]=='>' || lm_fd->lline[0]==';') {
- strncpy(str,lm_fd->lline+1,cnt);
- str[cnt-1]='\0';
- if ((bp = strchr(str,'\r'))!=NULL) *bp='\0';
- if ((bp = strchr(str,'\n'))!=NULL) *bp='\0';
- /*
- if ((bp = strchr(str,SFCHAR))!=NULL) *bp='\0';
- else if ((bp = strchr(str,'\001'))!=NULL) *bp='\0';
- else if ((bp = strchr(str,'\n'))!=NULL) *bp='\0';
- else str[cnt-1]='\0';
- */
- bp = str;
- while (*bp++) if (*bp=='\001' || *bp=='\t') *bp=' ';
- }
- else {
- str[0]='\0';
- }
- }
- else str[0]='\0';
-}
-
-void lget_ann(struct lmf_str *, char *, int);
-
-int
-lgetlib(unsigned char *seq,
- int maxs,
- char *libstr,
- int n_libstr,
- fseek_t *libpos,
- int *lcont,
- struct lmf_str *lm_fd,
- long *l_off)
-{
- register unsigned char *cp, *seqp;
- register int *ap;
- unsigned char *seqm, *seqm1;
- char *bp, *bp_gid;
-
- *l_off = 1;
-
- seqp = seq;
- seqm = &seq[maxs-11];
- seqm1 = seqm-1;
-
- ap = lm_fd->sascii;
-
- if (*lcont==0) {
- while (lm_fd->lline[0]!='L' || lm_fd->lline[1]!='O' ||
- strncmp(lm_fd->lline,"LOCUS",5)) { /* find LOCUS */
- lm_fd->lpos = FTELL(lm_fd->libf);
- if (fgets(lm_fd->lline,MAX_STR,lm_fd->libf)==NULL) return (-1);
- if (lm_fd->lfflag) getc(lm_fd->libf);
- }
- *libpos= lm_fd->lpos;
-
- if (n_libstr <= 21) {
- strncpy(libstr,&lm_fd->lline[12],12);
- libstr[12]='\0';
- }
- else {
- lget_ann(lm_fd,libstr,n_libstr);
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- }
-
- while (lm_fd->lline[0]!='O' || lm_fd->lline[1]!='R' ||
- strncmp(lm_fd->lline,"ORIGIN",6)) { /* find ORIGIN */
- if (fgets(lm_fd->lline,MAX_STR,lm_fd->libf)==NULL) return (-1);
- if (lm_fd->lfflag) getc(lm_fd->libf);
- }
- }
- else {
- for (cp= lm_fd->cpsave; seqp<seqm1; ) {
- if ((*seqp++=ap[*cp++])<NA) continue;
- if (*(--seqp)>NA) break;
- }
- }
-
- lm_fd->lline[0]='\0';
- while (seqp<seqm1 && fgets(lm_fd->lline,MAX_STR,lm_fd->libf)!=NULL) {
- if (lm_fd->lfflag) getc(lm_fd->libf);
- if (lm_fd->lline[0]=='/') goto new;
- for (cp= (unsigned char *)&lm_fd->lline[10]; seqp<seqm1; ) {
- if ((*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA) continue;
- if (*(--seqp)>NA) break;
- }
- }
- goto done;
-new:
- lm_fd->lpos = FTELL(lm_fd->libf);
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- if (lm_fd->lfflag) getc(lm_fd->libf);
-
-done:
- if (seqp>=seqm1) {
- lm_fd->cpsave = cp;
- (*lcont)++;
- }
- else *lcont=0;
-
- *seqp = EOSEQ;
- /* if ((int)(seqp-seq)==0) return 1; */
- return (int)(seqp-seq);
-}
-
-void
-lget_ann(struct lmf_str *lm_fd, char *libstr, int n_libstr) {
- char *bp, *bp_gid, locus[120], desc[120], acc[120], ver[120];
-
- /* copy in locus from lm_fd->lline */
- strncpy(locus,&lm_fd->lline[12],sizeof(locus));
