Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / iupred / getquery.c

diff --git a/website/archive/binaries/mac/src/iupred/getquery.c b/website/archive/binaries/mac/src/iupred/getquery.c
new file mode 100644 (file)
index 0000000..79e9bc5
--- /dev/null
+++ b/website/archive/binaries/mac/src/iupred/getquery.c
@@ -0,0 +1,120 @@
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <ctype.h>
+
+#include "getquery.h"
+#include "gjutil.h"
+
+/* get the next sequence entry from a fasta format file and
+   return a pointer to a structure containing this information.
+
+   Format expected of the input file is:
+
+   >IDENT Title here 
+   ONE LETTER CODE SEQUENCE ON SEVERAL LINES
+   LIKE THIS
+   >NEXTIDENT  Next title etc.
+
+   The routine reads lines from the file until it finds one that starts
+   in '>'.  It then reads this line as an ID, title line before reading
+   all alphabetic characters that follow as the amino acid sequence.  
+   The sequence is terminated by the next '>' or End of File.
+
+   This means that the must ONLY contain sequences.  PIR format permits 
+   more flexibility in the input file.
+
+   NOTE:  This routine assumes that no line will be longer than the 
+   p->MAX_BUFFER_LEN.  Any program that calls this routine should
+   have p->MAX_BUFFER_LEN set suitably big.  This can be done by 
+   pre-checking the database file for line lengths.
+
+   Author: G. J. Barton (October 1995)
+
+*/
+   
+SEQS *gseq_fasta(FILE *seqfile)
+{
+
+  char *buff,*tbuff;
+  SEQS *ret_val;
+  int MAX_BUFFER_LEN = 10000;  
+  int MAX_SEQ_LEN = 10000; 
+  char *ident = NULL;
+  char *title = NULL;
+
+  GJ_S_COUNT j;
+  int c;
+  STD_FILES;
+
+  buff = (char *) GJmalloc(sizeof(char) * MAX_BUFFER_LEN);
+  tbuff = buff;
+
+  while((buff = fgets(buff,MAX_BUFFER_LEN,seqfile)) != NULL) {
+    if(buff[0] == '>') {
+      ret_val = (SEQS *) GJmalloc(sizeof(SEQS));
+      ident = strtok(&buff[1]," ");
+      if(ident != NULL) {
+       ident=GJremovechar2(ident,'\n');
+       ret_val->id = GJstrdup(ident);
+       ret_val->ilen = strlen(ident);
+      }else {
+       GJerror("Something strange with sequence identifier in fasta file");
+       fprintf(std_err,"Line:%s\n",buff);
+       return NULL;
+      }
+      title = strtok(NULL,"\n");
+      if(title != NULL) {
+       ret_val->title = GJstrdup(title);
+       ret_val->tlen = strlen(title);
+      }else {
+       /*      GJerror("Something strange with sequence title in fasta file");*/
+       /*      fprintf(std_err,"Line:%s\n",buff);*/
+       /*if(p->VERBOSE > 10)fprintf(std_err,"Title missing in FASTA file - Inserting dummy: %s\n",buff);*/
+       ret_val->title = GJstrdup("-");
+       ret_val->tlen = strlen(ret_val->title);
+       /*      return NULL;*/
+      }
+      ret_val->seq = (char *) GJmalloc(sizeof(char) * MAX_SEQ_LEN);
+      ret_val->seq[0] = ' ';
+      j = 0;
+      for(;;) {
+       c = fgetc(seqfile);
+       if(c == EOF || c == '>') {
+         ungetc(c,seqfile);
+         ret_val->seq[j] = '\0';
+         ret_val->slen = j;
+         ret_val->seq = (char *) GJrealloc(ret_val->seq,sizeof(char) * ret_val->slen);
+         GJfree(buff);
+         return ret_val;
+       }else if(isalpha(c)) {
+         if(j == (MAX_SEQ_LEN - 3)){
+           fprintf(std_err,"Sequence too long: %s (> %d residues):  Increase MAX_SEQ_LEN\n",
+                   ret_val->id,j);
+           exit(-1);
+         }
+         ret_val->seq[j++] = toupper(c);
+       }
+      }
+    }
+  }
+  GJfree(tbuff);
+  return(NULL);
+}
+
+/*
+int main(int argc, char **argv)
+{
+   FILE *fasta; 
+   SEQS *seq; 
+   fasta = fopen("/homes/pvtroshin/large.fasta", "r");
+       
+   do{
+     seq = gseq_fasta(fasta); 
+     if(seq!=NULL) printf("Seq: %s\n",seq->id );
+   } while(seq != NULL);
+
+   fclose(fasta);
+  return 0;
+}
+*/