added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / venn.cpp

diff --git a/venn.cpp b/venn.cpp
index 8370701f9e4910fac97ff3849cd8a1c89ed28d0a..986c68db1f4942e8242aef7514f78441ef0e37e0 100644 (file)
--- a/venn.cpp
+++ b/venn.cpp
@@ -16,7 +16,7 @@
 
 
 //**********************************************************************************************************************
-Venn::Venn(){
+Venn::Venn(string o) : outputDir(o) {
        try {
                globaldata = GlobalData::getInstance();
 
@@ -31,7 +31,7 @@ void Venn::getPic(SAbundVector* sabund, vector<Calculator*> vCalcs) {
        try {
                                
                for(int i=0;i<vCalcs.size();i++){
-                       string filenamesvg = globaldata->inputFileName + ".venn." + sabund->getLabel() + vCalcs[i]->getName() + ".svg";
+                       string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + ".venn." + sabund->getLabel() + vCalcs[i]->getName() + ".svg";
                        openOutputFile(filenamesvg, outsvg);
 
                        vector<double> data = vCalcs[i]->getValues(sabund);
@@ -73,7 +73,7 @@ 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 = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
+                               string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
                                openOutputFile(filenamesvg, outsvg);
                        
                                //in essence you want to run it like a single 
@@ -122,7 +122,7 @@ 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 = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
+                               string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
                                openOutputFile(filenamesvg, outsvg);
                                
                                //get estimates for sharedAB
@@ -191,7 +191,7 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                        for(int i=0;i<vCalcs.size();i++){
                        
                                                                                                
-                               string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
+                               string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
                                openOutputFile(filenamesvg, outsvg);
                                
                                if (vCalcs[i]->getName() == "sharedace") {
@@ -446,7 +446,7 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                                
                                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(); }
                                else{
-                                       string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
+                                       string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
                                        openOutputFile(filenamesvg, outsvg);