fixed clearcut version bug, added group count output to get.groups and remove.groups

[mothur.git] / clusterdoturcommand.cpp

diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index 56fbd5c0d6c2b8e9380959bd6ba97435b28fcd70..5bcfe03416f90700a02a4ff3d58ad312f788bb96 100644 (file)
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -25,8 +25,7 @@ vector<string> ClusterDoturCommand::getValidParameters(){
 //**********************************************************************************************************************
 ClusterDoturCommand::ClusterDoturCommand(){    
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["list"] = tempOutNames;
                outputTypes["rabund"] = tempOutNames;
@@ -65,10 +64,10 @@ vector<string> ClusterDoturCommand::getRequiredFiles(){
 ClusterDoturCommand::ClusterDoturCommand(string option)  {
        try{
                
-               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
@@ -189,7 +188,7 @@ ClusterDoturCommand::~ClusterDoturCommand(){}
 int ClusterDoturCommand::execute(){
        try {
        
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                if(namefile != ""){     
                        nameMap = new NameAssignment(namefile);
@@ -272,6 +271,25 @@ int ClusterDoturCommand::execute(){
                //      m->mothurOut("changed cutoff to " + toString(cutoff)); 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->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }