added phylip as output file type for commands that output distance matrices. added...

[mothur.git] / pairwiseseqscommand.cpp

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index 1fa96e3e9d4c6cf8ce9a4e99af30d01c5562a009..f69faff477aee954801f0d04bb3bce67f785d1e5 100644 (file)
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -19,7 +19,7 @@ vector<string> PairwiseSeqsCommand::setParameters(){
                CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
                CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-               CommandParameter poutput("output", "Multiple", "column-lt-square", "column", "", "", "",false,false); parameters.push_back(poutput);
+               CommandParameter poutput("output", "Multiple", "column-lt-square-phylip", "column", "", "", "",false,false); parameters.push_back(poutput);
                CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "",false,false); parameters.push_back(pcalc);
                CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcountends);
                CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcompress);
@@ -249,6 +249,7 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
                        align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
                        
                        output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "column"; }
+            if (output=="phylip") { output = "lt"; }
                        if ((output != "column") && (output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are column, lt and square. I will use column."); m->mothurOutEndLine(); output = "column"; }
                        
                        calc = validParameter.validFile(parameters, "calc", false);