Delete unneeded directory

[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
deleted file mode 100644 (file)
index 79e9bc5..0000000
--- a/website/archive/binaries/mac/src/iupred/getquery.c
+++ /dev/null
@@ -1,120 +0,0 @@
-#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;
-}
-*/