bellerophon.h

   1 #ifndef BELLEROPHON_H
   2 #define BELLEROPHON_H
   3
   4 /*
   5  *  bellerophon.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 "chimera.h"
  15 #include "sparsematrix.hpp"
  16 #include "sequence.hpp"
  17 #include "dist.h"
  18
  19 typedef list<PCell>::iterator MatData;
  20 typedef map<int, float> SeqMap;  //maps sequence to all distance for that seqeunce
  21
  22 /***********************************************************/
  23
  24 class Bellerophon : public Chimera {
  25
  26         public:
  27                 Bellerophon(string, bool, bool, int, int, int, string); //fastafile, filter, correction, window, increment, processors, outputDir);
  28                 ~Bellerophon() { delete distCalculator; for (int i = 0; i < seqs.size(); i++) { delete seqs[i];  }  seqs.clear(); }
  29
  30                 int getChimeras();
  31                 int print(ostream&, ostream&, string);
  32
  33                 #ifdef USE_MPI
  34                 int print(MPI_File&, MPI_File&, string);
  35                 #endif
  36
  37         private:
  38                 struct linePair {
  39                         unsigned long long start;
  40                         int num;
  41                         linePair(unsigned long long i, int j) : start(i), num(j) {}
  42                 };
  43
  44                 vector<linePair> lines;
  45
  46                 Dist* distCalculator;
  47                 vector<Sequence*> seqs;
  48                 vector< vector<Preference> > pref; //pref[0] = preference scores for all seqs in window 0.
  49                 string fastafile;
  50                 int iters, count, window, increment, numSeqs, processors; //iters = number of windows
  51                 bool correction;
  52
  53                 int generatePreferences(vector<SeqMap>, vector<SeqMap>, int);
  54                 int createSparseMatrix(int, int, SparseMatrix*, vector<Sequence>);
  55                 vector<Preference> getBestPref();
  56                 int driverChimeras(vector<int>, linePair);
  57                 int createProcesses(vector<int>);
  58                 int writePrefs(string, linePair);
  59                 int readPrefs(string);
  60                 vector<string> getBestWindow(linePair line);
  61                 int fillPref(int, vector<string>&);
  62 };
  63
  64 /***********************************************************/
  65
  66 #endif
  67