--- /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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