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                         unsigned long int start;
  81                         unsigned long int end;
  82                         linePair(unsigned long int i, unsigned long 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                 virtual ~Chimera(){     for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i];  } };
  94                 virtual bool getUnaligned()                             {       return unaligned;                       }
  95                 virtual int getLength()                                 {   return length;      }
  96                 virtual vector<Sequence*> readSeqs(string);
  97                 virtual void setMask(string);
  98                 virtual map<int, int> runFilter(Sequence*);
  99                 virtual string createFilter(vector<Sequence*>, float);
 100                 virtual void printHeader(ostream&){};
 101                 virtual int getChimeras(Sequence*){ return 0; }
 102                 virtual int getChimeras(){ return 0; }
 103                 virtual int print(ostream&, ostream&){  return 0; }
 104
 105                 #ifdef USE_MPI
 106                 virtual int print(MPI_File&, MPI_File&){  return 0; }
 107                 #endif
 108
 109
 110         protected:
 111
 112                 vector<Sequence*> templateSeqs;
 113                 bool filter, unaligned;
 114                 int length;
 115                 string seqMask, filterString, outputDir, templateFileName;
 116                 Sequence* getSequence(string);  //find sequence from name
 117                 MothurOut* m;
 118 };
 119
 120 /***********************************************************************/
 121
 122 #endif
 123