+++ /dev/null
-/* ncbl_lib.c functions to read ncbi-blast format files from
- setdb (blastp 1.3.2) format files
-
- copyright (c) 1992 William R. Pearson
-*/
-
-/* $Name: fa_34_26_5 $ - $Id: ncbl_lib.c,v 1.9 2006/10/05 18:22:07 wrp Exp $ */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
-#ifndef WIN32
-#define RBSTR "r"
-#else
-#define RBSTR "rb"
-#endif
-
-#define XTERNAL
-#include "uascii.h"
-#include "upam.h"
-#include "ncbl_head.h"
-#include "mm_file.h"
-
-int ncbl_getliba(char *, int, char *, int, fseek_t *, int *, struct lmf_str *, long *);
-int ncbl_getlibn(char *, int, char *, int, fseek_t *, int *, struct lmf_str *, long *);
-
-void src_ulong_read();
-
-#ifndef NCBL13_ONLY
-static void src_char_read();
-static void newname(char *, char *, char *, int);
-#else
-void src_char_read();
-void newname(char *, char *, char *, int);
-#endif
-
-/* nt_btoa maps from blast 2bit format to ascii characters */
-static char nt_btoa[5] = {"ACGT"};
-
-static char aa_btoa[27]= {"-ARNDCQEGHILKMFPSTWYVBZX*"};
-static int aa_btof[32]; /* maps to fasta alphabet */
-
-static FILE *tfile=NULL, /* table of offsets, also DB info */
- *hfile=NULL, /* description lines */
- *sfile=NULL; /* binary sequence data */
-
-static unsigned long lib_cnt, max_cnt, totlen, mxlen, dbline_len;
-static unsigned long *seq_beg, *hdr_beg;
-static unsigned char *ambiguity_ray;
-static long seq_format, dbtype, dbformat;
-static char dline[512];
-
-#define NCBIBL13 11
-
-struct lmf_str *
-ncbl_openlib(char *name, int ldnaseq)
-{
- char hname[256];
- char sname[256];
- char tname[256];
- long title_len;
- char *title_str;
- int rdtmp;
- int i;
- unsigned long line_len, c_len, clean_count;
-
- if (ldnaseq!=1) {
- newname(tname,name,AA_TABLE_EXT,(int)sizeof(tname));
- if ((tfile = fopen(tname,RBSTR))==NULL) {
- fprintf(stderr," cannot open %s (%s.%s) table file\n",
- name,tname,NT_TABLE_EXT);
- return (-1);
- }
- seq_format = AAFORMAT;
- }
- else {
- newname(tname,name,NT_TABLE_EXT,(int)sizeof(tname));
- if ((tfile = fopen(tname,RBSTR))==NULL) {
- fprintf(stderr," cannot open %s (%s.%s) table file\n",
- name,tname,NT_TABLE_EXT);
- return (-1);
- }
- seq_format = NTFORMAT;
- }
-
- src_ulong_read(tfile,&dbtype);
- src_ulong_read(tfile,&dbformat);
-
- if (seq_format == AAFORMAT && (dbformat != seq_format || dbtype !=
- DB_TYPE_PRO)) {
- fprintf(stderr,"error - %s wrong type (%ld/%d) or format (%ld/%ld)\n",
- tname,dbtype,DB_TYPE_PRO,dbformat,seq_format);
- return (-1);
- }
- else if (seq_format == NTFORMAT && (dbformat != seq_format || dbtype !=
- DB_TYPE_NUC)) {
- fprintf(stderr,"error - %s wrong type (%ld/%d) or format (%ld/%ld)\n",
- tname,dbtype,DB_TYPE_NUC,dbformat,seq_format);
- return (-1);
- }
-
- if (seq_format == AAFORMAT) {
- newname(hname,name,AA_HEADER_EXT,(int)sizeof(hname));
- if ((hfile = fopen(hname,RBSTR))==NULL) {
- fprintf(stderr," cannot open %s header file\n",hname);
- return (-1);
- }
- newname(sname,name,AA_SEARCHSEQ_EXT,(int)sizeof(sname));
- if ((sfile = fopen(sname,RBSTR))==NULL) {
- fprintf(stderr," cannot open %s sequence file\n",sname);
- return (-1);
- }
- }
- else {
- newname(hname,name,NT_HEADER_EXT,(int)sizeof(hname));
- if ((hfile = fopen(hname,RBSTR))==NULL) {
- fprintf(stderr," cannot open %s header file\n",hname);
- return (-1);
- }
- newname(sname,name,NT_SEARCHSEQ_EXT,(int)sizeof(sname));
- if ((sfile = fopen(sname,RBSTR))==NULL) {
- fprintf(stderr," cannot open %s sequence file\n",sname);
- return (-1);
- }
- }
-
-/* all files should be open */
-
- src_ulong_read(tfile,&title_len);
- rdtmp = title_len + ((title_len%4 !=0 ) ? 4-(title_len%4) : 0);
- if ((title_str = calloc((size_t)rdtmp,sizeof(char)))==NULL) {
- fprintf(stderr," cannot allocate title string (%d)\n",rdtmp);
- return(-1);
- }
- fread(title_str,(size_t)1,(size_t)rdtmp,tfile);
-
- lib_cnt = 0;
- if (seq_format == AAFORMAT) {
- src_ulong_read(tfile,&max_cnt);
- src_ulong_read(tfile,&totlen);
- src_ulong_read(tfile,&mxlen);
-
- /* fprintf(stderr," max_cnt: %d, totlen: %d\n",max_cnt,totlen); */
-
- if ((seq_beg=(unsigned long *)calloc((size_t)max_cnt+1,sizeof(long)))==NULL) {
- fprintf(stderr," cannot allocate sequence pointers\n");
- return -1;
- }
- if ((hdr_beg=(unsigned long *)calloc((size_t)max_cnt+1,sizeof(long)))==NULL) {
- fprintf(stderr," cannot allocate header pointers\n");
- return -1;
- }
- for (i=0; i<max_cnt+1; i++) src_ulong_read(tfile,&seq_beg[i]);
- for (i=0; i<max_cnt+1; i++) src_ulong_read(tfile,&hdr_beg[i]);
-
- for (i=0; i<sizeof(aa_btoa); i++) {
- if ((rdtmp=aascii[aa_btoa[i]])<NA) aa_btof[i]=rdtmp;
- else aa_btof[i]=aascii['X'];
- }
- }
- else if (seq_format == NTFORMAT) {
- src_ulong_read(tfile,&dbline_len); /* length of uncompress DB lines */
- src_ulong_read(tfile,&max_cnt); /* number of entries */
- src_ulong_read(tfile,&mxlen); /* maximum length sequence */
- src_ulong_read(tfile,&totlen); /* total count */
- src_ulong_read(tfile,&c_len); /* compressed db length */
- src_ulong_read(tfile,&clean_count); /* count of nt's cleaned */
-
- fseek(tfile,(size_t)((clean_count)*4),1);
- /* seek over clean_count */
- if ((seq_beg=(unsigned long *)calloc((size_t)max_cnt+1,sizeof(long)))==NULL) {
- fprintf(stderr," cannot allocate sequence pointers\n");
- return -1;
- }
- if ((hdr_beg=(unsigned long *)calloc((size_t)max_cnt+1,sizeof(long)))==NULL) {
- fprintf(stderr," cannot allocate header pointers\n");
- return -1;
- }
- if ((ambiguity_ray=
- (unsigned char *)calloc((size_t)max_cnt/CHAR_BIT+1,sizeof(char)))==NULL) {
- fprintf(stderr," cannot allocate ambiguity_ray\n");
- return -1;
- }
-
- for (i=0; i<max_cnt+1; i++) src_ulong_read(tfile,&seq_beg[i]);
- fseek(tfile,(size_t)((max_cnt+1)*4),1);
- /* seek over seq_beg */
- for (i=0; i<max_cnt+1; i++) src_ulong_read(tfile,&hdr_beg[i]);
- for (i=0; i<max_cnt/CHAR_BIT+1; i++)
- src_char_read(tfile,&ambiguity_ray[i]);
- }
- return 1;
-}
-
-void ncbl_closelib()
-{
- if (tfile !=NULL ) {fclose(tfile); tfile=NULL;}
- if (hfile !=NULL ) {fclose(hfile); hfile=NULL;}
- if (sfile !=NULL ) {fclose(sfile); sfile=NULL;}
-}
-
-int
-ncbl_getliba(char *seq, int maxs,
- char *libstr, int n_libstr,
- fseek_t *libpos,
- int lcont)
-{