- if ((bp=strchr(locus,' '))!=NULL) *(bp+1) = '\0';
-
- /* get description */
- fgets(desc,sizeof(desc),lm_fd->libf);
- while (desc[0]!='D' || desc[1]!='E' || strncmp(desc,"DEFINITION",10))
- fgets(desc,sizeof(desc),lm_fd->libf);
- if ((bp = strchr(&desc[12],'\n'))!=NULL) *bp='\0';
-
- /* get accession */
- fgets(acc,sizeof(acc),lm_fd->libf);
- while (acc[0]!='A' || acc[1]!='C' || strncmp(acc,"ACCESSION",9)) {
- fgets(acc,sizeof(acc),lm_fd->libf);
- if (acc[0]=='O' && acc[1]=='R' && strncmp(acc,"ORIGIN",6)==0)
- break;
- }
- if ((bp = strchr(&acc[12],'\n'))!=NULL) *bp='\0';
- if ((bp = strchr(&acc[12],' '))!=NULL) *bp='\0';
-
- /* get version */
- fgets(ver,sizeof(ver),lm_fd->libf);
- while (ver[0]!='V' || ver[1]!='E' || strncmp(ver,"VERSION",7)) {
- fgets(ver,sizeof(ver),lm_fd->libf);
- if (ver[0]=='O' && ver[1]=='R' && strncmp(ver,"ORIGIN",6)==0)
- break;
- }
- if ((bp = strchr(&ver[12],'\n'))!=NULL) *bp='\0';
-
- /* extract gi:123456 from version line */
- bp_gid = strchr(&ver[12],':');
- if (bp_gid != NULL) {
- if ((bp=strchr(bp_gid+1,' '))!=NULL) *bp='\0';
- bp_gid++;
- }
- if ((bp = strchr(&ver[12],' '))!=NULL) *bp='\0';
-
- /* build up FASTA header line */
- if (bp_gid != NULL) {
- strncpy(libstr,"gi|",n_libstr-1);
- strncat(libstr,bp_gid,n_libstr-4);
- strncat(libstr,"|gb|",n_libstr-20);
- }
- else {libstr[0]='\0';}
-
- /* if we have a version number, use it, otherwise accession,
- otherwise locus/description */
-
- if (ver[0]=='V') {
- strncat(libstr,&ver[12],n_libstr-1-strlen(libstr));
- strncat(libstr,"|",n_libstr-1-strlen(libstr));
- }
- else if (acc[0]=='A') {
- strncat(libstr,&acc[12],n_libstr-1-strlen(libstr));
- strncat(libstr," ",n_libstr-1-strlen(libstr));
- }
-
- strncat(libstr,locus,n_libstr-1-strlen(libstr));
- strncat(libstr,&desc[11],n_libstr-1-strlen(libstr));
- libstr[n_libstr-1]='\0';
-}
-
-
-/* this code seeks to provide both the various accession numbers
- necessary to identify the sequence, and also some description.
-
- Unfortunately, the various contributors to Genbank use three
- slightly different formats for including the accession number.
-
-(1)LOCUS HSJ214M20 107422 bp DNA HTG 16-JUN-2000
- DEFINITION Homo sapiens chromosome 6 clone RP1-214M20 map p12.1-12.3, ***
- SEQUENCING IN PROGRESS ***, in unordered pieces.
- ACCESSION AL121969
-
-(2)LOCUS AL359201 117444 bp DNA HTG 15-JUN-2000
- DEFINITION Homo sapiens chromosome 1 clone RP4-671C13 map p13.2-21.1, ***
- SEQUENCING IN PROGRESS ***, in unordered pieces.
- ACCESSION AL359201
-
-(3)LOCUS BB067000 280 bp mRNA EST 19-JUN-2000
- DEFINITION BB067000 RIKEN full-length enriched, 15 days embryo male testis Mus
- musculus cDNA clone 8030456L01 3', mRNA sequence.
