X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mgclustercommand.cpp;h=e5681efb220d1635382ea6b077a36ea4e0f50226;hb=8772a51e7ab31b1c49dada6d38baf1474444943c;hp=870536d4640e5a0de07d24d4fd8799e218359a34;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96;p=mothur.git

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 870536d..e5681ef 100644
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -224,15 +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 = createRabund(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; }
 		
@@ -699,7 +709,19 @@ void MGClusterCommand::sortHclusterFiles(string unsortedDist, string unsortedOve
 
 //**********************************************************************************************************************
 
+RAbundVector MGClusterCommand::createRabund(ListVector list, map<string, int> nameMapCounts){
+    try {
+        RAbundVector rav;
+        for(int i = 0; i < list->getNumBins(); i++) {   rav.push_back(nameMapCounts[i]);    }
+        return rav;
+    }
+    catch(exception& e) {
+		m->errorOut(e, "MGClusterCommand", "createRabund");
+		exit(1);
+	}
+    
+}
 
-
+//**********************************************************************************************************************