added sparseDistanceMatrix class. Modified cluster commands to use the new sparse...

[mothur.git] / readmatrix.hpp

diff --git a/readmatrix.hpp b/readmatrix.hpp
index 49ae2946fda42c49c8475b040ac8f7e3f5617499..5ef8afa9d7846a18957ac30cb483e0be98f6450f 100644 (file)
--- a/readmatrix.hpp
+++ b/readmatrix.hpp
@@ -12,27 +12,26 @@
 
 #include "mothur.h"
 #include "listvector.hpp"
-#include "sparsematrix.hpp"
 #include "nameassignment.hpp"
+#include "sparsedistancematrix.h"
 
 class SparseMatrix;
 
 class ReadMatrix {
 
 public:
-       ReadMatrix(){   D = new SparseMatrix();  m = MothurOut::getInstance();  }
+       ReadMatrix(){ DMatrix = new SparseDistanceMatrix(); m = MothurOut::getInstance();  }
        virtual ~ReadMatrix() {}
        virtual int read(NameAssignment*){ 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;
        float cutoff;
        MothurOut* m;