added cutoff change to hcluster

[mothur.git] / hclustercommand.cpp

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index d98f5c69926f795cb75510853184197676647ab9..ec4d35ceef2d37172d21d4d40a2ca6cfb9737404 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -310,11 +310,17 @@ int HClusterCommand::execute(){
                                return 0;  
                }
 
+               float saveCutoff = cutoff;
                
                while (seqs.size() != 0){
                
                        seqs = cluster->getSeqs();
                        
+                       //to account for cutoff change in average neighbor
+                       if (seqs.size() != 0) {
+                               if (seqs[0].dist > cutoff) { break; }
+                       }
+                       
                        if (m->control_pressed) {  
                                delete cluster;
                                sabundFile.close();
@@ -327,7 +333,7 @@ int HClusterCommand::execute(){
                        for (int i = 0; i < seqs.size(); i++) {  //-1 means skip me
                                
                                if (seqs[i].seq1 != seqs[i].seq2) {
-                                       cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
+                                       cutoff = cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
                                        
                                        if (m->control_pressed) {  
                                                delete cluster;
@@ -388,6 +394,14 @@ int HClusterCommand::execute(){
                        return 0;  
                }
                
+               
+               if (saveCutoff != cutoff) { 
+                       if (hard)       {  saveCutoff = m->ceilDist(saveCutoff, precision);     }
+                       else            {       saveCutoff = m->roundDist(saveCutoff, precision);  }
+                       
+                       m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine(); 
+               }
+               
                //set list file as new current listfile
                string current = "";
                itTypes = outputTypes.find("list");