JPRED-2 Add alscript to the Git repository

[jpred.git] / sources / alscript / src / agetbloc.c

diff --git a/sources/alscript/src/agetbloc.c b/sources/alscript/src/agetbloc.c
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+/****************************************************************************
+
+ AGETBLOC - a routine to read an AMPS block file
+
+   Copyright:  Geoffrey J. Barton (1992,1997)
+
+   email: geoff@ebi.ac.uk
+
+   Please see README for conditions of use.
+
+****************************************************************************
+
+History:
+
+15th November 1992 - ANSI C version - also uses GJ... routines.
+This version adapted with error messages for alscript.
+
+11th June 1992.
+Agetbloc:  like getbloc, but does not require that every character read into
+the seqs structure is an alphabetic character.  Also does not contain the 
+option to convert the "sequences" read in into integer format
+
+getbloc:  Read an AMPS style block file into the seqs array
+the nbloc aligned sequences are stored in positions 1-nbloc.
+
+This is a straight-ish translation of the fortran routine fbloc.f, hence
+the non-C like goto's...
+
+Sequence lengths are actual length +1 + 1.  This allows position 0 to 
+be reserved for future use, and preserves the '\0' for output.
+
+18/Feb/1993:Fix (i) to (i+1) in realloc.  Spotted by RBR.
+
+ $Id: agetbloc.c,v 1.2 1998/09/17 16:54:58 geoff Exp $
+ $Log: agetbloc.c,v $
+ Revision 1.2  1998/09/17 16:54:58  geoff
+ Check consistency with archive
+
+
+*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+#include "array.h"
+#include "gjutil.h"
+
+
+int Agetbloc(FILE *bfile,struct seqdat *bloc,int *nbloc)
+
+{
+    int i,llen;
+    extern int MAXnseq, MAXslen, MAXilen, MAXtlen, MAXnbloc;
+    char *buff;
+    extern FILE *std_in,*std_out,*std_err;
+
+    char *idstart, *idend, *bstart, sident = 0;
+    int idlen,totseq = 0,k,j;
+
+    buff = (char *) GJmalloc(sizeof(char) * MAXtlen);
+
+l1: 
+    buff = fgets(buff,MAXtlen,bfile);
+    if(buff == NULL){
+       fprintf(std_err,"Premature end of BLOCK FILE\n");
+       return 0;
+    }
+    if((idstart = strchr(buff,'>')) != NULL){
+       if(++totseq == MAXnbloc){
+           fprintf(std_err,
+           "Max Number of block file sequences exceeded: %d\n",
+           totseq);
+           fprintf(std_err,"Use MAX_NSEQ command to increase value");
+           return 0;
+       }
+       sident = 1;
+       idend = strchr(idstart,' ');
+       if(idend == NULL){
+         idend = strchr(idstart,'\0');
+       }
+       if(idend == NULL){
+         fprintf(std_err,"Error reading identifier:%s\n",idstart);
+         error("Exiting",1);
+       }
+       idlen = (idend - idstart) + 1;
+       bloc[totseq].id = (char *) malloc(sizeof(char) * idlen);
+       bloc[totseq].id = GJstrblank(bloc[totseq].id,idlen);
+       strncpy(bloc[totseq].id,idstart+1,idlen-1);   /* don't copy the ">" symbol */
+       bloc[totseq].ilen = idlen-1;
+       bloc[totseq].id[idlen-1] = '\0';
+
+       bloc[totseq].tlen = strlen(idend)+1;
+       bloc[totseq].title = (char *) GJmalloc(sizeof(char) * bloc[totseq].tlen);
+       bloc[totseq].title = GJstrblank(bloc[totseq].title,bloc[totseq].tlen);
+       strcpy(bloc[totseq].title,idend);
+
+       bloc[totseq].seq = (char *) GJmalloc(sizeof(char) * MAXslen);
+        bloc[totseq].seq[0] = ' ';
+       goto l1;
+    } else if(sident){
+       if((idstart = strchr(buff,'*')) != NULL){
+           i = 0;
+           while((buff = fgets(buff,MAXtlen,bfile)) != NULL){
+               if(*idstart == '*'){
+/*                 fprintf(stdout,"Blocfile read: Length: %d\n",i);*/
+                   ++i;
+                   for(k=1;k<totseq+1;++k){
+                       bloc[k].slen = i;
+                       bloc[k].seq[i] = '\0';
+                       bloc[k].seq = (char *) realloc(bloc[k].seq,sizeof(char)*(i+1)); /*i+1 fix suggested by rbr*/
+                   }
+                   *nbloc = totseq;
+                   free(buff);
+                   return 1;
+               }
+               bstart = idstart;
+               ++i;
+               if(i==MAXslen)error("Max Sequence length exceeded - use MAX_SEQ_LEN command to increase",1);
+               for(j=1;j<totseq+1;++j){
+                   /*cope with short lines */
+/*                 if(!isalnum(*bstart)) *bstart = ' '; */
+                   bloc[j].seq[i] = *bstart++;
+               }
+           }
+           fprintf(std_err,"No terminating * in blocfile\n");
+           return 0;
+       }else{
+         goto l1;
+       }
+    } else {
+       goto l1;
+    }
+}
+