fixed bug with getting sharedrabunds for venn, heatmap and tree.shared commands,...

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index de30d3c5ac2e30ab6e44cb0f84cdb9e47c1eaf73..047ea6173103b5c2ad82c19c6213ab5bab9ed978 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -89,11 +89,12 @@ int TreeGroupCommand::execute(){
                if (treeCalculators.size() == 0) { return 0; }
 
                if (format == "sharedfile") {
+                       //you have groups
                        read = new ReadOTUFile(globaldata->inputFileName);      
                        read->read(&*globaldata); 
                        
                        input = globaldata->ginput;
-                       order = input->getSharedOrderVector();
+                       lookup = input->getSharedRAbundVectors();
                }else {
                        //you are using a list and a groupfile
                        read = new ReadOTUFile(globaldata->inputFileName);      
@@ -101,11 +102,11 @@ int TreeGroupCommand::execute(){
                
                        input = globaldata->ginput;
                        SharedList = globaldata->gSharedList;
-                       order = SharedList->getSharedOrderVector();
+                       lookup = SharedList->getSharedRAbundVector();
                }
                
-               //set users groups
-               util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "treegroup");
+               if (lookup.size() < 2) { cout << "You have not provided enough valid groups.  I cannot run the command." << endl; }
+               
                numGroups = globaldata->Groups.size();
                groupNames = "";
                for (int i = 0; i < numGroups; i++) { groupNames += globaldata->Groups[i]; }
@@ -121,12 +122,11 @@ int TreeGroupCommand::execute(){
                tmap->makeSim(globaldata->gGroupmap);
                globaldata->gTreemap = tmap;
                        
-               while(order != NULL){
+               while(lookup[0] != NULL){
                
-                       if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){                       
+                       if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){                   
                                
-                               cout << order->getLabel() << '\t' << count << endl;
-                               util->getSharedVectors(globaldata->Groups, lookup, order);  //fills group vectors from order vector.
+                               cout << lookup[0]->getLabel() << '\t' << count << endl;
                                
                                //for each calculator                                                                                           
                                for(int i = 0 ; i < treeCalculators.size(); i++) {
@@ -145,7 +145,7 @@ int TreeGroupCommand::execute(){
                                        for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
                
                                        //create a new filename
-                                       outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + order->getLabel() + ".tre";
+                                       outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + lookup[0]->getLabel() + ".tre";
                                                        
                                        for (int k = 0; k < lookup.size(); k++) { 
                                                for (int l = k; l < lookup.size(); l++) {
@@ -170,17 +170,7 @@ int TreeGroupCommand::execute(){
                        }
                
                        //get next line to process
-                       if (format == "sharedfile") {
-                               order = input->getSharedOrderVector();
-                       }else {
-                               //you are using a list and a groupfile
-                               SharedList = input->getSharedListVector(); //get new list vector to process
-                               if (SharedList != NULL) {
-                                       order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
-                               }else {
-                                       break;
-                               }
-                       }
+                       lookup = input->getSharedRAbundVectors();
                        count++;
                }