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

[mothur.git] / hclustercommand.cpp

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index 94082dfc74dfe0969e769572fc6df219ecaa69d2..128dee379080ddf32704367789c916d3bce14f41 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -395,7 +395,26 @@ int HClusterCommand::execute(){
                        for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
                        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();