- ACCESSION BB067000
-
-This makes it more difficult to both provide the accession number in a
-standard location and to conserve definition space
-*/
-
-void
-lranlib(char *str,
- int cnt,
- fseek_t seek,
- char *libstr,
- struct lmf_str *lm_fd)
-{
- char *bp, acc[MAX_STR], desc[MAX_STR];
-
- FSEEK(lm_fd->libf, seek, 0);
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- if (lm_fd->lfflag) getc(lm_fd->libf);
-
- lget_ann(lm_fd, str, cnt);
- str[cnt-1]='\0';
-
- FSEEK(lm_fd->libf,seek,0);
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- if (lm_fd->lfflag) getc(lm_fd->libf);
-}
-
-int
-pgetlib(unsigned char *seq,
- int maxs,
- char *libstr,
- int n_libstr,
- fseek_t *libpos,
- int *lcont,
- struct lmf_str *lm_fd,
- long *l_off)
-{
- int ic;
- register unsigned char *cp, *seqp;
- register int *ap;
- unsigned char *seqm, *seqm1;
-
- *l_off = 1;
-
- seqp = seq;
- seqm = &seq[maxs-11];
- seqm1 = seqm-1;
-
- ap = lm_fd->sascii;
-
- if (*lcont==0) {
- while (lm_fd->lline[0]!='E' || lm_fd->lline[1]!='N' || strncmp(lm_fd->lline,"ENTRY",5))
- { /* find ENTRY */
- lm_fd->lpos = FTELL(lm_fd->libf);
- if (fgets(lm_fd->lline,MAX_STR,lm_fd->libf)==NULL) return (-1);
- }
- strncpy(libstr,&lm_fd->lline[16],8);
- libstr[8]='\0';
- *libpos = lm_fd->lpos;
- while (lm_fd->lline[2]!='Q' || lm_fd->lline[0]!='S' || strncmp(lm_fd->lline,"SEQUENCE",8))
- { /* find SEQUENCE */
- if (fgets(lm_fd->lline,MAX_STR,lm_fd->libf)==NULL) return (-1);
- }
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf); /* get the extra line */
- }
- else {
- for (cp= lm_fd->cpsave; seqp<seqm1; ) {
- if ((*seqp++=ap[*cp++])<NA) continue;
- if (*(--seqp)>NA) break;
- }
- if (*seqp==ES) goto done;
- }
-
- lm_fd->lline[0]='\0';
- while (seqp<seqm1 && fgets(lm_fd->lline,MAX_STR,lm_fd->libf)!=NULL) {
- if (lm_fd->lline[0]=='/') goto new;
- for (cp= (unsigned char *)&lm_fd->lline[8]; seqp<seqm1; ) {
- if ((*seqp++=ap[*cp++])<NA) continue;
- if (*(--seqp)>NA) break;
- };
- if (*seqp==ES) goto done;
- }
- goto done;
-new:
- lm_fd->lpos = FTELL(lm_fd->libf);
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
-
-done:
- if (seqp>=seqm1) {
- lm_fd->cpsave = cp;
- (*lcont)++;
- }
- else *lcont=0;
-
- *seqp = EOSEQ;
- /* if ((int)(seqp-seq)==0) return 1; */
- return (int)(seqp-seq);
-}
-
-void
-pranlib(char *str,
- int cnt,
- fseek_t seek,
- char *libstr,
- struct lmf_str *lm_fd)
-{
- char *bp;
-
- FSEEK(lm_fd->libf, seek, 0);
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
-
- strncpy(str,&lm_fd->lline[16],8);
- str[8]='\0';
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- while (lm_fd->lline[0]!='T' || lm_fd->lline[1]!='I' || strncmp(lm_fd->lline,"TITLE",5))
