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

[jabaws.git] / binaries / src / clustalw / src / interface / CommandLineParser.cpp

diff --git a/binaries/src/clustalw/src/interface/CommandLineParser.cpp b/binaries/src/clustalw/src/interface/CommandLineParser.cpp
index 3d58c58..b970c70 100644 (file)
--- a/binaries/src/clustalw/src/interface/CommandLineParser.cpp
+++ b/binaries/src/clustalw/src/interface/CommandLineParser.cpp
@@ -116,7 +116,7 @@ CommandLineParser::CommandLineParser(StringArray* args, bool xmenus)
         seqNoArg = new StringArray(3);
         seqNoRangeArg = new StringArray(3);
         scoreArg = new StringArray(3);
-        outputArg = new StringArray(7);
+        outputArg = new StringArray(8);
         outputTreeArg = new StringArray(5);
         outputSecStrArg = new StringArray(5);
         cmdLineType = new StringArray(6);
@@ -167,7 +167,8 @@ CommandLineParser::CommandLineParser(StringArray* args, bool xmenus)
     (*outputArg)[3] = "phylip";
     (*outputArg)[4] = "nexus";
     (*outputArg)[5] = "fasta";
-    (*outputArg)[6] = "";
+    (*outputArg)[6] = "clustal";
+    (*outputArg)[7] = "";
     
     (*outputTreeArg)[0] = "nj";
     (*outputTreeArg)[1] = "phylip";
@@ -1479,8 +1480,8 @@ void CommandLineParser::setOptionalParam()
         #endif          
         if((*paramArg)[setOutput].length() > 0) 
         {
-            temp = findMatch((*paramArg)[setOutput], outputArg, 6);
-            if (temp >= 0 && temp <= 5) 
+            temp = findMatch((*paramArg)[setOutput], outputArg, 7);
+            if (temp >= 0 && temp <= 6) 
             {
                 userParameters->setOutputClustal(false);
                 userParameters->setOutputGCG(false);
@@ -1507,9 +1508,12 @@ void CommandLineParser::setOptionalParam()
                 case 4: // NEXUS
                     userParameters->setOutputNexus(true);
                     break;
-                case 5: // NEXUS
+                case 5: // FASTA
                     userParameters->setOutputFasta(true);
                     break;
+                case 6: // CLUSTAL
+                    userParameters->setOutputClustal(true);
+                    break;
                 default:
                     // FIXME AW: 1.83 behaves the same, but shouldnt
                     // we exit here?