filterseqscommand.h

   1 #ifndef FILTERSEQSCOMMAND_H
   2 #define FILTERSEQSCOMMAND_H
   3
   4 /*
   5  *  filterseqscommand.h
   6  *  Mothur
   7  *
   8  *  Created by Thomas Ryabin on 5/4/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "mothur.h"
  15 #include "globaldata.hpp"
  16 #include "readfasta.h"
  17 #include "readnexus.h"
  18 #include "readclustal.h"
  19 #include "readseqsphylip.h"
  20
  21 using namespace std;
  22
  23 class FilterSeqsCommand : public Command {
  24
  25 public:
  26         FilterSeqsCommand() {};
  27         ~FilterSeqsCommand() {};
  28         int execute();
  29
  30 private:
  31         void doTrump();
  32         void doSoft();
  33         void doFilter();
  34
  35         GlobalData* globaldata;
  36         string filename, trump, filter;
  37
  38         ReadSeqs* readSeqs;
  39
  40         vector<bool> columnsToRemove;
  41         SequenceDB* db;
  42         double soft;
  43 };
  44
  45 #endif