- register char *sptr;
- long seqcnt;
- long tmp;
- char ch;
- static long seq_len;
-
- *libpos = lib_cnt;
- if (*lcont==0) {
- if (lib_cnt >= max_cnt) return -1;
- seq_len = seq_beg[lib_cnt+1] - seq_beg[lib_cnt] -1;
- tmp=(long)fgetc(sfile); /* skip the null byte */
- if (tmp!=NULLB)
- fprintf(stderr," phase error: %ld:%ld found\n",lib_cnt,tmp);
- libstr[0]='\0';
- }
-
- if (seq_len < maxs) {
- if ((tmp=fread(seq,(size_t)1,(size_t)seq_len,sfile))!=(size_t)seq_len) {
- fprintf(stderr," could not read sequence record: %ld %ld != %ld\n",
- *libpos,tmp,seq_len);
- goto error;
- }
- if (aa_btoa[seq[seq_len-1]]=='*') seqcnt = seq_len-1;
- else seqcnt=seq_len;
- lib_cnt++;
- *lcont = 0;
- }
- else {
- if (fread(seq,(size_t)1,(size_t)(maxs-1),sfile)!=(size_t)(maxs-1)) {
- fprintf(stderr," could not read sequence record: %ld %ld\n",
- *libpos,seq_len);
- goto error;
- }
- (*lcont)++;
- seqcnt = maxs-1;
- seq_len -= seqcnt;
- }
- sptr = seq+seqcnt;
-
- while (--sptr >= seq) *sptr = aa_btof[*sptr];
-
- seq[seqcnt]= EOSEQ;
- return (seqcnt);
-
-error: fprintf(stderr," error reading %ld at %ld\n",libstr,*libpos);
- fflush(stderr);
- return (-1);
-}
-
-int
-ncbl_getlibn(char *seq, int maxs,
- char *libstr, int n_libstr,
- fseek_t *libpos, int *lcont)
-{
- register char *sptr, *tptr, stmp;
- long seqcnt;
- long tmp;
- char ch;
- static long seq_len;
- static int c_len,c_pad;
-
- *libpos = lib_cnt;
- if (*lcont==0) {
- if (lib_cnt >= max_cnt) return -1;
- c_len = seq_beg[lib_cnt+1]/(CHAR_BIT/NBPN)
- - seq_beg[lib_cnt]/(CHAR_BIT/NBPN);
- c_len -= NSENTINELS;
-
- seq_len = c_len*(CHAR_BIT/NBPN);
- c_pad = seq_beg[lib_cnt] & ((CHAR_BIT/NBPN)-1);
- if (c_pad != 0) seq_len -= ((CHAR_BIT/NBPN) - c_pad);
-
- tmp=fgetc(sfile); /* skip the null byte */
- if (tmp!=NT_MAGIC_BYTE) {
- fprintf(stderr," phase error: %ld:%ld (%ld/%d) found\n",
- lib_cnt,seq_len,tmp,NT_MAGIC_BYTE);
- goto error;
- }
- libstr[0]='\0';
- }
-
- if (seq_len < maxs-3) {
- seqcnt=(seq_len+3)/4;
- if (seqcnt==0) seqcnt++;
- if ((tmp=fread(seq,(size_t)1,(size_t)seqcnt,sfile))
- !=(size_t)seqcnt) {
- fprintf(stderr,
- " could not read sequence record: %s %ld %ld != %ld: %d\n",
- libstr,*libpos,tmp,seqcnt,*seq);
- goto error;
- }
- tmp=fgetc(sfile); /* skip the null byte */
- if (tmp!=(unsigned char)NT_MAGIC_BYTE) {
- fprintf(stderr," phase2 error: %ld:%ld (%ld/%d) next ",
- lib_cnt,seqcnt,tmp,NT_MAGIC_BYTE);
-
- goto error;
- }
- *lcont = 0;
- lib_cnt++;
- }
- else {
- seqcnt = ((maxs+3)/4)-1;
- if (fread(seq,(size_t)1,(size_t)(seqcnt),sfile)!=(size_t)(seqcnt)) {
- fprintf(stderr," could not read sequence record: %s %ld %ld\n",
- libstr,*libpos,seqcnt);
- goto error;
- }
- (*lcont)++;
- }
-
- /* point to the last packed byte and to the end of the array
- seqcnt is the exact number of bytes read
- tptr points to the destination, use multiple of 4 to simplify math
- sptr points to the source, note that the last byte will be read 4 cycles
- before it is written
- */
-
- sptr = seq + seqcnt;
- tptr = seq + 4*seqcnt;
- while (sptr>seq) {
- stmp = *--sptr;
- *--tptr = (stmp&3) +1;
