added set.current and get.current commands and modified existing commands to update...

[mothur.git] / matrixoutputcommand.cpp

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index baf449e34d8bac9e67ab424ba02539fb053033e6..ef2c23688e09e37167e8bd8421a0a493a4c4f943 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -402,6 +402,13 @@ int MatrixOutputCommand::execute(){
                //reset groups parameter
                globaldata->Groups.clear();  
                
+               //set phylip file as new current phylipfile
+               string current = "";
+               itTypes = outputTypes.find("phylip");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
+               }
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }