added modify names parameter to set.dir

[mothur.git] / fileoutput.h

diff --git a/fileoutput.h b/fileoutput.h
index 3b73b148d88c7052421d48358c8ccdf0b39035ed..170ee68a8151e9252788364c13a09de58b192815 100644 (file)
--- a/fileoutput.h
+++ b/fileoutput.h
@@ -2,17 +2,15 @@
 #define FILEOUTPUT_H
 
 #include "mothur.h"
-#include "globaldata.hpp"
-
-using namespace std;
+#include "mothurout.h"
 
 /***********************************************************************/
 
 class FileOutput {
        
 public:
-       FileOutput(){};
-       ~FileOutput(){};
+       FileOutput(){ m = MothurOut::getInstance(); }
+       virtual ~FileOutput(){};
        
        virtual void initFile(string) = 0;
        virtual void initFile(string, vector<string>) = 0;
@@ -22,8 +20,8 @@ public:
        virtual string getFileName() = 0;
 
 protected:
-       GlobalData* globaldata;
        int renameOk;
+       MothurOut* m;
 
 };     
        
@@ -32,7 +30,7 @@ protected:
 class ThreeColumnFile : public FileOutput {
        
 public:
-       ThreeColumnFile(string n) : FileOutput(), inName(n), counter(0), outName(getPathName(n) + ".temp." + getSimpleName(n)) { };
+       ThreeColumnFile(string n) : FileOutput(), inName(n), counter(0), outName(n + ".temp") { };
        ~ThreeColumnFile();
        void initFile(string);
        void output(int, vector<double>);
@@ -56,7 +54,7 @@ class OneColumnFile : public FileOutput {
        
        
 public:
-       OneColumnFile(string n) : inName(n), counter(0), outName(getPathName(n) + ".temp." + getSimpleName(n)) {};
+       OneColumnFile(string n) : inName(n), counter(0), outName(n + ".temp") {};
        ~OneColumnFile();
        void output(int, vector<double>);
        void initFile(string);
@@ -80,7 +78,7 @@ class SharedOneColumnFile : public FileOutput {
        
        
 public:
-       SharedOneColumnFile(string n) : inName(n), counter(0), outName(getPathName(n) + ".temp." + getSimpleName(n)) {};
+       SharedOneColumnFile(string n) : inName(n), counter(0), outName(n + ".temp") {};
        ~SharedOneColumnFile();
        void output(int, vector<double>);
        void initFile(string);
@@ -105,7 +103,7 @@ private:
 class SharedThreeColumnFile : public FileOutput {
        
 public:
-       SharedThreeColumnFile(string n, string groups) : FileOutput(), groupLabel(groups), inName(n), counter(0), numGroup(1), outName(getPathName(n) + ".temp." + getSimpleName(n)) {  };
+       SharedThreeColumnFile(string n, string groups) : FileOutput(), groupLabel(groups), inName(n), counter(0), numGroup(1), outName(n + ".temp") {   };
        ~SharedThreeColumnFile();
        void initFile(string);
        void output(int, vector<double>);
@@ -125,11 +123,11 @@ private:
 };
 
 /***********************************************************************/
-
+//used by parsimony, unifrac.weighted and unifrac.unweighted
 class ColumnFile : public FileOutput {
        
 public:
-       ColumnFile(string n) : FileOutput(), inName(n), counter(0), outName(getPathName(n) + ".temp." + getSimpleName(n)) { globaldata = GlobalData::getInstance(); };
+       ColumnFile(string n, string i) : FileOutput(), iters(i), inName(n), counter(0), outName(n + ".temp") {};
        ~ColumnFile();
        
        //to make compatible with parent class
@@ -146,8 +144,9 @@ private:
        ifstream inFile;
        ofstream outFile;
        int counter;
+       string iters;
 };
 
-/***********************************************************************/
+
 
 #endif