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- strncpy(&str[8],&lm_fd->lline[16],cnt-9);
- str[cnt-9]='\0';
- if ((bp = strchr(str,'\n'))!=NULL) *bp='\0';
-
- FSEEK(lm_fd->libf,seek,0);
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
-}
-
-int
-egetlib(unsigned char *seq,
- int maxs,
- char *libstr,
- int n_libstr,
- fseek_t *libpos,
- int *lcont,
- struct lmf_str *lm_fd,
- long *l_off)
-{
- int ll;
- int ic;
- register unsigned char *cp, *seqp;
- register int *ap;
- unsigned char *seqm, *seqm1;
- char id[11]; /* Holds Identifier */
-
- *l_off=1;
-
- seqp = seq;
- seqm = &seq[maxs-11];
- seqm1 = seqm-1;
-
- ap = lm_fd->sascii;
-
- if (*lcont==0) {
- while (lm_fd->lline[0]!='I' || lm_fd->lline[1]!='D') { /* find ID */
- lm_fd->lpos = FTELL(lm_fd->libf);
- if (fgets(lm_fd->lline,MAX_STR,lm_fd->libf)==NULL) return (-1);
- if (lm_fd->lfflag) getc(lm_fd->libf);
- }
- sscanf(&lm_fd->lline[5],"%s",id);
- sprintf(libstr,"%-12.12s",id);
- libstr[12]='\0';
- *libpos = lm_fd->lpos;
- while (lm_fd->lline[0]!='S' || lm_fd->lline[1]!='Q') { /* find ORIGIN */
- if (fgets(lm_fd->lline,MAX_STR,lm_fd->libf)==NULL) return (-1);
- if (lm_fd->lfflag) getc(lm_fd->libf);
- }
- sscanf(&lm_fd->lline[14],"%ld",&lm_fd->gcg_len);
- }
- else {
- for (cp= lm_fd->cpsave; seqp<seqm1; ) {
- if ((*seqp++=ap[*cp++])<NA) continue;
- if (*(--seqp)>NA) break;
- }
- if (*seqp==ES) goto done;
- }
-
- lm_fd->lline[0]='\0';
- while (seqp<seqm1 && fgets(lm_fd->lline,MAX_STR,lm_fd->libf)!=NULL) {
- if (lm_fd->lfflag) getc(lm_fd->libf);
- if (lm_fd->lline[0]=='/') goto new;
- lm_fd->lline[70]='\0';
- for (cp= (unsigned char *)&lm_fd->lline[5]; seqp<seqm1; ) {
- if ((*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA) continue;
- if (*(--seqp)>NA) break;
- }
- if (*seqp==ES) goto done;
- }
- goto done;
-new: lm_fd->lpos = FTELL(lm_fd->libf);
-fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
-if (lm_fd->lfflag) getc(lm_fd->libf);
-goto done;
-
-done: if (seqp>=seqm1) {
- lm_fd->cpsave = cp;
- (*lcont)++;
- lm_fd->gcg_len -= (long)(seqp-seq);
-}
-else *lcont=0;
-
-*seqp = EOSEQ;
-/* if ((int)(seqp-seq)==0) return 1; */
-/* if (*lcont==0 && (long)(seqp-seq)!=lm_fd->gcg_len)
- printf("%s read %d of %d\n",libstr,(int)(seqp-seq),lm_fd->gcg_len);
- */
-return (int)(seqp-seq);
-}
-
-void
-eranlib(char *str,
- int cnt,
- fseek_t seek,
- char *libstr,
- struct lmf_str *lm_fd)
-{
- char *bp;
- char id[11]; /* Holds Identifier */
-
- FSEEK(lm_fd->libf, seek, 0);
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- if (lm_fd->lfflag) getc(lm_fd->libf);
-
- sscanf(&lm_fd->lline[5],"%s",id);
- sprintf(str,"%-10.10s ",id);
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- if (lm_fd->lfflag) getc(lm_fd->libf);
