removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / venn.cpp

diff --git a/venn.cpp b/venn.cpp
index cf77a921e3c58cb6c6db8fbd6c38d5a0a369bff6..cd14785b776723d10672f6c5de11505bfc5bdafe 100644 (file)
--- a/venn.cpp
+++ b/venn.cpp
@@ -17,11 +17,9 @@
 
 
 //**********************************************************************************************************************
-Venn::Venn(string o, bool n) : outputDir(o), nseqs(n) {
+Venn::Venn(string o, bool n, string f) : outputDir(o), nseqs(n), inputfile(f) {
        try {
-               globaldata = GlobalData::getInstance();
                m = MothurOut::getInstance();
-
        }
        catch(exception& e) {
                m->errorOut(e, "Venn", "Venn");
@@ -35,7 +33,7 @@ vector<string> Venn::getPic(SAbundVector* sabund, vector<Calculator*> vCalcs) {
                vector<string> outputNames;
 
                for(int i=0;i<vCalcs.size();i++){
-                       string filenamesvg = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "." + sabund->getLabel() + "." + vCalcs[i]->getName() + ".svg";
+                       string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "." + sabund->getLabel() + "." + vCalcs[i]->getName() + ".svg";
                        outputNames.push_back(filenamesvg);
                        m->openOutputFile(filenamesvg, outsvg);
                        
@@ -93,7 +91,7 @@ vector<string> Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculato
                        
                        //make a file for each calculator
                        for(int i=0;i<vCalcs.size();i++){
-                               string filenamesvg = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + ".svg";
+                               string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + ".svg";
                                outputNames.push_back(filenamesvg);
                                m->openOutputFile(filenamesvg, outsvg);
                                
@@ -149,7 +147,7 @@ vector<string> Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculato
                        
                        //make a file for each calculator
                        for(int i=0;i<vCalcs.size();i++){
-                               string filenamesvg = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + ".svg";
+                               string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + ".svg";
 
                                outputNames.push_back(filenamesvg);
                                m->openOutputFile(filenamesvg, outsvg);
@@ -250,7 +248,7 @@ vector<string> Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculato
                        //make a file for each calculator
                        for(int i=0;i<vCalcs.size();i++){
                        
-                               string filenamesvg = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + "-" + lookup[2]->getGroup() + ".svg";
+                               string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + "-" + lookup[2]->getGroup() + ".svg";
 
                                outputNames.push_back(filenamesvg);
                                m->openOutputFile(filenamesvg, outsvg);
@@ -571,7 +569,7 @@ vector<string> Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculato
                                
                                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 + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + "-" + lookup[2]->getGroup() + "-" + lookup[3]->getGroup() + ".svg";
+                                       string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + "-" + lookup[2]->getGroup() + "-" + lookup[3]->getGroup() + ".svg";
                                        outputNames.push_back(filenamesvg);
                                        m->openOutputFile(filenamesvg, outsvg);