secondarystructurecommand.h

   1 #ifndef SECONDARYSTRUCTURECHECKERCOMMAND_H
   2 #define SECONDARYSTRUCTURECHECKERCOMMAND_H
   3
   4 /*
   5  *  secondarystructurecommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 9/18/09.
   9  *  Copyright 2009 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14
  15 /**************************************************************************************************/
  16
  17 struct statData {
  18         int pound;
  19         int tilde;
  20         int dash;
  21         int plus;
  22         int equal;
  23         int loop;
  24         int total;
  25         statData() : pound(0), loop(0), tilde(0), dash(0), plus(0), equal(0), total(0) {};
  26 };
  27
  28 /**************************************************************************************************/
  29
  30
  31 class AlignCheckCommand : public Command {
  32
  33         public:
  34
  35                 AlignCheckCommand(string);
  36                 ~AlignCheckCommand(){};
  37                 int execute();
  38                 void help();
  39
  40         private:
  41                 vector<int> structMap;
  42                 string mapfile, fastafile, outputDir;
  43                 bool abort;
  44                 int seqLength;
  45
  46                 void readMap();
  47                 statData getStats(string sequence);
  48 };
  49
  50 /**************************************************************************************************/
  51 #endif
  52