X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustersplitcommand.cpp;h=b02bd20063e9f70bb422fa541403013d6a1976ab;hb=cd1a91833339b19a107ce769ee67b5fc74c93ce4;hp=74867ebdeb0ec271d07d727b7cf9c8d19aa13284;hpb=af0a94ea8f02421b2b73e77e68753a2b4c37768e;p=mothur.git

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 74867eb..b02bd20 100644
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -843,9 +843,12 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> us
 			if (itLabel->first == -1) { thisLabel = "unique"; }
 			else { thisLabel = toString(itLabel->first,  length-1);  } 
 			
-			outList << thisLabel << '\t' << itLabel->second << '\t';
+			//outList << thisLabel << '\t' << itLabel->second << '\t';
             
             RAbundVector* rabund = NULL;
+            ListVector completeList;
+            completeList.setLabel(thisLabel);
+            
             if (countfile == "") {
                 rabund = new RAbundVector();
                 rabund->setLabel(thisLabel);
@@ -854,7 +857,8 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> us
 			//add in singletons
 			if (listSingle != NULL) {
 				for (int j = 0; j < listSingle->getNumBins(); j++) {
-					outList << listSingle->get(j) << '\t';
+					//outList << listSingle->get(j) << '\t';
+                    completeList.push_back(listSingle->get(j));
 					if (countfile == "") { rabund->push_back(m->getNumNames(listSingle->get(j))); }
 				}
 			}
@@ -871,7 +875,8 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> us
 				if (list == NULL) { m->mothurOut("Error merging listvectors in file " + listNames[k]); m->mothurOutEndLine();  }	
 				else {		
 					for (int j = 0; j < list->getNumBins(); j++) {
-						outList << list->get(j) << '\t';
+						//outList << list->get(j) << '\t';
+                        completeList.push_back(list->get(j));
 						if (countfile == "") { rabund->push_back(m->getNumNames(list->get(j))); }
 					}
 					delete list;
@@ -884,7 +889,8 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> us
                 sabund.print(outSabund);
                 rabund->print(outRabund);
             }
-			outList << endl;
+			//outList << endl;
+            completeList.print(outList);
 			
 			if (rabund != NULL) { delete rabund; }
 		}
@@ -1324,9 +1330,10 @@ string ClusterSplitCommand::clusterFile(string thisDistFile, string thisNamefile
         m->mothurOutEndLine(); m->mothurOut("Clustering " + thisDistFile); m->mothurOutEndLine();
 		
         //create cluster
-        if (method == "furthest")	{	cluster = new CompleteLinkage(rabund, list, matrix, cutoff, method); }
-        else if(method == "nearest"){	cluster = new SingleLinkage(rabund, list, matrix, cutoff, method); }
-        else if(method == "average"){	cluster = new AverageLinkage(rabund, list, matrix, cutoff, method);	}
+        float adjust = -1.0;
+        if (method == "furthest")	{	cluster = new CompleteLinkage(rabund, list, matrix, cutoff, method, adjust); }
+        else if(method == "nearest"){	cluster = new SingleLinkage(rabund, list, matrix, cutoff, method, adjust); }
+        else if(method == "average"){	cluster = new AverageLinkage(rabund, list, matrix, cutoff, method, adjust);	}
         tag = cluster->getTag();
 		
         if (outputDir == "") { outputDir += m->hasPath(thisDistFile); }