- while (lm_fd->lline[0]!='D' || lm_fd->lline[1]!='E') fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- strncpy(&str[11],&lm_fd->lline[5],cnt-11);
- str[cnt-11]='\0';
- if ((bp = strchr(str,'\r'))!=NULL) *bp='\0';
- if ((bp = strchr(str,'\n'))!=NULL) *bp='\0';
-
- FSEEK(lm_fd->libf,seek,0);
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- if (lm_fd->lfflag) getc(lm_fd->libf);
-}
-
-int
-igetlib(unsigned char *seq,
- int maxs,
- char *libstr,
- int n_libstr,
- fseek_t *libpos,
- int *lcont,
- struct lmf_str *lm_fd,
- long *l_off)
-{
- register unsigned char *cp, *seqp;
- register int *ap;
- unsigned char *seqm, *seqm1;
- char *bp;
-
- *l_off = 1;
-
- seqp = seq;
- seqm = &seq[maxs-9];
- seqm1 = seqm-1;
-
- ap = lm_fd->sascii;
-
- if (*lcont==0) {
- while (lm_fd->lline[0]!=';') {
- lm_fd->lpos = FTELL(lm_fd->libf);
- if (fgets(lm_fd->lline,MAX_STR,lm_fd->libf)==NULL) return (-1);
- }
- *libpos = lm_fd->lpos;
- while (lm_fd->lline[0]==';') fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- strncpy(libstr,lm_fd->lline+1,12);
- libstr[12]='\0';
- if((bp=strchr(libstr,'\n'))!=NULL) *bp='\0';
- }
-
- lm_fd->lline[0]='\0';
- while (seqp<seqm1 && fgets((char *)seqp,(size_t)(seqm-seqp),lm_fd->libf)!=NULL) {
- if (*seqp=='>') goto new;
- if (*seqp==';') {
- if (strchr((char *)seqp,'\n')==NULL) goto cont;
- continue;
- }
- for (cp=seqp; seqp<seqm1; ) {
- if ((*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA) continue;
- if (*(--seqp)>NA) break;
- }
- if (*seqp==ES) goto done;
- lm_fd->lpos = FTELL(lm_fd->libf);
- }
- goto done;
-new: strncpy(lm_fd->lline,(char *)seqp,MAX_STR);
- lm_fd->lline[MAX_STR-1]='\0';
- if (strchr((char *)seqp,'\n')==NULL)
- fgets(lm_fd->lline,MAX_STR-strlen(lm_fd->lline),lm_fd->libf);
- goto done;
-
-cont:
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- seqm1 = seqp;
-
-done: if (seqp>=seqm1) {
- (*lcont)++;
- }
- else {
- *lcont=0;
- }
-
-
- *seqp = EOSEQ;
- /* if ((int)(seqp-seq)==0) return 1; */
- return (int)(seqp-seq);
- }
-
-void
-iranlib(char *str,
- int cnt,
- fseek_t seek,
- char *libstr,
- struct lmf_str *lm_fd)
-{
- char *bp;
- char tline[MAX_FN];
-
- FSEEK(lm_fd->libf, seek, 0);
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
-
- if (lm_fd->lline[0]=='>' || lm_fd->lline[0]==';') {
- strncpy(tline,lm_fd->lline+1,sizeof(tline));
- tline[sizeof(tline)-1]='\0';
- if ((bp = strchr(tline,'\n'))!=NULL) *bp='\0';
- }
- else {
- tline[0]='\0';
- }
-
- while (lm_fd->lline[0]==';') fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- if ((bp=strchr(lm_fd->lline,'\n'))!=NULL) *bp=0;
- if ((bp=strchr(lm_fd->lline,' '))!=NULL) *bp=0;
- strncpy(str,lm_fd->lline,cnt);
- str[cnt-1]='\0';
