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 "globaldata.hpp"
  15 #include "readfasta.h"
  16 #include "readnexus.h"
  17 #include "readclustal.h"
  18 #include "readseqsphylip.h"
  19
  20
  21 class FilterSeqsCommand : public Command {
  22
  23 public:
  24         FilterSeqsCommand();
  25         ~FilterSeqsCommand() {};
  26         int execute();
  27
  28 private:
  29         void doTrump();
  30         void doSoft();
  31         void doHard();
  32         void doVertical();
  33         string filter;
  34         int alignmentLength;
  35
  36         char trump;
  37         bool vertical;
  38
  39         GlobalData* globaldata;
  40 //      ReadSeqs* readSeqs;
  41 //      SequenceDB* db;
  42
  43
  44 };
  45
  46 #endif