working on testing

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index eb3c33481d4ef68199f2b42e452ea93c1679bbf4..637eccedfc77e74556de6bf3f201270b28874d96 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -50,6 +50,8 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       globaldata->newRead();
+                       
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
                        if (inputDir == "not found"){   inputDir = "";          }
@@ -244,7 +246,8 @@ int TreeGroupCommand::execute(){
                if (format == "sharedfile") {
                        //if the users entered no valid calculators don't execute command
                        if (treeCalculators.size() == 0) { m->mothurOut("You have given no valid calculators."); m->mothurOutEndLine(); return 0; }
-
+                       
+                       if (globaldata->gGroupmap != NULL) {  delete globaldata->gGroupmap;   globaldata->gGroupmap = NULL;  }
                        //you have groups
                        read = new ReadOTUFile(globaldata->inputFileName);      
                        read->read(&*globaldata); 
@@ -258,17 +261,17 @@ int TreeGroupCommand::execute(){
                        //used in tree constructor 
                        globaldata->runParse = false;
                        
-                       //clear globaldatas old tree names if any
-                       globaldata->Treenames.clear();
-               
-                       //fills globaldatas tree names
-                       globaldata->Treenames = globaldata->Groups;
-               
                        //create treemap class from groupmap for tree class to use
                        tmap = new TreeMap();
                        tmap->makeSim(globaldata->gGroupmap);
                        globaldata->gTreemap = tmap;
                        
+                       //clear globaldatas old tree names if any
+                       globaldata->Treenames.clear();
+                       
+                       //fills globaldatas tree names
+                       globaldata->Treenames = globaldata->Groups;
+               
                        if (m->control_pressed) { return 0; }
                        
                        //create tree file
@@ -606,7 +609,7 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                                                                subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]); 
                                                                
                                                                data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
-                                                               
+                                               //cout << thisLookup[k]->getGroup() << '\t' << thisLookup[l]->getGroup() << '\t' << (1.0 - data[0]) << endl;
                                                                if (m->control_pressed) { return 1; }
                                                                
                                                                //save values in similarity matrix