broke up globaldata and moved error checking and help into commands

[mothur.git] / heatmap.cpp

diff --git a/heatmap.cpp b/heatmap.cpp
index 8a1837ae8365106d24c587dd94a64ccb56a37b70..e707b604a76d204571dc599f7734de817758d7ee 100644 (file)
--- a/heatmap.cpp
+++ b/heatmap.cpp
@@ -10,11 +10,12 @@
 #include "heatmap.h"
 
 //**********************************************************************************************************************
-HeatMap::HeatMap(){
+HeatMap::HeatMap(string sort, string scale){
        try {
                globaldata = GlobalData::getInstance();
                format = globaldata->getFormat();
-               sorted = globaldata->getSorted();
+               sorted = sort;
+               scaler = scale;
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -30,8 +31,7 @@ HeatMap::HeatMap(){
 
 void HeatMap::getPic(RAbundVector* rabund) {
        try {
-               //get users scaling method
-               scaler = globaldata->getScale();
+               
                
                float maxRelAbund = 0.0;                
                
@@ -40,7 +40,6 @@ void HeatMap::getPic(RAbundVector* rabund) {
                        if(relAbund > maxRelAbund){     maxRelAbund = relAbund; }
                }
                
-               scaler = globaldata->getScale();
                
                vector<string> scaleRelAbund(rabund->size(), "");
                
@@ -121,8 +120,6 @@ void HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
                        if(maxRelAbund[i] > superMaxRelAbund){  superMaxRelAbund = maxRelAbund[i];      }
                }
                
-               scaler = globaldata->getScale();
-               
                scaleRelAbund.resize(lookup.size());
                for(int i=0;i<lookup.size();i++){
                        scaleRelAbund[i].assign(lookup[i]->size(), "");