- strncat(str," ",cnt-strlen(str)-1);
- strncat(str,tline,cnt-strlen(str)-1);
-
- FSEEK(lm_fd->libf,seek,0);
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- }
-
-int
-vgetlib(unsigned char *seq,
- int maxs,
- char *libstr,
- int n_libstr,
- fseek_t *libpos,
- int *lcont,
- struct lmf_str *lm_fd,
- long *l_off)
-{
- int i, ich;
- register unsigned char *cp, *seqp;
- register int *ap;
- unsigned char *seqm, *seqm1;
- char *bp, *tp;
-
- *l_off = 1;
-
- seqp = seq;
- seqm = &seq[maxs-9];
- seqm1 = seqm-1;
-
- ap = lm_fd->sascii;
-
- if (*lcont==0) {
- while (lm_fd->lline[0]!='>' && lm_fd->lline[0]!=';') {
- lm_fd->lpos = FTELL(lm_fd->libf);
- if (fgets(lm_fd->lline,MAX_STR,lm_fd->libf)==NULL) return (-1);
- if (lm_fd->lfflag) getc(lm_fd->libf);
- }
-
-#ifdef SUPERFAMNUM
- if ((bp=strchr(&lm_fd->lline[1],' ')) &&
- (bp=strchr(bp+1,SFCHAR))) {
- i=0;
- if ((tp = strtok(bp+1," \t\n"))!=NULL) sfnum[i++] = atoi(tp);
- while ((tp = strtok(NULL," \t")) != NULL) {
- sfnum[i++] = atoi(tp);
- if (i>=10) break;
- }
- sfnum[nsfnum=i]= 0;
- if (nsfnum>1) sf_sort(sfnum,nsfnum);
- else {
- if (nsfnum < 1) fprintf(stderr," found | but no sfnum: %s\n",libstr);
- }
- }
- else sfnum[0]=nsfnum=0;
-#endif
-
- if ((bp=strchr(lm_fd->lline,'\n'))!=NULL) *bp='\0';
- strncpy(libstr,&lm_fd->lline[4],12);
- libstr[12]='\0';
- if ((bp=strchr(libstr,' '))!=NULL) *bp='\0';
- if ((bp=strchr(libstr,'\n'))!=NULL) *bp='\0';
-
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- if (lm_fd->lfflag) getc(lm_fd->libf);
-
- if (n_libstr > 21) {
- strcat(libstr," ");
- strncat(libstr,lm_fd->lline,n_libstr-1-strlen(libstr));
- if ((bp=strchr(libstr,'\n'))!=NULL) *bp='\0';
- libstr[n_libstr-1]='\0';
- }
- *libpos = lm_fd->lpos;
- }
-
- lm_fd->lline[0]='\0';
- while (seqp<seqm1 && fgets((char *)seqp,(size_t)(seqm-seqp),lm_fd->libf)!=NULL) {
- if (lm_fd->lfflag && (ich=getc(lm_fd->libf))!=LFCHAR) ungetc(ich,lm_fd->libf);
- if (*seqp=='>') goto new;
- if (*seqp==';') {
- if (strchr((char *)seqp,'\n')==NULL) goto cont;
- continue;
- }
- for (cp=seqp; seqp<seqm1; ) {
- if ((*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA) continue;
- if (*(--seqp)>NA) break;
- }
- if (*seqp==ES) goto done;
- lm_fd->lpos = FTELL(lm_fd->libf);
- }
- goto done;
-new:
- strncpy(lm_fd->lline,(char *)seqp,MAX_STR);
- lm_fd->lline[MAX_STR-1]='\0';
- if (strchr((char *)seqp,'\n')==NULL) {
- fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR-strlen(lm_fd->lline),lm_fd->libf);
- if (lm_fd->lfflag && (ich=getc(lm_fd->libf))!=LFCHAR) ungetc(ich,lm_fd->libf);
- }
- goto done;
-
-cont:
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- if (lm_fd->lfflag && (ich=getc(lm_fd->libf))!=LFCHAR) ungetc(ich,lm_fd->libf);
