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 "sharedlistvector.h"
  16 #include "sparsematrix.hpp"
  17 #include "nameassignment.hpp"
  18 #include "inputdata.h"
  19 #include "globaldata.hpp"
  20 #include "sabundvector.hpp"
  21 #include "groupmap.h"
  22
  23 class SparseMatrix;
  24
  25 class ReadMatrix {
  26
  27 public:
  28         ReadMatrix(){   D = new SparseMatrix(); }
  29         virtual void read(NameAssignment*){};
  30         virtual void read(GlobalData* globaldata){};
  31         void setCutoff(float c)                 {       cutoff = c;             }
  32         SparseMatrix* getMatrix()               {       return D;               }
  33         ListVector* getListVector()             {       return list;    }
  34 //      OrderVector* getOrderVector()   {       return order;   }
  35
  36         int successOpen;
  37
  38 protected:
  39         SparseMatrix* D;
  40         ListVector* list;
  41         GlobalData* globaldata;
  42         OrderVector* order;
  43         InputData* input;
  44         float cutoff;
  45 };
  46
  47
  48
  49 class ReadPhylipMatrix : public ReadMatrix {
  50
  51 public:
  52         ReadPhylipMatrix(string);
  53         ~ReadPhylipMatrix();
  54         void read(NameAssignment*);
  55 private:
  56         ifstream fileHandle;
  57         string distFile;
  58 };
  59
  60
  61
  62 class ReadColumnMatrix : public ReadMatrix {
  63
  64 public:
  65         ReadColumnMatrix(string);
  66         ~ReadColumnMatrix();
  67         void read(NameAssignment*);
  68 private:
  69         ifstream fileHandle;
  70         string distFile;
  71 };
  72
  73
  74 class ReadPhilFile : public ReadMatrix {
  75
  76 public:
  77         ReadPhilFile(string);
  78         ~ReadPhilFile();
  79         void read(GlobalData* globaldata);
  80 private:
  81         ifstream fileHandle;
  82         string philFile;
  83         InputData* input;
  84         InputData* inputSabund;
  85         InputData* inputList;
  86         ListVector* list;
  87         SharedListVector* SharedList;
  88         OrderVector* order;
  89         SAbundVector* sabund;
  90         GlobalData* globaldata;
  91         // InputData* getInput()                        {       return input;   }
  92 };
  93
  94
  95
  96 #endif