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

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 99e89bafecdf8c2d5740aeb12446d04b8d9e4fdd..16407d59b9819183edb70748d0b3a0ca1ff9acda 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -15,7 +15,7 @@ vector<string> DistanceCommand::setParameters(){
                CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "OldFastaColumn",false,false); parameters.push_back(pcolumn);
                CommandParameter poldfasta("oldfasta", "InputTypes", "", "", "none", "none", "OldFastaColumn",false,false); parameters.push_back(poldfasta);
                CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
-               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);
@@ -210,6 +210,7 @@ DistanceCommand::DistanceCommand(string option) {
                        convert(temp, compress);
 
                        output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "column"; }
+            if (output == "phylip") { output = "lt";  }
                        
                        if (((column != "") && (oldfastafile == "")) || ((column == "") && (oldfastafile != ""))) { m->mothurOut("If you provide column or oldfasta, you must provide both."); m->mothurOutEndLine(); abort=true; }