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

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index ec6b1d3828c38019085101abaa4a0599c539f974..731f981f7a7b9c14d7f0f9033671cc274b43595b 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -321,6 +321,18 @@ int SharedCommand::execute(){
                                return 1; 
                }
                
+               //set rabund file as new current rabundfile
+               string current = "";
+               itTypes = outputTypes.find("rabund");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+               }
+               
+               itTypes = outputTypes.find("shared");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
+               }       
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }