X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readmatrix.hpp;h=90d5b430de4a1ce73e5a9c03880333c4b39febad;hb=5a4ac4f954c4b4445bcee272f1f8220ddcc9c1e4;hp=66480e7a6999ed90830f45a730c49ab4b850c73f;hpb=154e089bcd37c2c2f773e53ffb88a20170b27037;p=mothur.git

diff --git a/readmatrix.hpp b/readmatrix.hpp
index 66480e7..90d5b43 100644
--- a/readmatrix.hpp
+++ b/readmatrix.hpp
@@ -12,30 +12,32 @@
 
 #include "mothur.h"
 #include "listvector.hpp"
-#include "sparsematrix.hpp"
 #include "nameassignment.hpp"
-#include "globaldata.hpp"
+#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;
 	float cutoff;
+	MothurOut* m;
+	bool sim;
 };