started shared utilities, updates to venn and heatmap added tree.groups command

[mothur.git] / heatmapcommand.cpp

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index 10264c87951668a890b92903d87073fed2b0aa03..82aa12ce66821443c9cedce4628fad3e43d01674 100644 (file)
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -17,6 +17,7 @@ HeatMapCommand::HeatMapCommand(){
                globaldata = GlobalData::getInstance();
                heatmap = new HeatMap();
                format = globaldata->getFormat();
+               util = new SharedUtil();
                
        }
        catch(exception& e) {
@@ -34,6 +35,7 @@ HeatMapCommand::~HeatMapCommand(){
        delete input;
        delete read;
        delete heatmap;
+       delete util;
 }
 
 //**********************************************************************************************************************
@@ -65,12 +67,14 @@ int HeatMapCommand::execute(){
                        ordersingle = globaldata->gorder;
                        input = globaldata->ginput;
                }
-
                
+                               
                if (format != "list") { 
-                       
-                       setGroups();
-                       
+               
+                       util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "heat");
+                       globaldata->setGroups("");
+
+
                        while(order != NULL){
                
                                if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){                       
@@ -96,7 +100,7 @@ int HeatMapCommand::execute(){
                        }
                        
                        //reset groups parameter
-                       globaldata->Groups.clear();  globaldata->setGroups("");
+                       globaldata->Groups.clear();  
                        
                }else{
                        while(ordersingle != NULL){
@@ -126,50 +130,5 @@ int HeatMapCommand::execute(){
 }
 
 //**********************************************************************************************************************
-void HeatMapCommand::setGroups() {
-       try {
-               //if the user has not entered specific groups to analyze then do them all
-               if (globaldata->Groups.size() != 0) {
-                       if (globaldata->Groups[0] != "all") {
-                               //check that groups are valid
-                               for (int i = 0; i < globaldata->Groups.size(); i++) {
-                                       if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
-                                               cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
-                                               // erase the invalid group from globaldata->Groups
-                                               globaldata->Groups.erase(globaldata->Groups.begin()+i);
-                                       }
-                               }
-                       
-                               //if the user only entered invalid groups
-                               if (globaldata->Groups.size() == 0) { 
-                                       cout << "When using the groups parameter you must have at least 1 valid groups. I will run the command using all the groups in your groupfile." << endl; 
-                                       for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
-                                               globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
-                                       }
-                               }
-                       }else{//user has enter "all" and wants the default groups
-                               globaldata->Groups.clear();
-                               for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
-                                       globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
-                               }
-                               globaldata->setGroups("");
-                       }
-               }else {
-                       for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
-                               globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
-                       }
-               }
-               
-       }
-       catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the HeatMapCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 
-}
-/***********************************************************/