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

[mothur.git] / mgclustercommand.cpp

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 3ed9bf2131a45ac7a4b0ac44d959b16bfe28cd36..23f359eae8ab7fe84e9b86faf96d54d33ac8dcd3 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -25,8 +25,7 @@ vector<string> MGClusterCommand::getValidParameters(){
 //**********************************************************************************************************************
 MGClusterCommand::MGClusterCommand(){  
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["list"] = tempOutNames;
                outputTypes["rabund"] = tempOutNames;
@@ -64,10 +63,10 @@ vector<string> MGClusterCommand::getRequiredFiles(){
 MGClusterCommand::MGClusterCommand(string option) {
        try {
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -202,7 +201,7 @@ MGClusterCommand::~MGClusterCommand(){}
 int MGClusterCommand::execute(){
        try {
                
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //read names file
                if (namefile != "") {
@@ -508,6 +507,26 @@ int MGClusterCommand::execute(){
                m->mothurOut(fileroot+ tag + ".sabund"); m->mothurOutEndLine(); outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund");
                m->mothurOutEndLine();
                
+               //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->mothurOut("It took " + toString(time(NULL) - start) + " seconds to cluster."); m->mothurOutEndLine();
                        
                return 0;