chimeraseqscommand.h

   1 #ifndef CHIMERACOMMAND_H
   2 #define CHIMERACOMMAND_H
   3
   4 /*
   5  *  chimeraseqscommand.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 6/29/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14 #include "command.hpp"
  15 #include "filterseqscommand.h"
  16 #include "sequence.hpp"
  17 #include "sparsematrix.hpp"
  18 #include "dist.h"
  19
  20 typedef list<PCell>::iterator MatData;
  21 typedef map<int, float> SeqMap;  //maps sequence to all distance for that seqeunce
  22
  23 /***********************************************************/
  24
  25 class ChimeraSeqsCommand : public Command {
  26 public:
  27         ChimeraSeqsCommand(string);
  28         ~ChimeraSeqsCommand();
  29         int execute();
  30         void help();
  31
  32 private:
  33         //Dist* distCalculator;
  34
  35         struct Preference {
  36                 string leftParent;
  37                 string rightParent;
  38                 float score;
  39
  40         };
  41
  42         Dist* distCalculator;
  43         bool abort;
  44         string method, fastafile;
  45         bool filter, correction;
  46         int processors, midpoint;
  47         FilterSeqsCommand* filterSeqs;
  48         vector<Sequence> seqs;
  49         vector<Preference> pref;
  50
  51         int findAverageMidPoint();
  52         void readSeqs();
  53         void generatePreferences(SparseMatrix*, SparseMatrix*);
  54         int createSparseMatrix(int, int, SparseMatrix*, vector<Sequence>);
  55
  56
  57 };
  58
  59 /***********************************************************/
  60
  61 #endif
  62