working on pam

[mothur.git] / readmatrix.hpp

diff --git a/readmatrix.hpp b/readmatrix.hpp
index 9c71732f87a712eef8660748926e7a1ceb64c6c6..bc3874e7f424d24a4a3dbf1465559c916d7423f0 100644 (file)
--- a/readmatrix.hpp
+++ b/readmatrix.hpp
@@ -10,82 +10,33 @@
  *
  */
 
-#include "rabundvector.hpp"
+#include "mothur.h"
 #include "listvector.hpp"
-#include "sparsematrix.hpp"
 #include "nameassignment.hpp"
-#include "inputdata.h"
-#include "globaldata.hpp"
-#include "sabundvector.hpp"
-#include "groupmap.h"
+#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;
-       OrderVector* order;
-       InputData* input;
        float cutoff;
-};
-
-
-
-class ReadPhylipMatrix : public ReadMatrix {
-       
-public:
-       ReadPhylipMatrix(string);
-       ~ReadPhylipMatrix();
-       void read(NameAssignment*);
-private:
-       ifstream fileHandle;
-       string distFile;
-};
-
-
-
-class ReadColumnMatrix : public ReadMatrix {
-       
-public:
-       ReadColumnMatrix(string);
-       ~ReadColumnMatrix();
-       void read(NameAssignment*);
-private:
-       ifstream fileHandle;
-       string distFile;
-};
-
-
-class ReadPhilFile : public ReadMatrix {
-       
-public:
-       ReadPhilFile(string);
-       ~ReadPhilFile();
-       void read(GlobalData* globaldata);
-private:
-       ifstream fileHandle;
-       string philFile;
-       InputData* input;
-       InputData* inputSabund;
-       ListVector* list;
-       OrderVector* order;
-       SAbundVector* sabund;
-       GlobalData* globaldata;
-       // InputData* getInput()                        {       return input;   }
+       MothurOut* m;
+       bool sim;
 };