changed heatmap and venn command to use vector of sharedrabunds instead of order...

[mothur.git] / heatmapcommand.cpp

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index b8b38207277789ae9181e688f5a648e96ffe337c..be25f091516022e5a6414184c7ecb58518e60a94 100644 (file)
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -17,8 +17,6 @@ HeatMapCommand::HeatMapCommand(){
                globaldata = GlobalData::getInstance();
                heatmap = new HeatMap();
                format = globaldata->getFormat();
-               util = new SharedUtil();
-               
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -35,7 +33,6 @@ HeatMapCommand::~HeatMapCommand(){
        delete input;
        delete read;
        delete heatmap;
-       delete util;
 }
 
 //**********************************************************************************************************************
@@ -50,7 +47,7 @@ int HeatMapCommand::execute(){
                        read->read(&*globaldata); 
                        
                        input = globaldata->ginput;
-                       order = input->getSharedOrderVector();
+                       lookup = input->getSharedRAbundVectors();
                }else if (format == "shared") {
                        //you are using a list and a groupfile
                        read = new ReadOTUFile(globaldata->inputFileName);      
@@ -58,43 +55,28 @@ int HeatMapCommand::execute(){
                
                        input = globaldata->ginput;
                        SharedList = globaldata->gSharedList;
-                       order = SharedList->getSharedOrderVector();
+                       lookup = SharedList->getSharedRAbundVector();
                }else if (format == "list") {
                        //you are using just a list file and have only one group
                        read = new ReadOTUFile(globaldata->inputFileName);      
                        read->read(&*globaldata); 
                        
-                       ordersingle = globaldata->gorder;
-                       input = globaldata->ginput;
+                       rabund = globaldata->rabund;
+                       input = globaldata->ginput;             
                }
                
                if (format != "list") { 
                
-                       util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "heat");
-                       globaldata->setGroups("");
-
-
-                       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;
-                                       heatmap->getPic(order);
-
+                                       cout << lookup[0]->getLabel() << '\t' << count << endl;
+                                       heatmap->getPic(lookup);
                                }
                                                
                                //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++;
                        }
                        
@@ -102,20 +84,21 @@ int HeatMapCommand::execute(){
                        globaldata->Groups.clear();  
                        
                }else{
-                       while(ordersingle != NULL){
                
-                               if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(ordersingle->getLabel()) == 1){                 
+                       while(rabund != NULL){
+               
+                               if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(rabund->getLabel()) == 1){                      
        
-                                       cout << ordersingle->getLabel() << '\t' << count << endl;
-                                       heatmap->getPic(ordersingle);
-                                       
+                                       cout << rabund->getLabel() << '\t' << count << endl;
+                                       heatmap->getPic(rabund);
                                }
                                
-                               ordersingle = (input->getOrderVector());
+                               rabund = input->getRAbundVector();
                                count++;
                        }
                }
                
+               globaldata->setGroups("");
                return 0;
        }
        catch(exception& e) {