X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fileoutput.h;h=170ee68a8151e9252788364c13a09de58b192815;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=d7c4726e3f3d2b13786ebcf8bf6afa792b39fe52;hpb=50ed3b6104d5821d6184f882e1e1423d47dcbf10;p=mothur.git

diff --git a/fileoutput.h b/fileoutput.h
index d7c4726..170ee68 100644
--- 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") { };
+	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") {};
+	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") {};
+	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") {	};
+	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>);
@@ -129,7 +127,7 @@ private:
 class ColumnFile : public FileOutput {
 	
 public:
-	ColumnFile(string n) : FileOutput(), inName(n), counter(0), outName(getPathName(n) + ".temp") { 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