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