X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=fileoutput.h;h=170ee68a8151e9252788364c13a09de58b192815;hp=3f90cd59a8225f94d94aee928fd5c24fa289e108;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed

diff --git a/fileoutput.h b/fileoutput.h
index 3f90cd5..170ee68 100644
--- a/fileoutput.h
+++ b/fileoutput.h
@@ -1,27 +1,28 @@
 #ifndef FILEOUTPUT_H
 #define FILEOUTPUT_H
 
-#include <iostream>
-#include <fstream>
-#include <iomanip>
-#include <vector>
-#include "utilities.hpp"
-#include "globaldata.hpp"
-
-using namespace std;
+#include "mothur.h"
+#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 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:
+	int renameOk;
+	MothurOut* m;
+
 };	
 	
 /***********************************************************************/
@@ -29,12 +30,16 @@ public:
 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 output(vector<double>) {};
+
 private:
 	string inName;
 	string outName;
@@ -49,12 +54,16 @@ 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);
 	void resetFile();
 	string getFileName()	{ return inName;	};
+	
+	void initFile(string, vector<string>) {};
+	void output(vector<double>) {};
+
 
 private:
 	string outName;
@@ -69,12 +78,16 @@ 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);
 	void resetFile();
 	string getFileName()	{ return inName;	};
+	
+	void initFile(string, vector<string>) {};
+	void output(vector<double>) {};
+
 
 private:
 	string outName;
@@ -90,12 +103,17 @@ 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>);
 	void resetFile();
 	string getFileName()	{ return inName;	};
+	
+	
+	void initFile(string, vector<string>) {};
+	void output(vector<double>) {};
+
 private:
 	string inName, groupLabel;
 	string outName;
@@ -104,6 +122,31 @@ private:
 	int counter, numGroup;
 };
 
+/***********************************************************************/
+//used by parsimony, unifrac.weighted and unifrac.unweighted
+class ColumnFile : public FileOutput {
+	
+public:
+	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>){};
+	void initFile(string){};
+	
+	void initFile(string, vector<string>);
+	void output(vector<double>);
+	void resetFile();
+	string getFileName()	{ return inName;	};
+private:
+	string inName;
+	string outName;
+	ifstream inFile;
+	ofstream outFile;
+	int counter;
+	string iters;
+};
+
 
 
 #endif