added ifelse for rabund

[mothur.git] / mgclustercommand.cpp

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 9c45afe95277b5c7106e3f87f64e60e53b9bf321..c4cdb50a303e6e814bf7c6e10ca5fcb76935b597 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -61,6 +61,28 @@ string MGClusterCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string MGClusterCommand::getOutputFileNameTag(string type, string inputName=""){       
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "list") {  outputFileName =  "list"; }
+            else if (type == "rabund") {  outputFileName =  "rabund"; }
+            else if (type == "sabund") {  outputFileName =  "sabund"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MGClusterCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 MGClusterCommand::MGClusterCommand(){  
        try {
                abort = true; calledHelp = true; 
@@ -202,15 +224,25 @@ int MGClusterCommand::execute(){
                string tag = "";
                time_t start;
                float previousDist = 0.00000;
-               float rndPreviousDist = 0.00000;
+               float rndPreviousDist = 0.00000; 
                
                //read blastfile - creates sparsematrices for the distances and overlaps as well as a listvector
                //must remember to delete those objects here since readBlast does not
                read = new ReadBlast(blastfile, cutoff, penalty, length, minWanted, hclusterWanted);
                read->read(nameMap);
-               
-               list = new ListVector(nameMap->getListVector());
-               RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
+        
+        list = new ListVector(nameMap->getListVector());
+        RAbundVector* rabund = NULL;
+        if(large) {
+            map<string, int> nameMapCounts = m->readNames(namefile);
+            RAbundVector* rabund = newFunctionToCreateRabund(list, nameMapCounts);
+        }else {
+            RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
+        }
+        
+        
+               //list = new ListVector(nameMap->getListVector());
+               //RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
                
                if (m->control_pressed) { outputTypes.clear(); delete nameMap; delete read; delete list; delete rabund; return 0; }
                
@@ -223,10 +255,13 @@ int MGClusterCommand::execute(){
                else if (method == "nearest")   { tag = "nn";  }
                else                                                    { tag = "an";  }
                
-               //open output files
-               m->openOutputFile(fileroot+ tag + ".list",  listFile);
-               m->openOutputFile(fileroot+ tag + ".rabund",  rabundFile);
-               m->openOutputFile(fileroot+ tag + ".sabund",  sabundFile);
+        string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
+        string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
+        string listFileName = fileroot+ tag + "." + getOutputFileNameTag("list");
+        
+               m->openOutputFile(sabundFileName,       sabundFile);
+               m->openOutputFile(rabundFileName,       rabundFile);
+               m->openOutputFile(listFileName, listFile);
                
                if (m->control_pressed) { 
                        delete nameMap; delete read; delete list; delete rabund; 
@@ -493,9 +528,9 @@ int MGClusterCommand::execute(){
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
-               m->mothurOut(fileroot+ tag + ".list"); m->mothurOutEndLine();   outputNames.push_back(fileroot+ tag + ".list"); outputTypes["list"].push_back(fileroot+ tag + ".list");
-               m->mothurOut(fileroot+ tag + ".rabund"); m->mothurOutEndLine(); outputNames.push_back(fileroot+ tag + ".rabund"); outputTypes["rabund"].push_back(fileroot+ tag + ".rabund");
-               m->mothurOut(fileroot+ tag + ".sabund"); m->mothurOutEndLine(); outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund");
+               m->mothurOut(listFileName); m->mothurOutEndLine();      outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
+               m->mothurOut(rabundFileName); m->mothurOutEndLine();    outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
+               m->mothurOut(sabundFileName); m->mothurOutEndLine();    outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
                m->mothurOutEndLine();
                
                if (saveCutoff != cutoff) {