X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mgclustercommand.cpp;h=508b05f01d432a83d387b9b5b072d59a4b0fdcd5;hb=9eb79e6942cf98f3a0296ff9f63b4a47731b49e8;hp=42f6d0ad72b7fcc35674b3734664f4c48b2e0fab;hpb=a8ff535f332ee97582f735a35ef8f3dfb04f8de1;p=mothur.git

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 42f6d0a..508b05f 100644
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -235,20 +235,20 @@ int MGClusterCommand::execute(){
 		read = new ReadBlast(blastfile, cutoff, penalty, length, minWanted, hclusterWanted);
 		read->read(nameMap);
         
-//        list = new ListVector(nameMap->getListVector());
-//        RAbundVector* rabund = NULL;
-//        
-//        if(large) {
-//            map<string, int> nameMapCounts = m->readNames(namefile);
-//            createRabund(nameMapCounts);
-//            rabund = &rav;
-//        }else {
-//            rabund = new RAbundVector(list->getRAbundVector());
-//        }
+        list = new ListVector(nameMap->getListVector());
+        RAbundVector* rabund = NULL;
+        
+        if(large) {
+            map<string, int> nameMapCounts = m->readNames(namefile);
+            createRabund(nameMapCounts);
+            rabund = &rav;
+        }else {
+            rabund = new RAbundVector(list->getRAbundVector());
+        }
         
                 
-		list = new ListVector(nameMap->getListVector());
-		RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
+		//list = new ListVector(nameMap->getListVector());
+		//rabund = new RAbundVector(list->getRAbundVector());
 		
 		if (m->control_pressed) { outputTypes.clear(); delete nameMap; delete read; delete list; delete rabund; return 0; }
 		
@@ -519,8 +519,8 @@ int MGClusterCommand::execute(){
 			m->mothurRemove(overlapFile);
 		}
 		
-		delete list; 
-		delete rabund;
+		delete list;
+		if (!large) {delete rabund;}
 		listFile.close();
 		sabundFile.close();
 		rabundFile.close();
@@ -714,22 +714,22 @@ void MGClusterCommand::sortHclusterFiles(string unsortedDist, string unsortedOve
 }
 
 //**********************************************************************************************************************
-//
-//void MGClusterCommand::createRabund(map<string, int> nameMapCounts){
-//    try {
-//        //RAbundVector rav;
-//        map<string,int>::iterator it;
-//        //it = nameMapCounts.begin();
-//        //for(int i = 0; i < list->getNumBins(); i++) {   rav.push_back((*it).second); it++;    }
-//        for ( it=nameMapCounts.begin(); it!=nameMapCounts.end(); it++ ) {    rav.push_back( it->second );    }
-//        //return rav;
-//    }
-//    catch(exception& e) {
-//		m->errorOut(e, "MGClusterCommand", "createRabund");
-//		exit(1);
-//	}
-//    
-//}
+
+void MGClusterCommand::createRabund(map<string, int> nameMapCounts){
+    try {
+        //RAbundVector rav;
+        map<string,int>::iterator it;
+        //it = nameMapCounts.begin();
+        //for(int i = 0; i < list->getNumBins(); i++) {   rav.push_back((*it).second); it++;    }
+        for ( it=nameMapCounts.begin(); it!=nameMapCounts.end(); it++ ) {    rav.push_back( it->second );    }
+        //return rav;
+    }
+    catch(exception& e) {
+		m->errorOut(e, "MGClusterCommand", "createRabund");
+		exit(1);
+	}
+    
+}
 
 //**********************************************************************************************************************