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

[jabaws.git] / binaries / src / clustalw / src / alignment / AlignmentOutput.cpp

diff --git a/binaries/src/clustalw/src/alignment/AlignmentOutput.cpp b/binaries/src/clustalw/src/alignment/AlignmentOutput.cpp
index a0b9de3..2e658ce 100644 (file)
--- a/binaries/src/clustalw/src/alignment/AlignmentOutput.cpp
+++ b/binaries/src/clustalw/src/alignment/AlignmentOutput.cpp
@@ -1067,6 +1067,9 @@ void AlignmentOutput::nexusOut(Alignment* alignPtr, outputRegion partToOutput)
         (*nexusOutFile) << "dimensions ntax=" << alignPtr->getNumSeqs() 
                         << " nchar=" << length << ";\n"; //- nige
         (*nexusOutFile) << "format missing=?\n";
+
+       // removed - bugzilla bug 204
+       /*
         (*nexusOutFile) << "symbols=\"";
         
         for(i = 0; i <= userParameters->getMaxAA(); i++)
@@ -1074,6 +1077,8 @@ void AlignmentOutput::nexusOut(Alignment* alignPtr, outputRegion partToOutput)
             (*nexusOutFile) << userParameters->getAminoAcidCode(i);
         }
         (*nexusOutFile) << "\"\n";
+       */
+
         (*nexusOutFile) << "interleave datatype=";
         bool _dnaFlag = userParameters->getDNAFlag();
         string _type = _dnaFlag ? "DNA " : "PROTEIN ";