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

[mothur.git] / venncommand.cpp

diff --git a/venncommand.cpp b/venncommand.cpp
index 5357c2560a7c75fe82f3238d482a443744b6a6f5..e9cb47aca2c0b6291cbf57902ceb56808137704e 100644 (file)
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -24,7 +24,6 @@ VennCommand::VennCommand(){
                globaldata = GlobalData::getInstance();
                format = globaldata->getFormat();
                validCalculator = new ValidCalculators();
-               util = new SharedUtil();
                
                int i;
                
@@ -81,7 +80,6 @@ VennCommand::~VennCommand(){
        delete input;
        delete read;
        delete venn;
-       delete util;
 }
 
 //**********************************************************************************************************************
@@ -99,7 +97,7 @@ int VennCommand::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);      
@@ -107,43 +105,36 @@ int VennCommand::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;
+                       sabund = globaldata->sabund;
                        input = globaldata->ginput;
                }
 
                
                if (format != "list") { 
                        
-                       util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "venn");
-                       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;
-                                       venn->getPic(order, vennCalculators);
-
+                                       cout << lookup[0]->getLabel() << '\t' << count << endl;
+                                       
+                                       if (lookup.size() > 4) {
+                                               cout << "Error: Too many groups chosen.  You may use up to 4 groups with the venn command.  I will use the first four groups in your groupfile." << endl;
+                                               for (int i = lookup.size(); i > 3; i--) { delete lookup[i]; lookup.pop_back(); }
+                                       }
+                                       
+                                       //util->getSharedVectors(globaldata->Groups, lookup, order);  //fills group vectors from order vector.
+                                       venn->getPic(lookup, vennCalculators);
                                }
                                                
                                //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++;
                        }
                        
@@ -151,20 +142,21 @@ int VennCommand::execute(){
                        globaldata->Groups.clear();  
                        
                }else{
-                       while(ordersingle != NULL){
                
-                               if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(ordersingle->getLabel()) == 1){                 
+                       while(sabund != NULL){
+               
+                               if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){                      
        
-                                       cout << ordersingle->getLabel() << '\t' << count << endl;
-                                       venn->getPic(ordersingle, vennCalculators);
-                                       
+                                       cout << sabund->getLabel() << '\t' << count << endl;
+                                       venn->getPic(sabund, vennCalculators);
                                }
                                
-                               ordersingle = (input->getOrderVector());
+                               sabund = input->getSAbundVector();
                                count++;
                        }
                }
                
+               globaldata->setGroups("");
                return 0;
        }
        catch(exception& e) {
@@ -177,5 +169,4 @@ int VennCommand::execute(){
        }               
 }
 
-//**********************************************************************************************************************
-
+//**********************************************************************************************************************
\ No newline at end of file