you can now use a distance matrix as input for the heatmap.sim command.

[mothur.git] / readmatrix.hpp

diff --git a/readmatrix.hpp b/readmatrix.hpp
index 9c71732f87a712eef8660748926e7a1ceb64c6c6..d8f9bd11eff62b07593c29e728c35c5ddcf2ac2f 100644 (file)
--- a/readmatrix.hpp
+++ b/readmatrix.hpp
@@ -10,14 +10,11 @@
  *
  */
 
-#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"
 
 class SparseMatrix;
 
@@ -25,6 +22,7 @@ class ReadMatrix {
 
 public:
        ReadMatrix(){   D = new SparseMatrix(); }
+       virtual ~ReadMatrix() {}
        virtual void read(NameAssignment*){};
        virtual void read(GlobalData* globaldata){};
        void setCutoff(float c)                 {       cutoff = c;             }
@@ -38,56 +36,9 @@ protected:
        SparseMatrix* D;
        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;   }
-};
-
-
-
 #endif