X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fileoutput.h;h=0c7999d2c901cc3c3c28357837e467dabb4a990a;hb=301b61cb98aaa4641f8701f43cf830c0fa44fac1;hp=6eb5e8d708eca6f102c7a562507ac92e1553e336;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/fileoutput.h b/fileoutput.h
index 6eb5e8d..0c7999d 100644
--- a/fileoutput.h
+++ b/fileoutput.h
@@ -1,14 +1,7 @@
 #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"
 
 /***********************************************************************/
 
@@ -16,12 +9,18 @@ class FileOutput {
 	
 public:
 	FileOutput(){};
-	~FileOutput(){};
-	virtual void output(int, vector<double>) = 0;
+	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;
+
 };	
 	
 /***********************************************************************/
@@ -29,12 +28,16 @@ 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(getPathName(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 +52,16 @@ 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(getPathName(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 +76,16 @@ class SharedOneColumnFile : public FileOutput {
 	
 	
 public:
-	SharedOneColumnFile(string n, vector<string> g) : inName(n), counter(0), outName(getPathName(n) + ".temp." + getSimpleName(n)) {};
+	SharedOneColumnFile(string n) : inName(n), counter(0), outName(getPathName(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 +101,17 @@ 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(getPathName(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;
@@ -104,7 +120,31 @@ 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(getPathName(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
-