- seqm1 = seqp;
-
-done:
- if (seqp>=seqm1) {
- (*lcont)++;
- }
- else {
- *lcont=0;
- }
-
- *seqp = EOSEQ;
- /* if ((int)(seqp-seq)==0) return 1;*/
- return (int)(seqp-seq);
-}
-
-void
-vranlib(char *str,
- int cnt,
- fseek_t seek,
- char *libstr,
- struct lmf_str *lm_fd)
-{
- char *bp, *llp;
-
- FSEEK(lm_fd->libf, seek, 0);
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- if (lm_fd->lfflag) getc(lm_fd->libf);
-
- if (lm_fd->lline[0]=='>'&&(lm_fd->lline[3]==';'||lm_fd->lline[3]=='>')) {
- strncpy(str,&lm_fd->lline[4],cnt-1);
- str[cnt-1]='\0';
-
- if ((bp = strchr(str,':'))!=NULL) *bp='\0';
- if ((bp=strchr(str,'\r'))!=NULL) *bp='\0';
- else if ((bp = strchr(str,'\n'))!=NULL) *bp='\0';
- else str[cnt-1]='\0';
-
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- if (lm_fd->lfflag) getc(lm_fd->libf);
-
- /* skip over redundant stuff */
- for (llp=lm_fd->lline,bp=str; *llp==*bp; llp++,bp++);
- if ((int)(llp-lm_fd->lline)<5) llp = lm_fd->lline;
-
- if ((bp=strchr(llp,'\r'))!=NULL) *bp=' ';
- if ((bp=strchr(llp,'\n'))!=NULL) *bp='\0';
- strncat(str," ",(size_t)1);
- strncat(str,llp,(size_t)cnt-strlen(str)-1);
- }
- else {
- str[0]='\0';
- }
-
- FSEEK(lm_fd->libf,seek,0);
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- if (lm_fd->lfflag) getc(lm_fd->libf);
-}
-
-static int gcg_bton[4]={2,4,1,3};
-
-int
-gcg_getlib(unsigned char *seq,
- int maxs,
- char *libstr,
- int n_libstr,
- fseek_t *libpos,
- int *lcont,
- struct lmf_str *lm_fd,
- long *l_off)
-{
- char dummy[20];
- char gcg_date[10];
- register unsigned char *cp, *seqp, stmp;
- register int *ap;
- char gcg_type[10];
- unsigned char *seqm, *seqm1;
- long r_block, b_block;
- char *bp;
-
- *l_off = 1;
-
- seqp = seq;
- seqm = &seq[maxs-9];
- seqm1 = seqm-1;
-
- ap = lm_fd->sascii;
-
- if (*lcont==0) {
- while (lm_fd->lline[0]!='>' && lm_fd->lline[0]!=';') {
- lm_fd->lpos = FTELL(lm_fd->libf);
- if (fgets(lm_fd->lline,MAX_STR,lm_fd->libf)==NULL) return (-1);
- }
- sscanf(&lm_fd->lline[4],"%s %s %s %s %ld",
- libstr,gcg_date,gcg_type,dummy,&(lm_fd->gcg_len));
-
- lm_fd->gcg_binary = (gcg_type[0]=='2');
-
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- while (strchr((char *)lm_fd->lline,'\n')==NULL) {
- if (strlen(lm_fd->lline)<MAX_STR/2)
- fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR/2,lm_fd->libf);
- else
- fgets(&lm_fd->lline[strlen(lm_fd->lline)-MAX_STR/2],MAX_STR/2,lm_fd->libf);
- }
- lm_fd->lline[MAX_STR-1]='\0';
- if (n_libstr <= 21) {
- libstr[12]='\0';
- }
- else {
- strncat(libstr," ",1);
- strncat(libstr,lm_fd->lline,n_libstr-1-strlen(libstr));
- if ((bp = strchr(libstr,'\n'))!=NULL) *bp='\0';
- libstr[n_libstr-1]='\0';
- }
- *libpos = lm_fd->lpos;
- }
