From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Thu, 16 Jun 2011 13:35:08 +0000 (+0000)
Subject: Improvements to the code
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0a982a5ec8f74cf8bcaf923e4a747c863968858d;p=jabaws.git

Improvements to the code

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4273 e3abac25-378b-4346-85de-24260fe3988d
---

diff --git a/binaries/src/iupred/iupred b/binaries/src/iupred/iupred
index e02c906..ca86ab3 100644
Binary files a/binaries/src/iupred/iupred and b/binaries/src/iupred/iupred differ
diff --git a/binaries/src/iupred/iupred.c b/binaries/src/iupred/iupred.c
index 2d8b274..c5e25a2 100644
--- a/binaries/src/iupred/iupred.c
+++ b/binaries/src/iupred/iupred.c
@@ -85,9 +85,10 @@ int main(int argc, char **argv)
   if (argc<2) {
     printf(" Usage: %s seqfile type \n",argv[0]);
     printf("      where type stands for one of the options of \n");
-    printf("      \"long\", \"short\", \"glob\" or \"all\"\n");
+    printf("      \"long\", \"short\", \"glob\". If no type is provided the program assumes all types\n");
     exit(1);
   }
+
   if ((path=getenv("IUPred_PATH"))==NULL) {
     fprintf(stderr,"IUPred_PATH environment variable is not set\n");
     path="./";
@@ -105,8 +106,10 @@ int main(int argc, char **argv)
   printf("#\n");
   printf("#\n");
 
-
-  if ((strncmp(argv[2],"long",4))==0) {
+  if(argv[2]==NULL) {
+    type=3;
+  }
+  else if ((strncmp(argv[2],"long",4))==0) {
     type=0;   
   }
   else if ((strncmp(argv[2],"short",5))==0) {
@@ -115,22 +118,23 @@ int main(int argc, char **argv)
   else if ((strncmp(argv[2],"glob",4))==0) {
     type=2;   
   }
-  else if ((strncmp(argv[2],"all",3))==0) {
-    type=3;   
-  }
   else {
-    printf("No disorder type is given assuming long\n");
+    printf("Cannot recognise disorder type assuming long\n");
     type=0;
   }
 
+  FILE *fasta; 
+
+  if ((fasta=fopen(argv[1],"r"))==NULL) {
+    printf("Could not open %s\n",argv[1]),exit(1);
+  }
+
 /* Creating output files depending on the type */  
   createOutputFiles(type);
 
-
 /* Read input file sequence by sequence */
-   FILE *fasta; 
+
    SEQS *fastaseq; 
-   fasta = fopen(argv[1], "r");
 
    do {