added warning about average neighbor merges around cutoff. fixed little bugs.

[mothur.git] / hclustercommand.cpp

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index bdec48e788121bc2d88519d98e1e8135d32020d5..c39b002ccfc0096197cd59ced3f4bb7fa21cce6b 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -178,9 +178,6 @@ int HClusterCommand::execute(){
                
                print_start = true;
                start = time(NULL);
-       
-               //ifstream in;
-               //openInputFile(distfile, in);
                                
                cluster = new HCluster(rabund, list, method, distfile, globaldata->nameMap, cutoff);
                vector<seqDist> seqs; seqs.resize(1); // to start loop
@@ -192,19 +189,17 @@ int HClusterCommand::execute(){
                        for (int i = 0; i < seqs.size(); i++) {  //-1 means skip me
 
                                if (seqs[i].seq1 != seqs[i].seq2) {
-                                       bool clustered = cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
+                                       cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
                                        
                                        float rndDist = roundDist(seqs[i].dist, precision);
                                        
-                                       if (clustered) {
-                                               if((previousDist <= 0.0000) && (seqs[i].dist != previousDist)){
-                                                       printData("unique");
-                                               }
-                                               else if((rndDist != rndPreviousDist)){
-                                                       printData(toString(rndPreviousDist,  length-1));
-                                               }
+                                       if((previousDist <= 0.0000) && (seqs[i].dist != previousDist)){
+                                               printData("unique");
                                        }
-                                       
+                                       else if((rndDist != rndPreviousDist)){
+                                               printData(toString(rndPreviousDist,  length-1));
+                                       }
+                               
                                        previousDist = seqs[i].dist;
                                        rndPreviousDist = rndDist;
                                        oldRAbund = *rabund;
@@ -212,8 +207,6 @@ int HClusterCommand::execute(){
                                }
                        }
                }
-               
-               //in.close();
 
                if(previousDist <= 0.0000){
                        printData("unique");