X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mgclustercommand.cpp;h=9a1ac215388e09e6477fffa034e0542c38c208b1;hb=2df35fdeea85f574630d75b11fb5b08c39aec31a;hp=f8f3c78e6fc68c507bcc896bf0789a2ba2d7e373;hpb=3102812d94898439646131cecdb64fc542913c87;p=mothur.git

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index f8f3c78..9a1ac21 100644
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -208,7 +208,7 @@ int MGClusterCommand::execute(){
 				listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
 				return 0; 
 			}
-			
+		
 			//cluster using cluster classes
 			while (distMatrix->getSmallDist() < cutoff && distMatrix->getNNodes() > 0){
 				
@@ -227,7 +227,6 @@ int MGClusterCommand::execute(){
 				}else{
 					rndDist = roundDist(dist, precision); 
 				}
-
 				
 				if(previousDist <= 0.0000 && dist != previousDist){
 					oldList.setLabel("unique");
@@ -235,7 +234,6 @@ int MGClusterCommand::execute(){
 				}
 				else if(rndDist != rndPreviousDist){
 					if (merge) {
-						Seq2Bin = cluster->getSeqtoBin();
 						ListVector* temp = mergeOPFs(oldSeq2Bin, rndPreviousDist);
 						
 						if (m->control_pressed) { 
@@ -252,11 +250,11 @@ int MGClusterCommand::execute(){
 						printData(&oldList);
 					}
 				}
-				
+	
 				previousDist = dist;
-	cout << "prev distance = " << previousDist << " dist = " << dist << endl;
 				rndPreviousDist = rndDist;
 				oldList = *list;
+				Seq2Bin = cluster->getSeqtoBin();
 				oldSeq2Bin = Seq2Bin;
 			}
 			
@@ -266,7 +264,6 @@ int MGClusterCommand::execute(){
 			}
 			else if(rndPreviousDist<cutoff){
 				if (merge) {
-					Seq2Bin = cluster->getSeqtoBin();
 					ListVector* temp = mergeOPFs(oldSeq2Bin, rndPreviousDist);
 					
 					if (m->control_pressed) { 
@@ -359,7 +356,6 @@ int MGClusterCommand::execute(){
 						}
 						else if((rndDist != rndPreviousDist)){
 							if (merge) {
-								Seq2Bin = hcluster->getSeqtoBin();
 								ListVector* temp = mergeOPFs(oldSeq2Bin, rndPreviousDist);
 								
 								if (m->control_pressed) { 
@@ -382,6 +378,7 @@ int MGClusterCommand::execute(){
 						previousDist = seqs[i].dist;
 						rndPreviousDist = rndDist;
 						oldList = *list;
+						Seq2Bin = cluster->getSeqtoBin();
 						oldSeq2Bin = Seq2Bin;
 					}
 				}
@@ -394,7 +391,6 @@ int MGClusterCommand::execute(){
 			}
 			else if(rndPreviousDist<cutoff){
 				if (merge) {
-					Seq2Bin = hcluster->getSeqtoBin();
 					ListVector* temp = mergeOPFs(oldSeq2Bin, rndPreviousDist);
 					
 					if (m->control_pressed) { 
@@ -415,8 +411,8 @@ int MGClusterCommand::execute(){
 			}
 			
 			delete hcluster;
-			//remove(distFile.c_str());
-			//remove(overlapFile.c_str());
+			remove(distFile.c_str());
+			remove(overlapFile.c_str());
 		}
 		
 		delete list; 
@@ -475,6 +471,7 @@ ListVector* MGClusterCommand::mergeOPFs(map<string, int> binInfo, float dist){
 	try {
 		//create new listvector so you don't overwrite the clustering
 		ListVector* newList = new ListVector(oldList);
+
 		bool done = false;
 		ifstream inOverlap;
 		int count = 0;
@@ -503,13 +500,16 @@ ListVector* MGClusterCommand::mergeOPFs(map<string, int> binInfo, float dist){
 					float overlapDistance;
 					inOverlap >> firstName >> secondName >> overlapDistance; gobble(inOverlap);
 					
-					map<string,int>::iterator itA = nameMap->find(firstName);
-					map<string,int>::iterator itB = nameMap->find(secondName);
-					if(itA == nameMap->end()){  cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1);  }
-					if(itB == nameMap->end()){  cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);  }
+					//commented out because we check this in readblast already
+					//map<string,int>::iterator itA = nameMap->find(firstName);
+					//map<string,int>::iterator itB = nameMap->find(secondName);
+					//if(itA == nameMap->end()){  cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1);  }
+					//if(itB == nameMap->end()){  cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);  }
 					
-					overlapNode.seq1 = itA->second;
-					overlapNode.seq2 = itB->second;
+					//overlapNode.seq1 = itA->second;
+					//overlapNode.seq2 = itB->second;
+					overlapNode.seq1 = nameMap->get(firstName);
+					overlapNode.seq2 = nameMap->get(secondName);
 					overlapNode.dist = overlapDistance;
 				}else { inOverlap.close(); break; }
 			} 
@@ -520,21 +520,24 @@ ListVector* MGClusterCommand::mergeOPFs(map<string, int> binInfo, float dist){
 				string name2 = nameMap->get(overlapNode.seq2);
 			
 				//use binInfo to find out if they are already in the same bin
-				map<string, int>::iterator itBin1 = binInfo.find(name1);
-				map<string, int>::iterator itBin2 = binInfo.find(name2);
+				//map<string, int>::iterator itBin1 = binInfo.find(name1);
+				//map<string, int>::iterator itBin2 = binInfo.find(name2);
 				
-				if(itBin1 == binInfo.end()){  cerr << "AAError: Sequence '" << name1 << "' does not have any bin info.\n"; exit(1);  }
-				if(itBin2 == binInfo.end()){  cerr << "ABError: Sequence '" << name2 << "' does not have any bin info.\n"; exit(1);  }
+				//if(itBin1 == binInfo.end()){  cerr << "AAError: Sequence '" << name1 << "' does not have any bin info.\n"; exit(1);  }
+				//if(itBin2 == binInfo.end()){  cerr << "ABError: Sequence '" << name2 << "' does not have any bin info.\n"; exit(1);  }
 
-				int binKeep = itBin1->second;
-				int binRemove = itBin2->second;
+				//int binKeep = itBin1->second;
+				//int binRemove = itBin2->second;
 				
+				int binKeep = binInfo[name1];
+				int binRemove = binInfo[name2];
+			
 				//if not merge bins and update binInfo
 				if(binKeep != binRemove) {
 		
 					//save names in old bin
 					string names = newList->get(binRemove);
-					
+		
 					//merge bins into name1s bin
 					newList->set(binKeep, newList->get(binRemove)+','+newList->get(binKeep));
 					newList->set(binRemove, "");