*
*/
-#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;
class ReadMatrix {
public:
- ReadMatrix(){ D = new SparseMatrix(); }
- virtual void read(NameAssignment*){};
- virtual void read(GlobalData* globaldata){};
+ ReadMatrix(){ D = new SparseMatrix(); m = MothurOut::getInstance(); }
+ virtual ~ReadMatrix() {}
+ virtual int read(NameAssignment*){ return 1; }
+
void setCutoff(float c) { cutoff = c; }
SparseMatrix* getMatrix() { return D; }
ListVector* getListVector() { return list; }
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; }
+ MothurOut* m;
+ bool sim;
};