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                 string leftParent; //keep the name of closest left
  21                 string rightParent; //keep the name of closest
  22                 float score;  //preference score
  23                 float closestLeft;  //keep the closest left
  24                 float closestRight; //keep the closest right
  25                 int midpoint;
  26                 Preference() { name = ""; leftParent = ""; rightParent = ""; score = 0.0; closestLeft = 10000.0; closestRight = 10000.0; midpoint = 0;  }
  27                 ~Preference() {}
  28 };
  29 /***********************************************************************/
  30 struct score_struct {
  31         int prev;
  32         int score;
  33         int row;
  34         int col;
  35 };
  36 /***********************************************************************/
  37 struct trace_struct {
  38         int col;
  39         int oldCol;
  40         int row;
  41 };
  42 /***********************************************************************/
  43 struct results {
  44         int regionStart;
  45         int regionEnd;
  46         int nastRegionStart;
  47         int nastRegionEnd;
  48         string parent;
  49         string parentAligned;
  50         float queryToParent;
  51         float queryToParentLocal;
  52         float divR;
  53 };
  54 /***********************************************************************/
  55 struct SeqDist {
  56         Sequence* seq;
  57         float dist;
  58         int index;
  59 };
  60 //********************************************************************************************************************
  61 //sorts lowest to highest
  62 inline bool compareRegionStart(results left, results right){
  63         return (left.nastRegionStart < right.nastRegionStart);
  64 }
  65 //********************************************************************************************************************
  66 //sorts lowest to highest
  67 inline bool compareSeqDist(SeqDist left, SeqDist right){
  68         return (left.dist < right.dist);
  69 }
  70 //********************************************************************************************************************
  71
  72 struct sim {
  73                 string leftParent;
  74                 string rightParent;
  75                 float score;
  76                 int midpoint;
  77 };
  78
  79 struct linePair {
  80                         int start;
  81                         int end;
  82                         linePair(int i, int j) : start(i), end(j) {}
  83                         linePair(){}
  84 };
  85
  86 /***********************************************************************/
  87
  88 class Chimera {
  89
  90         public:
  91
  92                 Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false; }
  93                 //Chimera(string) { m = MothurOut::getInstance(); }
  94                 //Chimera(string, bool, string) { m = MothurOut::getInstance(); }
  95                 //Chimera(string, string) { m = MothurOut::getInstance(); }
  96                 virtual ~Chimera(){     for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i];  } };
  97                 //virtual void setFilter(bool f)                        {       filter = f;                     }
  98                 //virtual void setCorrection(bool c)            {       correction = c;         }
  99                 //virtual void setProcessors(int p)             {       processors = p;         }
 100                 //virtual void setWindow(int w)                 {       window = w;                     }
 101                 //virtual void setIncrement(int i)              {       increment = i;          }
 102                 //virtual void setNumWanted(int n)              {       numWanted = n;          }
 103                 //virtual void setKmerSize(int k)                       {       kmerSize = k;           }
 104                 //virtual void setSVG(int s)                            {       svg = s;                        }
 105                 //virtual void setName(string n)                        {       name = n;                       }
 106                 //virtual void setMatch(int m)                  {       match = m;                      }
 107                 //virtual void setMisMatch(int m)                       {       misMatch = m;           }
 108                 //virtual void setDivR(float d)                 {       divR = d;                       }
 109                 //virtual void setParents(int p)                        {       parents = p;            }
 110                 //virtual void setMinSim(int s)                 {       minSim = s;                     }
 111                 //virtual void setMinCoverage(int c)            {       minCov = c;                     }
 112                 //virtual void setMinBS(int b)                  {       minBS = b;                      }
 113                 //virtual void setMinSNP(int s)                 {       minSNP = s;                     }
 114                 //virtual void setIters(int i)                  {       iters = i;                      }
 115                 virtual bool getUnaligned()                             {       return unaligned;                       }
 116                 //virtual void setTemplateFile(string t)        {   templateFileName = t;       templateSeqs = readSeqs(t);  }
 117                 virtual int getLength()                                 {   return length;      }
 118
 119                 //virtual void setCons(string){};
 120                 //virtual void setQuantiles(string){};
 121                 //virtual int doPrep(){ return 0; }
 122                 virtual vector<Sequence*> readSeqs(string);
 123                 //virtual vector< vector<float> > readQuantiles();
 124                 virtual void setMask(string);
 125                 virtual map<int, int> runFilter(Sequence*);
 126                 virtual string createFilter(vector<Sequence*>, float);
 127
 128                 virtual void printHeader(ostream&){};
 129                 virtual int getChimeras(Sequence*){ return 0; }
 130                 virtual int getChimeras(){ return 0; }
 131                 virtual int print(ostream&, ostream&){  return 0; }
 132
 133                 #ifdef USE_MPI
 134                 virtual int print(MPI_File&, MPI_File&){  return 0; }
 135                 #endif
 136
 137
 138         protected:
 139
 140                 vector<Sequence*> templateSeqs;
 141                 bool filter, unaligned; //  correction, svg,
 142                 int length; //processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters,
 143                 //float divR;
 144                 string seqMask, filterString, outputDir, templateFileName; //quanfile, name,
 145                 Sequence* getSequence(string);  //find sequence from name
 146                 MothurOut* m;
 147 };
 148
 149 /***********************************************************************/
 150
 151 #endif
 152