fixed bug in hcluster command

[mothur.git] / hclustercommand.cpp

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index 38559500b0a81f25716b983b2274b88332e3ff56..dbc0e1bb9917b0d2cfdebfa83a5a97a17b6eb905 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -21,7 +21,7 @@ HClusterCommand::HClusterCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"cutoff","precision","method","showabund","timing","phylip","column","name","sorted"};
+                       string Array[] =  {"cutoff","precision","method","phylip","column","name","sorted","showabund","timing"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -114,7 +114,7 @@ HClusterCommand::HClusterCommand(string option){
 
 void HClusterCommand::help(){
        try {
-               mothurOut("The hcluster command parameter options are cutoff, precision, method, showabund, timing, phylip, column, name and sorted. Phylip or column and name are required.\n");
+               mothurOut("The hcluster command parameter options are cutoff, precision, method, phylip, column, name, showabund, timing and sorted. Phylip or column and name are required.\n");
                mothurOut("The phylip and column parameter allow you to enter your distance file, and sorted indicates whether your column distance file is already sorted. \n");
                mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n");
                mothurOut("The hcluster command should be in the following format: \n");
@@ -161,7 +161,7 @@ int HClusterCommand::execute(){
        
                mothurOut("It took " + toString(time(NULL) - estart) + " seconds to sort. "); mothurOutEndLine();
                estart = time(NULL);
-               
+       
                //list vector made by read contains all sequence names
                if(list != NULL){
                        rabund = new RAbundVector(list->getRAbundVector());
@@ -177,7 +177,7 @@ int HClusterCommand::execute(){
                print_start = true;
                start = time(NULL);
                
-//cout << "here" << endl;      
+       
                ifstream in;
                openInputFile(distfile, in);
                string firstName, secondName;
@@ -187,7 +187,7 @@ int HClusterCommand::execute(){
                bool clusteredSomething;
                vector<seqDist> seqs; seqs.resize(1); // to start loop
                exitedBreak = false;  //lets you know if there is a distance stored in next
-               
+       
                while (seqs.size() != 0){
                
                        seqs = getSeqs(in);
@@ -205,12 +205,12 @@ int HClusterCommand::execute(){
                                        print_start = false;
                                }
                                
-       ///cout << "before cluster update" << endl;
+       //cout << "before cluster update" << endl;
                                if (seqs[i].seq1 != seqs[i].seq2) {
                                        clusteredSomething = cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
                                        
                                        float rndDist = roundDist(seqs[i].dist, precision);
-                                       //cout << "after cluster update clusterSomething = " << clusteredSomething << " rndDist = " << rndDist << " rndPreviousDist = " << rndPreviousDist << endl;                     
+               //cout << "after cluster update clusterSomething = " << clusteredSomething << " rndDist = " << rndDist << " rndPreviousDist = " << rndPreviousDist << endl;                     
                                        
                                        
                                        if((previousDist <= 0.0000) && (seqs[i].dist != previousDist)){
@@ -325,7 +325,8 @@ vector<seqDist> HClusterCommand::getSeqs(ifstream& filehandle){
                        
                        //save first one
                        if (prevDistance == -1) { prevDistance = distance; }
-                       
+       //cout << prevDistance << endl; 
+//if (globaldata->nameMap == NULL) { cout << "null" << endl; }
                        map<string,int>::iterator itA = globaldata->nameMap->find(firstName);
                        map<string,int>::iterator itB = globaldata->nameMap->find(secondName);
                        
@@ -335,7 +336,7 @@ vector<seqDist> HClusterCommand::getSeqs(ifstream& filehandle){
                        if(itB == globaldata->nameMap->end()){
                                cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);
                        }
-                       
+       //cout << "here" << endl;               
                        //using cutoff
                        if (distance > cutoff) { break; }