- *--tptr = ((stmp >>= 2)&3)+1;
- *--tptr = ((stmp >>= 2)&3)+1;
- *--tptr = ((stmp >>= 2)&3)+1;
- }
- /*
- for (sptr=seq; sptr < seq+seq_len; sptr++) {
- printf("%c",nt[*sptr]);
- if ((int)(sptr-seq) % 60 == 59) printf("\n");
- }
- printf("\n");
- */
- if (seqcnt*4 >= seq_len) { /* there was enough room */
- seq[seq_len]= EOSEQ;
- /* printf("%d\n",seq_len); */
- return seq_len;
- }
- else { /* not enough room */
- seq[seqcnt*4]=EOSEQ;
- seq_len -= 4*seqcnt;
- return (4*seqcnt);
- }
-
-error: fprintf(stderr," error reading %ld at %ld\n",libstr,*libpos);
- fflush(stderr);
- return (-1);
-}
-
-void
-ncbl_ranlib(str,cnt,libpos)
- char *str; int cnt;
- long libpos;
-{
- char hline[256], *bp, *bp0;
- int llen;
- long spos;
-
- lib_cnt = libpos;
- llen = hdr_beg[lib_cnt+1]-hdr_beg[lib_cnt];
- if (llen > sizeof(hline)) llen = sizeof(hline);
- fseek(hfile,hdr_beg[lib_cnt]+1,0);
-
- fread(hline,(size_t)1,(size_t)(llen-1),hfile);
- hline[llen-1]='\0';
-
- if (hline[9]=='|' || hline[10]=='|') {
- bp0 = strchr(hline+3,'|');
- if ((bp=strchr(bp0+1,' '))!=NULL) *bp='\0';
- if (dbformat == NTFORMAT &&
- (ambiguity_ray[lib_cnt/CHAR_BIT]&(1<<lib_cnt%CHAR_BIT))) {
- sprintf(str,"*%-9s ",bp0+1);
- }
- else sprintf(str,"%-10s ",bp0+1);
- strncat(str+11,bp+1,cnt-strlen(str));
- }
- else {
- if (dbformat == NTFORMAT &&
- (ambiguity_ray[lib_cnt/CHAR_BIT]&(1<<lib_cnt%CHAR_BIT))) {
- str[0]='*';
- strncpy(str+1,hline,cnt-1);
- }
- else strncpy(str,hline,cnt);
- }
- str[cnt-1]='\0';
-
- if (dbformat == AAFORMAT)
- fseek(sfile,seq_beg[lib_cnt]-1,0);
- else {
- spos = (seq_beg[lib_cnt])/(CHAR_BIT/NBPN);
- fseek(sfile,spos-1,0);
- }
-}
-
-void src_ulong_read(fd, val)
- FILE *fd;
- unsigned long *val;
-{
-#ifdef IS_BIG_ENDIAN
- fread((char *)val,(size_t)4,(size_t)1,fd);
-#else
- unsigned char b[4];
-
- fread((char *)&b[0],(size_t)1,(size_t)4,fd);
- *val = 0;
- *val = (unsigned long)((unsigned long)((unsigned long)(b[0]<<8) +
- (unsigned long)b[1]<<8) + (unsigned long)b[2]<<8)+(unsigned long)b[3];
-#endif
-}
-
-void src_long_read(fd,val)
- FILE *fd;
- long *val;
-{
-#ifdef IS_BIG_ENDIAN
- fread((char *)val,(size_t)4,(size_t)1,fd);
-#else
- unsigned char b[4];
-
- fread((char *)&b[0],(size_t)1,(size_t)4,fd);
- *val = 0;
- *val = (long)((long)((long)(b[0]<<8)+(long)b[1]<<8)+(long)b[2]<<8)
- +(long)b[3];
-#endif
-}
-
-#ifndef NCBL13_ONLY
-static void
-#else
-void
-#endif
-src_char_read(fd, val)
- FILE *fd;
- char *val;
-{
- fread(val,(size_t)1,(size_t)1,fd);
-}
-
-#ifndef NCBL13_ONLY
-static void
-#else
-void
-#endif
-src_fstr_read(fd, val, slen)
- FILE *fd;
- char *val;
- long slen;
-{
- fread(val,(size_t)slen,(size_t)1,fd);
-}
-
-#ifndef NCBL13_ONLY
-static void
-#else
-void
-#endif
-newname(char *nname, char *oname, char *suff, int maxn)
-{
- char *tptr;
-
- if (oname[0]=='@') strncpy(nname,&oname[1],maxn);
- else strncpy(nname,oname,maxn);
- for (tptr=nname; *tptr=='.' && *tptr; tptr++);
- for (; *tptr!='.'&& *tptr; tptr++); /* get to '.' or EOS */
- *tptr++='.'; *tptr='\0';
- strncat(nname,suff,maxn);
-}
-
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