added ifelse for rabund

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 61e130647c6734ee49ba99b0bcded20804ee103d..c4cdb50a303e6e814bf7c6e10ca5fcb76935b597 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -230,9 +230,19 @@ int MGClusterCommand::execute(){
                //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; }