X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readmatrix.hpp;fp=readmatrix.hpp;h=9c71732f87a712eef8660748926e7a1ceb64c6c6;hb=20a2d0350a737a434c89f303662d64a8eeea7b05;hp=0000000000000000000000000000000000000000;hpb=bbb5879a7e566935c23d63d42bb945072424b939;p=mothur.git

diff --git a/readmatrix.hpp b/readmatrix.hpp
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+++ b/readmatrix.hpp
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+#ifndef READMATRIX_HPP
+#define READMATRIX_HPP
+
+/*
+ *  readmatrix.hpp
+ *  
+ *
+ *  Created by Pat Schloss on 8/13/08.
+ *  Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+#include "rabundvector.hpp"
+#include "listvector.hpp"
+#include "sparsematrix.hpp"
+#include "nameassignment.hpp"
+#include "inputdata.h"
+#include "globaldata.hpp"
+#include "sabundvector.hpp"
+#include "groupmap.h"
+
+class SparseMatrix;
+
+class ReadMatrix {
+
+public:
+	ReadMatrix(){	D = new SparseMatrix();	}
+	virtual void read(NameAssignment*){};
+	virtual void read(GlobalData* globaldata){};
+	void setCutoff(float c)			{	cutoff = c;		}
+	SparseMatrix* getMatrix()		{	return D;		}
+	ListVector* getListVector()		{	return list;	}
+//	OrderVector* getOrderVector()   {	return order;	}
+
+	int successOpen;
+	
+protected:
+	SparseMatrix* D;
+	ListVector* list;
+	GlobalData* globaldata;
+	OrderVector* order;
+	InputData* input;
+	float cutoff;
+};
+
+
+
+class ReadPhylipMatrix : public ReadMatrix {
+	
+public:
+	ReadPhylipMatrix(string);
+	~ReadPhylipMatrix();
+	void read(NameAssignment*);
+private:
+	ifstream fileHandle;
+	string distFile;
+};
+
+
+
+class ReadColumnMatrix : public ReadMatrix {
+	
+public:
+	ReadColumnMatrix(string);
+	~ReadColumnMatrix();
+	void read(NameAssignment*);
+private:
+	ifstream fileHandle;
+	string distFile;
+};
+
+
+class ReadPhilFile : public ReadMatrix {
+	
+public:
+	ReadPhilFile(string);
+	~ReadPhilFile();
+	void read(GlobalData* globaldata);
+private:
+	ifstream fileHandle;
+	string philFile;
+	InputData* input;
+	InputData* inputSabund;
+	ListVector* list;
+	OrderVector* order;
+	SAbundVector* sabund;
+	GlobalData* globaldata;
+	// InputData* getInput()			{	return input;	}
+};
+
+
+
+#endif