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 "sequence.hpp"
  16
  17
  18 struct Preference {
  19                 string name;
  20                 vector<string> leftParent; //keep the name of closest left associated with the two scores
  21                 vector<string> rightParent; //keep the name of closest right associated with the two scores
  22                 vector<float> score;  //so you can keep last score and calc this score and keep whichever is bigger.
  23                 vector<float> closestLeft;  //keep the closest left associated with the two scores
  24                 vector<float> closestRight; //keep the closest right associated with the two scores
  25                 int midpoint;
  26
  27 };
  28
  29 struct SeqDist {
  30         Sequence* seq;
  31         float dist;
  32 };
  33
  34 //********************************************************************************************************************
  35 //sorts lowest to highest
  36 inline bool compareSeqDist(SeqDist left, SeqDist right){
  37         return (left.dist < right.dist);
  38 }
  39 //********************************************************************************************************************
  40
  41 struct sim {
  42                 string leftParent;
  43                 string rightParent;
  44                 float score;
  45                 int midpoint;
  46 };
  47
  48 struct linePair {
  49                         int start;
  50                         int end;
  51                         linePair(int i, int j) : start(i), end(j) {}
  52                         linePair(){}
  53 };
  54
  55 /***********************************************************************/
  56
  57 class Chimera {
  58
  59         public:
  60
  61                 Chimera(){};
  62                 Chimera(string);
  63                 Chimera(string, string);
  64                 virtual ~Chimera(){};
  65                 virtual void setFilter(bool f)                  {       filter = f;                     }
  66                 virtual void setCorrection(bool c)              {       correction = c;         }
  67                 virtual void setProcessors(int p)               {       processors = p;         }
  68                 virtual void setWindow(int w)                   {       window = w;                     }
  69                 virtual void setIncrement(int i)                {       increment = i;          }
  70                 virtual void setNumWanted(int n)                {       numWanted = n;          }
  71                 virtual void setKmerSize(int k)                 {       kmerSize = k;           }
  72                 virtual void setSVG(int s)                              {       svg = s;                        }
  73                 virtual void setName(string n)                  {       name = n;                       }
  74                 virtual void setMatch(int m)                    {       match = m;                      }
  75                 virtual void setMisMatch(int m)                 {       misMatch = m;           }
  76                 virtual void setDivR(float d)                   {       divR = d;                       }
  77                 virtual void setParents(int p)                  {       parents = p;            }
  78                 virtual void setMinSim(int s)                   {       minSim = s;                     }
  79                 virtual void setIters(int i)                    {       iters = i;                      }
  80
  81
  82                 virtual void setCons(string){};
  83                 virtual void setQuantiles(string){};
  84                 virtual vector<Sequence*> readSeqs(string);
  85                 virtual vector< vector<float> > readQuantiles();
  86                 virtual void setMask(string);
  87                 virtual void runFilter(vector<Sequence*>);
  88                 virtual void createFilter(vector<Sequence*>);
  89
  90
  91                 //pure functions
  92                 virtual void getChimeras() = 0;
  93                 virtual void print(ostream&) = 0;
  94
  95         protected:
  96
  97                 bool filter, correction, svg;
  98                 int processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, parents, iters;
  99                 float divR;
 100                 string seqMask, quanfile, filterString, name;
 101
 102
 103 };
 104
 105 /***********************************************************************/
 106
 107 #endif
 108