JWS-112 Bumping version of ClustalW (src, binaries and windows) to version 2.1.

[jabaws.git] / binaries / src / clustalw / src / Clustal.cpp

diff --git a/binaries/src/clustalw/src/Clustal.cpp b/binaries/src/clustalw/src/Clustal.cpp
index 646b34a..453bcc0 100644 (file)
--- a/binaries/src/clustalw/src/Clustal.cpp
+++ b/binaries/src/clustalw/src/Clustal.cpp
@@ -1043,8 +1043,11 @@ int Clustal::profile2Input(string profile2Name)
     userParameters->setSeqName(profile2Name);
     userParameters->setProfile2Name(profile2Name);
 
+
     FileReader readProfileFile;
+    cout << "before profileInput\n";
     code = readProfileFile.profileInput(&alignmentObj);
+    cout << "after profileInput\n";
 
     if(!userParameters->getInteractive())
     {
@@ -1058,7 +1061,9 @@ int Clustal::profile2Input(string profile2Name)
             else
                 cerr << "ERROR: Unhandled error code (" << code << ") returned from profileInput.\n";
             // AW: should we really exit here? What if called from clustalx?
-            exit(2);
+            // DD: fixed
+            if(!userParameters->getGui())
+                exit(2);
         }
     }
     return code;