worked on hcluster. made .single command run using a sharedfile. and various other...

[mothur.git] / hclustercommand.cpp

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index 506ba544045c7c14e8944ef02d2b99a6e061acf3..bdec48e788121bc2d88519d98e1e8135d32020d5 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -179,39 +179,30 @@ int HClusterCommand::execute(){
                print_start = true;
                start = time(NULL);
        
-               ifstream in;
-               openInputFile(distfile, in);
-               string firstName, secondName;
-               float distance;
-               
-               cluster = new HCluster(rabund, list, method);
+               //ifstream in;
+               //openInputFile(distfile, in);
+                               
+               cluster = new HCluster(rabund, list, method, distfile, globaldata->nameMap, cutoff);
                vector<seqDist> seqs; seqs.resize(1); // to start loop
                
                while (seqs.size() != 0){
                
-                       seqs = cluster->getSeqs(in, globaldata->nameMap, cutoff);
+                       seqs = cluster->getSeqs();
                                
                        for (int i = 0; i < seqs.size(); i++) {  //-1 means skip me
 
-                               if (print_start && isTrue(timing)) {
-                                       mothurOut("Clustering (" + tag + ") dist " + toString(distance) + "/" 
-                                                         + toString(roundDist(distance, precision)) 
-                                                         + "\t(precision: " + toString(precision) + ")");
-                                       cout.flush();
-                                       print_start = false;
-                               }
-                               
-       
                                if (seqs[i].seq1 != seqs[i].seq2) {
-                                       cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
+                                       bool clustered = cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
                                        
                                        float rndDist = roundDist(seqs[i].dist, precision);
-                                                       
-                                       if((previousDist <= 0.0000) && (seqs[i].dist != previousDist)){
-                                               printData("unique");
-                                       }
-                                       else if((rndDist != rndPreviousDist)){
-                                               printData(toString(rndPreviousDist,  length-1));
+                                       
+                                       if (clustered) {
+                                               if((previousDist <= 0.0000) && (seqs[i].dist != previousDist)){
+                                                       printData("unique");
+                                               }
+                                               else if((rndDist != rndPreviousDist)){
+                                                       printData(toString(rndPreviousDist,  length-1));
+                                               }
                                        }
                                        
                                        previousDist = seqs[i].dist;
@@ -222,15 +213,8 @@ int HClusterCommand::execute(){
                        }
                }
                
-               in.close();
+               //in.close();
 
-               if (print_start && isTrue(timing)) {
-                       //mothurOut("Clustering (" + tag + ") for distance " + toString(previousDist) + "/" + toString(rndPreviousDist) 
-                                        //+ "\t(precision: " + toString(precision) + ", Nodes: " + toString(matrix->getNNodes()) + ")");
-                       cout.flush();
-                       print_start = false;
-               }
-       
                if(previousDist <= 0.0000){
                        printData("unique");
                }