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

[mothur.git] / phylotypecommand.cpp

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index 4b524dd09af79b7d9cc2653caec6eb9d4dfb36ad..c3aee4719859a4921ece77b25e7cf5dfe69d9aec 100644 (file)
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -305,6 +305,25 @@ int PhylotypeCommand::execute(){
                        return 0; 
                }
                
+               //set list file as new current listfile
+               string current = "";
+               itTypes = outputTypes.find("list");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+               }
+               
+               //set rabund file as new current rabundfile
+               itTypes = outputTypes.find("rabund");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+               }
+               
+               //set sabund file as new current sabundfile
+               itTypes = outputTypes.find("sabund");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
+               }               
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }