X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=fileoutput.h;h=170ee68a8151e9252788364c13a09de58b192815;hp=7e9d8d26144be2150d75358e67da2a72a6dafb32;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d

diff --git a/fileoutput.h b/fileoutput.h
index 7e9d8d2..170ee68 100644
--- a/fileoutput.h
+++ b/fileoutput.h
@@ -2,27 +2,26 @@
 #define FILEOUTPUT_H
 
 #include "mothur.h"
-#include "globaldata.hpp"
-
-using namespace std;
+#include "mothurout.h"
 
 /***********************************************************************/
 
 class FileOutput {
 	
 public:
-	FileOutput(){};
-	~FileOutput(){};
-	virtual void output(int, vector<double>) = 0;
+	FileOutput(){ m = MothurOut::getInstance(); }
+	virtual ~FileOutput(){};
+	
 	virtual void initFile(string) = 0;
-	virtual void resetFile() = 0;
-	virtual string getFileName() = 0;
 	virtual void initFile(string, vector<string>) = 0;
+	virtual void output(int, vector<double>) = 0;
 	virtual void output(vector<double>) = 0;
+	virtual void resetFile() = 0;
+	virtual string getFileName() = 0;
 
 protected:
-	GlobalData* globaldata;
 	int renameOk;
+	MothurOut* m;
 
 };	
 	
@@ -31,14 +30,14 @@ 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>);
 	void resetFile();
 	string getFileName()	{ return inName;	};
 	
-	void initFile(string, vector<string>) {};
+	void initFile(string, vector<string>){};
 	void output(vector<double>) {};
 
 private:
@@ -55,7 +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);
@@ -79,7 +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);
@@ -104,7 +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>);
@@ -124,12 +123,12 @@ private:
 };
 
 /***********************************************************************/
-
-class ThreeColumnFile2 : public FileOutput {
+//used by parsimony, unifrac.weighted and unifrac.unweighted
+class ColumnFile : public FileOutput {
 	
 public:
-	ThreeColumnFile2(string n) : FileOutput(), inName(n), counter(0), outName(getPathName(n) + ".temp." + getSimpleName(n)) { globaldata = GlobalData::getInstance(); };
-	~ThreeColumnFile2();
+	ColumnFile(string n, string i) : FileOutput(), iters(i), inName(n), counter(0), outName(n + ".temp") {};
+	~ColumnFile();
 	
 	//to make compatible with parent class
 	void output(int, vector<double>){};
@@ -145,8 +144,9 @@ private:
 	ifstream inFile;
 	ofstream outFile;
 	int counter;
+	string iters;
 };
 
-/***********************************************************************/
+
 
 #endif