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

[mothur.git] / indicatorcommand.cpp

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index 143135f18f7cd61d68f9750944dd70a8493e803c..654ec066f7610ae4def19f745c28512a71d3b196 100644 (file)
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -37,8 +37,7 @@ vector<string> IndicatorCommand::getRequiredParameters(){
 //**********************************************************************************************************************
 IndicatorCommand::IndicatorCommand(){  
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["tree"] = tempOutNames;
                outputTypes["summary"] = tempOutNames;
@@ -64,10 +63,10 @@ vector<string> IndicatorCommand::getRequiredFiles(){
 IndicatorCommand::IndicatorCommand(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
@@ -199,7 +198,7 @@ IndicatorCommand::~IndicatorCommand(){}
 int IndicatorCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
        
                //read designfile if given and set up globaldatas groups for read of sharedfiles
                if (designfile != "") {
@@ -326,6 +325,13 @@ int IndicatorCommand::execute(){
                        delete outputTree; delete globaldata->gTreemap;  return 0; 
                }
                
+               //set tree file as new current treefile
+               string current = "";
+               itTypes = outputTypes.find("tree");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
+               }
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }