readmatrix.hpp

   1 #ifndef READMATRIX_HPP
   2 #define READMATRIX_HPP
   3
   4 /*
   5  *  readmatrix.hpp
   6  *
   7  *
   8  *  Created by Pat Schloss on 8/13/08.
   9  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
  10  *
  11  */
  12
  13 #include "rabundvector.hpp"
  14 #include "listvector.hpp"
  15 #include "sparsematrix.hpp"
  16 #include "nameassignment.hpp"
  17 #include "inputdata.h"
  18 #include "globaldata.hpp"
  19 #include "sabundvector.hpp"
  20 #include "groupmap.h"
  21
  22 class SparseMatrix;
  23
  24 class ReadMatrix {
  25
  26 public:
  27         ReadMatrix(){   D = new SparseMatrix(); }
  28         virtual void read(NameAssignment*){};
  29         virtual void read(GlobalData* globaldata){};
  30         void setCutoff(float c)                 {       cutoff = c;             }
  31         SparseMatrix* getMatrix()               {       return D;               }
  32         ListVector* getListVector()             {       return list;    }
  33 //      OrderVector* getOrderVector()   {       return order;   }
  34
  35         int successOpen;
  36
  37 protected:
  38         SparseMatrix* D;
  39         ListVector* list;
  40         GlobalData* globaldata;
  41         OrderVector* order;
  42         InputData* input;
  43         float cutoff;
  44 };
  45
  46
  47
  48 class ReadPhylipMatrix : public ReadMatrix {
  49
  50 public:
  51         ReadPhylipMatrix(string);
  52         ~ReadPhylipMatrix();
  53         void read(NameAssignment*);
  54 private:
  55         ifstream fileHandle;
  56         string distFile;
  57 };
  58
  59
  60
  61 class ReadColumnMatrix : public ReadMatrix {
  62
  63 public:
  64         ReadColumnMatrix(string);
  65         ~ReadColumnMatrix();
  66         void read(NameAssignment*);
  67 private:
  68         ifstream fileHandle;
  69         string distFile;
  70 };
  71
  72
  73 class ReadPhilFile : public ReadMatrix {
  74
  75 public:
  76         ReadPhilFile(string);
  77         ~ReadPhilFile();
  78         void read(GlobalData* globaldata);
  79 private:
  80         ifstream fileHandle;
  81         string philFile;
  82         InputData* input;
  83         InputData* inputSabund;
  84         ListVector* list;
  85         OrderVector* order;
  86         SAbundVector* sabund;
  87         GlobalData* globaldata;
  88         // InputData* getInput()                        {       return input;   }
  89 };
  90
  91
  92
  93 #endif