X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=readmatrix.hpp;h=bc3874e7f424d24a4a3dbf1465559c916d7423f0;hp=4e26881d1c883d34b4262bb1c38935525cc6f565;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=f18d75f9c996cb619a5051a7664620c0c5ae05fb

diff --git a/readmatrix.hpp b/readmatrix.hpp
index 4e26881..bc3874e 100644
--- a/readmatrix.hpp
+++ b/readmatrix.hpp
@@ -10,85 +10,33 @@
  *
  */
 
-#include "rabundvector.hpp"
+#include "mothur.h"
 #include "listvector.hpp"
-#include "sharedlistvector.h"
-#include "sparsematrix.hpp"
 #include "nameassignment.hpp"
-#include "inputdata.h"
-#include "globaldata.hpp"
-#include "sabundvector.hpp"
-#include "groupmap.h"
+#include "counttable.h"
+#include "sparsedistancematrix.h"
 
-class SparseMatrix;
 
 class ReadMatrix {
 
 public:
-	ReadMatrix(){	D = new SparseMatrix();	}
-	virtual void read(NameAssignment*){};
-	virtual void read(GlobalData* globaldata){};
+	ReadMatrix(){ DMatrix = new SparseDistanceMatrix(); m = MothurOut::getInstance();  }
+	virtual ~ReadMatrix() {}
+	virtual int read(NameAssignment*){ return 1; }
+    virtual int read(CountTable*){ return 1; }
+	
 	void setCutoff(float c)			{	cutoff = c;		}
-	SparseMatrix* getMatrix()		{	return D;		}
+    SparseDistanceMatrix* getDMatrix()		{	return DMatrix;		}
 	ListVector* getListVector()		{	return list;	}
-//	OrderVector* getOrderVector()   {	return order;	}
 
 	int successOpen;
 	
 protected:
-	SparseMatrix* D;
+    SparseDistanceMatrix* DMatrix;
 	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;
-	InputData* inputList;
-	ListVector* list;
-	SharedListVector* SharedList;
-	OrderVector* order;
-	SAbundVector* sabund;
-	GlobalData* globaldata;
-	// InputData* getInput()			{	return input;	}
+	MothurOut* m;
+	bool sim;
 };