chimera.h

   1 #ifndef CHIMERA_H
   2 #define CHIMERA_H
   3
   4 /*
   5  *  chimera.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 7/9/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "mothur.h"
  15 #include "sparsematrix.hpp"
  16
  17 typedef list<PCell>::iterator MatData;
  18 typedef map<int, float> SeqMap;  //maps sequence to all distance for that seqeunce
  19
  20
  21 /***********************************************************************/
  22
  23 class Chimera {
  24
  25         public:
  26
  27                 Chimera(){};
  28                 Chimera(string);
  29                 virtual ~Chimera(){};
  30                 virtual void setFilter(bool f)                  {       filter = f;                     }
  31                 virtual void setCorrection(bool c)              {       correction = c;         }
  32                 virtual void setProcessors(int p)               {       processors = p;         }
  33                 virtual void setWindow(int w)                   {       window = w;                     }
  34                 virtual void setIncrement(int i)                {       increment = i;          }
  35                 virtual void setTemplate(string t)              {       templateFile = t;       }
  36
  37                 //pure functions
  38                 virtual void getChimeras() = 0;
  39                 virtual void print(ostream&) = 0;
  40
  41         protected:
  42
  43                 bool filter, correction;
  44                 int processors, window, increment;
  45                 string templateFile;
  46
  47
  48 };
  49
  50 /***********************************************************************/
  51
  52 #endif
  53