Initial revision

[mothur.git] / readmatrix.hpp

diff --git a/readmatrix.hpp 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