*** empty log message ***

[mothur.git] / heatmapcommand.cpp

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index 5da80d8179f4cb29f3c005490526ef6e8c5a93ab..09dfb5a15bde8e52a967c1ef9cdae0e4130a0b3a 100644 (file)
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -15,6 +15,7 @@
 HeatMapCommand::HeatMapCommand(){
        try {
                globaldata = GlobalData::getInstance();
+               heatmap = new HeatMap();
                format = globaldata->getFormat();
        }
        catch(exception& e) {
@@ -31,6 +32,7 @@ HeatMapCommand::HeatMapCommand(){
 HeatMapCommand::~HeatMapCommand(){
        delete input;
        delete read;
+       delete heatmap;
 }
 
 //**********************************************************************************************************************
@@ -38,72 +40,61 @@ HeatMapCommand::~HeatMapCommand(){
 int HeatMapCommand::execute(){
        try {
                int count = 1;  
-               
+       
                if (format == "sharedfile") {
                        //you have groups
-                       read = new ReadPhilFile(globaldata->inputFileName);     
+                       read = new ReadOTUFile(globaldata->inputFileName);      
                        read->read(&*globaldata); 
                        
                        input = globaldata->ginput;
-                       order = input->getSharedOrderVector();
-               }else if (format == "shared") {
-                       //you are using a list and a groupfile
-                       read = new ReadPhilFile(globaldata->inputFileName);     
-                       read->read(&*globaldata); 
-               
-                       input = globaldata->ginput;
-                       SharedList = globaldata->gSharedList;
-                       order = SharedList->getSharedOrderVector();
+                       lookup = input->getSharedRAbundVectors();
                }else if (format == "list") {
                        //you are using just a list file and have only one group
-                       read = new ReadPhilFile(globaldata->inputFileName);     
+                       read = new ReadOTUFile(globaldata->inputFileName);      
                        read->read(&*globaldata); 
-               
-                       ordersingle = globaldata->gorder;
-                       input = globaldata->ginput;
+                       
+                       rabund = globaldata->rabund;
+                       input = globaldata->ginput;             
                }
                
                if (format != "list") { 
-                       while(order != NULL){
                
-                               if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){                       
+                       while(lookup[0] != NULL){
+               
+                               if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){                   
        
-                                       cout << order->getLabel() << '\t' << count << endl;
-//call heatmap class to make file
+                                       cout << lookup[0]->getLabel() << '\t' << count << endl;
+                                       heatmap->getPic(lookup);
                                }
-                                               
+                               
+                               //prevent memory leak
+                               for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
+                               
                                //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++;
                        }
                        
                        //reset groups parameter
-                       globaldata->Groups.clear();  globaldata->setGroups("");
+                       globaldata->Groups.clear();  
                        
                }else{
-                       while(ordersingle != NULL){
                
-                               if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){                       
+                       while(rabund != NULL){
+               
+                               if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(rabund->getLabel()) == 1){                      
        
-                                       cout << order->getLabel() << '\t' << count << endl;
-//call heatmap class to make file
+                                       cout << rabund->getLabel() << '\t' << count << endl;
+                                       heatmap->getPic(rabund);
                                }
                                
-                               ordersingle = (input->getOrderVector());
+                               delete rabund;
+                               rabund = input->getRAbundVector();
                                count++;
                        }
                }
                
+               globaldata->setGroups("");
                return 0;
        }
        catch(exception& e) {
@@ -118,3 +109,4 @@ int HeatMapCommand::execute(){
 
 //**********************************************************************************************************************
 
+