added out.hierarchy command

[mothur.git] / mgclustercommand.cpp

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 07e3776e08adc3b85ee5b8c2bd3829d340eb9c82..81e80ccaf6ee82a0bbed8cd5a757a4502fd5449d 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -153,9 +153,9 @@ int MGClusterCommand::execute(){
                        delete read;
                
                        //create cluster
-                       if (method == "furthest")       {       cluster = new CompleteLinkage(rabund, list, distMatrix); }
-                       else if(method == "nearest"){   cluster = new SingleLinkage(rabund, list, distMatrix); }
-                       else if(method == "average"){   cluster = new AverageLinkage(rabund, list, distMatrix); }
+                       if (method == "furthest")       {       cluster = new CompleteLinkage(rabund, list, distMatrix, cutoff); }
+                       else if(method == "nearest"){   cluster = new SingleLinkage(rabund, list, distMatrix, cutoff); }
+                       else if(method == "average"){   cluster = new AverageLinkage(rabund, list, distMatrix, cutoff); }
                        cluster->setMapWanted(true);
                        
                        //cluster using cluster classes
@@ -220,16 +220,16 @@ int MGClusterCommand::execute(){
                        sortHclusterFiles(distFile, overlapFile);
                
                        //create cluster
-                       hcluster = new HCluster(rabund, list, method);
+                       hcluster = new HCluster(rabund, list, method, distFile, nameMap, cutoff);
                        hcluster->setMapWanted(true);
                        
                        vector<seqDist> seqs; seqs.resize(1); // to start loop
-                       ifstream inHcluster;
-                       openInputFile(distFile, inHcluster);
+                       //ifstream inHcluster;
+                       //openInputFile(distFile, inHcluster);
 
                        while (seqs.size() != 0){
                
-                               seqs = hcluster->getSeqs(inHcluster, nameMap, cutoff);
+                               seqs = hcluster->getSeqs();
                                
                                for (int i = 0; i < seqs.size(); i++) {  //-1 means skip me
                                        
@@ -262,7 +262,7 @@ int MGClusterCommand::execute(){
                                        }
                                }
                        }
-                       inHcluster.close();
+                       //inHcluster.close();
                        
                        if(previousDist <= 0.0000){
                                oldList.setLabel("unique");