made make.table alias to count.seqs command. added large parameter to count.seqs...

[mothur.git] / readmatrix.hpp

diff --git a/readmatrix.hpp b/readmatrix.hpp
index d8f9bd11eff62b07593c29e728c35c5ddcf2ac2f..49ae2946fda42c49c8475b040ac8f7e3f5617499 100644 (file)
--- a/readmatrix.hpp
+++ b/readmatrix.hpp
@@ -14,17 +14,16 @@
 #include "listvector.hpp"
 #include "sparsematrix.hpp"
 #include "nameassignment.hpp"
-#include "globaldata.hpp"
 
 class SparseMatrix;
 
 class ReadMatrix {
 
 public:
-       ReadMatrix(){   D = new SparseMatrix(); }
+       ReadMatrix(){   D = new SparseMatrix();  m = MothurOut::getInstance();  }
        virtual ~ReadMatrix() {}
-       virtual void read(NameAssignment*){};
-       virtual void read(GlobalData* globaldata){};
+       virtual int read(NameAssignment*){ return 1; }
+       
        void setCutoff(float c)                 {       cutoff = c;             }
        SparseMatrix* getMatrix()               {       return D;               }
        ListVector* getListVector()             {       return list;    }
@@ -35,8 +34,9 @@ public:
 protected:
        SparseMatrix* D;
        ListVector* list;
-       GlobalData* globaldata;
        float cutoff;
+       MothurOut* m;
+       bool sim;
 };