X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2Fclustalw%2Fsrc%2Falignment%2FAlignmentOutput.cpp;h=2e658ceb2092a336c4fb747de43a850035fd2ab8;hb=7c6018cf87e67d7ac21f5230284ef2162a19320f;hp=a0b9de3e5580f47f199f6adb769853e382309e11;hpb=1eab6cadc31107fabe7ef060de1ae91eeb4a025b;p=jabaws.git

diff --git a/binaries/src/clustalw/src/alignment/AlignmentOutput.cpp b/binaries/src/clustalw/src/alignment/AlignmentOutput.cpp
index a0b9de3..2e658ce 100644
--- 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 ";