changed raredisplay to use vectors instead of files

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index cb797d8d229fd0a2dfaff82d431b084bd0a227a5..ab81f42a08d80dfebb8cb7f784623bbd3e421100 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -227,7 +227,8 @@ int TreeGroupCommand::execute(){
                        lastLabel = lookup[0]->getLabel();
                        
                        if (lookup.size() < 2) { mothurOut("You have not provided enough valid groups.  I cannot run the command."); mothurOutEndLine(); return 0; }
-               
+                       
+                       //used in tree constructor 
                        globaldata->runParse = false;
                        
                        //create tree file
@@ -266,6 +267,7 @@ int TreeGroupCommand::execute(){
                        //fills globaldatas tree names
                        globaldata->Treenames = globaldata->Groups;
                        
+                       //used in tree constructor 
                        globaldata->runParse = false;
                        
                        makeSimsDist();
@@ -446,7 +448,7 @@ void TreeGroupCommand::makeSimsShared() {
                while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
                
                        if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){                       
-                               mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+                               mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
                                process(lookup);
                                
                                processedLabels.insert(lookup[0]->getLabel());
@@ -458,7 +460,7 @@ void TreeGroupCommand::makeSimsShared() {
                                for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
                                lookup = input->getSharedRAbundVectors(lastLabel);
 
-                               mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+                               mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
                                process(lookup);
                                        
                                processedLabels.insert(lookup[0]->getLabel());
@@ -491,7 +493,7 @@ void TreeGroupCommand::makeSimsShared() {
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
                        lookup = input->getSharedRAbundVectors(lastLabel);
 
-                       mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+                       mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
                        process(lookup);
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }         
                }