created mothurOut class to handle logfiles

[mothur.git] / venn.cpp

diff --git a/venn.cpp b/venn.cpp
index 986c68db1f4942e8242aef7514f78441ef0e37e0..43129f5e2d8713e1608be534915cbe61276d1ea5 100644 (file)
--- a/venn.cpp
+++ b/venn.cpp
@@ -19,19 +19,23 @@
 Venn::Venn(string o) : outputDir(o) {
        try {
                globaldata = GlobalData::getInstance();
+               m = MothurOut::getInstance();
 
        }
        catch(exception& e) {
-               errorOut(e, "Venn", "Venn");
+               m->errorOut(e, "Venn", "Venn");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-void Venn::getPic(SAbundVector* sabund, vector<Calculator*> vCalcs) {
+vector<string> Venn::getPic(SAbundVector* sabund, vector<Calculator*> vCalcs) {
        try {
-                               
+               
+               vector<string> outputNames;
+               
                for(int i=0;i<vCalcs.size();i++){
                        string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + ".venn." + sabund->getLabel() + vCalcs[i]->getName() + ".svg";
+                       outputNames.push_back(filenamesvg);
                        openOutputFile(filenamesvg, outsvg);
 
                        vector<double> data = vCalcs[i]->getValues(sabund);
@@ -53,17 +57,20 @@ void Venn::getPic(SAbundVector* sabund, vector<Calculator*> vCalcs) {
                        outsvg << "</g>\n</svg>\n";
                        outsvg.close();
                }
+               
+               return outputNames;
        }
        catch(exception& e) {
-               errorOut(e, "Venn", "getPic");
+               m->errorOut(e, "Venn", "getPic");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs) {
+vector<string> Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs) {
        try {
                
                vector<SharedRAbundVector*> subset;
+               vector<string> outputNames;
                
                /******************* 1 Group **************************/
                if (lookup.size() == 1) {
@@ -74,6 +81,7 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                        //make a file for each calculator
                        for(int i=0;i<vCalcs.size();i++){
                                string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
+                               outputNames.push_back(filenamesvg);
                                openOutputFile(filenamesvg, outsvg);
                        
                                //in essence you want to run it like a single 
@@ -123,6 +131,7 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                        //make a file for each calculator
                        for(int i=0;i<vCalcs.size();i++){
                                string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
+                               outputNames.push_back(filenamesvg);
                                openOutputFile(filenamesvg, outsvg);
                                
                                //get estimates for sharedAB
@@ -190,8 +199,8 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                        //make a file for each calculator
                        for(int i=0;i<vCalcs.size();i++){
                        
-                                                                                               
                                string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
+                               outputNames.push_back(filenamesvg);
                                openOutputFile(filenamesvg, outsvg);
                                
                                if (vCalcs[i]->getName() == "sharedace") {
@@ -444,9 +453,10 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                        //make a file for each calculator
                        for(int i=0;i<vCalcs.size();i++){
                                
-                               if ((vCalcs[i]->getName() != "sharedsobs") && (vCalcs[i]->getName() != "sharedchao")) { mothurOut(vCalcs[i]->getName() + " is not a valid calculator with four groups.  It will be disregarded. "); mothurOutEndLine(); }
+                               if ((vCalcs[i]->getName() != "sharedsobs") && (vCalcs[i]->getName() != "sharedchao")) { m->mothurOut(vCalcs[i]->getName() + " is not a valid calculator with four groups.  It will be disregarded. "); m->mothurOutEndLine(); }
                                else{
                                        string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
+                                       outputNames.push_back(filenamesvg);
                                        openOutputFile(filenamesvg, outsvg);
 
                                
@@ -625,9 +635,11 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                        }
                }
                
+               return outputNames;
+               
        }
        catch(exception& e) {
-               errorOut(e, "Venn", "getPic");
+               m->errorOut(e, "Venn", "getPic");
                exit(1);
        }
 }