moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / venn.cpp

diff --git a/venn.cpp b/venn.cpp
index 443c36ce95c0c8a8bb9233f2aa40c3518126e28d..dfa551966c66c46df5e28d48cce90eff7848986d 100644 (file)
--- a/venn.cpp
+++ b/venn.cpp
@@ -34,9 +34,9 @@ vector<string> Venn::getPic(SAbundVector* sabund, vector<Calculator*> vCalcs) {
                vector<string> outputNames;
                
                for(int i=0;i<vCalcs.size();i++){
-                       string filenamesvg = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "." + sabund->getLabel() + "." + vCalcs[i]->getName() + ".svg";
+                       string filenamesvg = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "." + sabund->getLabel() + "." + vCalcs[i]->getName() + ".svg";
                        outputNames.push_back(filenamesvg);
-                       openOutputFile(filenamesvg, outsvg);
+                       m->openOutputFile(filenamesvg, outsvg);
                        
                        if (m->control_pressed) { outsvg.close(); return outputNames; }
 
@@ -88,9 +88,9 @@ 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 + getRootName(getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + ".svg";
+                               string filenamesvg = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + ".svg";
                                outputNames.push_back(filenamesvg);
-                               openOutputFile(filenamesvg, outsvg);
+                               m->openOutputFile(filenamesvg, outsvg);
                                
                                if (m->control_pressed) { outsvg.close(); return outputNames; }
                                
@@ -140,10 +140,10 @@ 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 + getRootName(getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + ".svg";
+                               string filenamesvg = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + ".svg";
 
                                outputNames.push_back(filenamesvg);
-                               openOutputFile(filenamesvg, outsvg);
+                               m->openOutputFile(filenamesvg, outsvg);
                                
                                if (m->control_pressed) { outsvg.close(); return outputNames; }
                                
@@ -215,10 +215,10 @@ 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 + getRootName(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(globaldata->inputFileName)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + "-" + lookup[2]->getGroup() + ".svg";
 
                                outputNames.push_back(filenamesvg);
-                               openOutputFile(filenamesvg, outsvg);
+                               m->openOutputFile(filenamesvg, outsvg);
                                
                                if (m->control_pressed) { outsvg.close(); return outputNames; }
                                
@@ -477,9 +477,9 @@ 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 + getRootName(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(globaldata->inputFileName)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + "-" + lookup[2]->getGroup() + "-" + lookup[3]->getGroup() + ".svg";
                                        outputNames.push_back(filenamesvg);
-                                       openOutputFile(filenamesvg, outsvg);
+                                       m->openOutputFile(filenamesvg, outsvg);
 
                                        if (m->control_pressed) { outsvg.close(); return outputNames; }