-
- lm_fd->lline[0]='\0';
-
- r_block = b_block = min((size_t)(seqm-seqp),lm_fd->gcg_len);
- if (lm_fd->gcg_binary) { r_block = (r_block+3)/4; }
-
- fread((char *)seqp,(size_t)r_block,(size_t)1,lm_fd->libf);
- if (!lm_fd->gcg_binary)
- for (cp=seqp; seqp<seq+r_block; ) *seqp++ = ap[*cp++];
- else if (lm_fd->gcg_binary) {
- seqp = seq + r_block;
- cp = seq + 4*r_block;
- while (seqp > seq) {
- stmp = *--seqp;
- *--cp = gcg_bton[stmp&3];
- *--cp = gcg_bton[(stmp >>= 2)&3];
- *--cp = gcg_bton[(stmp >>= 2)&3];
- *--cp = gcg_bton[(stmp >>= 2)&3];
- }
- }
- if (4 * r_block >= lm_fd->gcg_len) {
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
- *lcont = 0;
- }
- else {
- if (lm_fd->gcg_binary) b_block = 4*r_block;
- lm_fd->gcg_len -= b_block;
- (*lcont)++;
- }
-
- seq[b_block] = EOSEQ;
- /* if (b_block==0) return 1; else */
- return b_block;
-}
-
-void
-gcg_ranlib(char *str,
- int cnt,
- fseek_t seek,
- char *libstr,
- struct lmf_str *lm_fd)
-{
- char *bp, *bp1, *llp;
-
- FSEEK(lm_fd->libf, seek, 0);
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
-
- if (lm_fd->lline[0]=='>'&&(lm_fd->lline[3]==';'||lm_fd->lline[3]=='>')) {
- strncpy(str,&lm_fd->lline[4],cnt-1);
- str[cnt-1]='\0';
- if ((bp = strchr(str,' '))!=NULL) *bp='\0';
- else if ((bp=strchr(str,'\r'))!=NULL) *bp='\0';
- else if ((bp = strchr(str,'\n'))!=NULL) *bp='\0';
- else str[cnt-1]='\0';
-
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
-
- /* check beginning of line it is a duplicate */
- for (llp=lm_fd->lline,bp=str; *llp == *bp; llp++,bp++);
- if ((int)(llp-lm_fd->lline)<5) llp = lm_fd->lline;
-
- /* here we would like to skip over some species stuff */
- /*
- if ((bp1 = strchr(llp,';'))!=NULL && (int)(bp1-llp)<50) {
- if ((bp2 = strchr(bp1+1,';'))!=NULL && (int)(bp2-bp1)<50) {
- *(bp2+1)='\0'; bp1 = bp2+2;
- }
- else {bp1=llp;}
- }
- else if ((bp1=strchr(llp,'.'))!=NULL && *(bp1+1)==' ') {
- *(bp1+1) = '\0'; bp1 += 2;}
- else bp1 = llp;
- */
-
- bp1 = llp;
- if ((bp=strchr(bp1,'\r'))!=NULL) *bp='\0';
- if ((bp=strchr(bp1,'\n'))!=NULL) *bp='\0';
- strncat(str," ",(size_t)1);
- strncat(str,bp1,(size_t)cnt-strlen(str));
- if (bp1!=llp) strncat(str,llp,(size_t)cnt-strlen(str));
- }
- else {
- str[0]='\0';
- }
-
- FSEEK(lm_fd->libf,seek,0);
- fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
-}
-
-void
-sf_sort(s,n)
- int *s, n;
-{
- int gap, i, j;
- int itmp;
-
- if (n == 1) return;
-
- for (i=0; i<n-1; i++)
- if (s[i]>s[i+1]) goto l2;
- return;
-
-l2:
- for (gap=n/2; gap>0; gap/=2)
- for (i=gap; i<n; i++)
- for (j=i-gap; j>=0; j -= gap) {
- if (s[j] <= s[j+gap]) break;
- itmp = s[j];
- s[j]=s[j+gap];
- s[j+gap]=itmp;
- }
-}
git://source.jalview.org / jabaws.git / blobdiff