working on pam

[mothur.git] / readmatrix.hpp

diff --git a/readmatrix.hpp b/readmatrix.hpp
index 2c47832f166ea0df47a7b5f5a8760c73f9ce2dfe..bc3874e7f424d24a4a3dbf1465559c916d7423f0 100644 (file)
--- a/readmatrix.hpp
+++ b/readmatrix.hpp
@@ -12,32 +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();  m = MothurOut::getInstance();  }
+       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;
 };