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 #include "sequence.hpp"
  17
  18 typedef list<PCell>::iterator MatData;
  19 typedef map<int, float> SeqMap;  //maps sequence to all distance for that seqeunce
  20
  21
  22 /***********************************************************************/
  23
  24 class Chimera {
  25
  26         public:
  27
  28                 Chimera(){};
  29                 Chimera(string);
  30                 Chimera(string, string);
  31                 virtual ~Chimera(){};
  32                 virtual void setFilter(bool f)                  {       filter = f;                     }
  33                 virtual void setCorrection(bool c)              {       correction = c;         }
  34                 virtual void setProcessors(int p)               {       processors = p;         }
  35                 virtual void setWindow(int w)                   {       window = w;                     }
  36                 virtual void setIncrement(int i)                {       increment = i;          }
  37
  38                 virtual void setCons(string) {};
  39                 virtual void setQuantiles(string) {};
  40
  41                 virtual vector<Sequence*> readSeqs(string file) {
  42                         try {
  43                                 ifstream in;
  44                                 openInputFile(file, in);
  45                                 vector<Sequence*> container;
  46
  47                                 //read in seqs and store in vector
  48                                 while(!in.eof()){
  49
  50                                         Sequence* current = new Sequence(in);
  51                                         container.push_back(current);
  52                                         gobble(in);
  53                                 }
  54
  55                                 in.close();
  56                                 return container;
  57                         }
  58                         catch(exception& e) {
  59                                 errorOut(e, "Chimera", "readSeqs");
  60                                 exit(1);
  61                         }
  62                 }
  63
  64
  65                 //pure functions
  66                 virtual void getChimeras() = 0;
  67                 virtual void print(ostream&) = 0;
  68
  69         protected:
  70
  71                 bool filter, correction;
  72                 int processors, window, increment;
  73
  74
  75 };
  76
  77 /***********************************************************************/
  78
  79 #endif
  80