X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=readmatrix.hpp;h=bc3874e7f424d24a4a3dbf1465559c916d7423f0;hp=d8f9bd11eff62b07593c29e728c35c5ddcf2ac2f;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=02909d6cae9963ba00dc746969a370fa8ca934fc

diff --git a/readmatrix.hpp b/readmatrix.hpp
index d8f9bd1..bc3874e 100644
--- a/readmatrix.hpp
+++ b/readmatrix.hpp
@@ -12,31 +12,31 @@
 
 #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();	}
+	ReadMatrix(){ DMatrix = new SparseDistanceMatrix(); m = MothurOut::getInstance();  }
 	virtual ~ReadMatrix() {}
-	virtual void read(NameAssignment*){};
-	virtual void read(GlobalData* globaldata){};
+	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;
 };