working on pca

[mothur.git] / clustersplitcommand.cpp

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 5998726fe3e4d48523ac6a771a9609dae328f739..f9d38227f2d59709235bfe69f87385067317b1ab 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -31,8 +31,7 @@ vector<string> ClusterSplitCommand::getValidParameters(){
 //**********************************************************************************************************************
 ClusterSplitCommand::ClusterSplitCommand(){    
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["list"] = tempOutNames;
                outputTypes["rabund"] = tempOutNames;
@@ -72,11 +71,11 @@ vector<string> ClusterSplitCommand::getRequiredFiles(){
 ClusterSplitCommand::ClusterSplitCommand(string option)  {
        try{
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                format = "";
                
                //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
@@ -290,7 +289,7 @@ ClusterSplitCommand::~ClusterSplitCommand(){}
 int ClusterSplitCommand::execute(){
        try {
        
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                time_t estart;
                vector<string> listFileNames;
@@ -380,7 +379,6 @@ int ClusterSplitCommand::execute(){
                                        
                        //for each file group figure out which process will complete it
                        //want to divide the load intelligently so the big files are spread between processes
-                       int count = 1;
                        for (int i = 0; i < distName.size(); i++) { 
                                int processToAssign = (i+1) % processors; 
                                if (processToAssign == 0) { processToAssign = processors; }
@@ -618,6 +616,25 @@ int ClusterSplitCommand::execute(){
                
                m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to merge."); 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();    }
@@ -1112,7 +1129,7 @@ int ClusterSplitCommand::createMergedDistanceFile(vector< map<string, string> >
                }
 #endif
                                
-                       
+               return 0;       
                
                
        }