test

[mothur.git] / heatmap.cpp

diff --git a/heatmap.cpp b/heatmap.cpp
index 3ed606f17be79024c72cf9834f499128a06d6a2e..2bd020e0c3cf8337c0671c1db515954e51177dd0 100644 (file)
--- a/heatmap.cpp
+++ b/heatmap.cpp
@@ -10,19 +10,16 @@
 #include "heatmap.h"
 
 //**********************************************************************************************************************
-HeatMap::HeatMap(string sort, string scale){
+HeatMap::HeatMap(string sort, string scale, string dir){
        try {
                globaldata = GlobalData::getInstance();
 //             format = globaldata->getFormat();
                sorted = sort;
                scaler = scale;
+               outputDir = dir;
        }
        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";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the HeatMap class function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "HeatMap", "HeatMap");
                exit(1);
        }
 }
@@ -61,11 +58,11 @@ void HeatMap::getPic(RAbundVector* rabund) {
                }
                
                
-               string filenamesvg = getRootName(globaldata->inputFileName) + rabund->getLabel() + ".heatmap.bin.svg";
+               string filenamesvg = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + rabund->getLabel() + ".heatmap.bin.svg";
                openOutputFile(filenamesvg, outsvg);
                
                //svg image
-               outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(300) + " " + toString((rabund->getNumBins()*5 + 120))  + "\">\n";
+               outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(300) + " " + toString((rabund->getNumBins()*5 + 120))  + "\">\n";
                outsvg << "<g>\n";
                
                //white backround
@@ -91,11 +88,7 @@ void HeatMap::getPic(RAbundVector* rabund) {
                
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "HeatMap", "getPic");
                exit(1);
        }
 }
@@ -141,11 +134,11 @@ void HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
                        }
                }
 
-               string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".heatmap.bin.svg";
+               string filenamesvg = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + ".heatmap.bin.svg";
                openOutputFile(filenamesvg, outsvg);
                
                //svg image
-               outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(lookup.size() * 300) + " " + toString((lookup[0]->getNumBins()*5 + 120))  + "\">\n";
+               outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(lookup.size() * 300) + " " + toString((lookup[0]->getNumBins()*5 + 120))  + "\">\n";
                outsvg << "<g>\n";
                
                //white backround
@@ -179,11 +172,7 @@ void HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
 
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "HeatMap", "getPic");
                exit(1);
        }
 }
@@ -243,7 +232,7 @@ void HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
                        //fill lookup
                        for (int j = 0; j < looktemp.size(); j++) {
                                //if they are not shared then push to back, if they are not insert in front
-                               if (count < 2)  { lookup[j]->push_back(looktemp[j]->getAbundance(i), i, looktemp[j]->getGroup()); }
+                               if (count < 2)  { lookup[j]->push_back(looktemp[j]->getAbundance(i), looktemp[j]->getGroup()); }
                                //they are shared by some
                                else {  lookup[j]->insert(looktemp[j]->getAbundance(i), place[count], looktemp[j]->getGroup());   updatePlace = true; }
                        }
@@ -263,14 +252,9 @@ void HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
                
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "HeatMap", "sortSharedVectors");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the HeatMap class function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       
 }
 
 //**********************************************************************************************************************
@@ -308,14 +292,9 @@ void HeatMap::printLegend(int y, float maxbin) {
        }
        
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function printLegend. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "HeatMap", "printLegend");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the HeatMap class function printLegend. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       
 }