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 struct Preference {
  24                 string name;
  25                 vector<string> leftParent; //keep the name of closest left associated with the two scores
  26                 vector<string> rightParent; //keep the name of closest right associated with the two scores
  27                 vector<float> score;  //so you can keep last score and calc this score and keep whichever is bigger.
  28                 vector<float> closestLeft;  //keep the closest left associated with the two scores
  29                 vector<float> closestRight; //keep the closest right associated with the two scores
  30                 int midpoint;
  31
  32 };
  33
  34
  35
  36 /***********************************************************/
  37
  38 class ChimeraSeqsCommand : public Command {
  39 public:
  40         ChimeraSeqsCommand(string);
  41         ~ChimeraSeqsCommand();
  42         int execute();
  43         void help();
  44
  45
  46 private:
  47
  48         Dist* distCalculator;
  49         bool abort;
  50         string method, fastafile;
  51         bool filter, correction;
  52         int processors, midpoint, averageLeft, averageRight, window, iters, increment;
  53         FilterSeqsCommand* filterSeqs;
  54         ListVector* list;
  55         vector<Sequence> seqs;
  56         vector<Preference> pref;
  57
  58         void readSeqs();
  59         void generatePreferences(vector<SeqMap>, vector<SeqMap>, int);
  60         int createSparseMatrix(int, int, SparseMatrix*, vector<Sequence>);
  61
  62
  63 };
  64
  65 /***********************************************************/
  66
  67 #endif
  68