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                 ~AlignCheckCommand(){}
  38
  39                 vector<string> setParameters();
  40                 string getCommandName()                 { return "align.check";                         }
  41                 string getCommandCategory()             { return "Sequence Processing";         }
  42
  43         string getHelpString();
  44     string getOutputPattern(string);
  45                 string getCitation() { return "http://www.mothur.org/wiki/Align.check"; }
  46                 string getDescription()         { return "calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment"; }
  47
  48
  49                 int execute();
  50                 void help() { m->mothurOut(getHelpString()); }
  51
  52         private:
  53                 vector<int> structMap;
  54                 string mapfile, fastafile, outputDir, namefile, countfile;
  55                 bool abort;
  56                 int seqLength, haderror;
  57                 vector<string> outputNames;
  58                 map<string, int> nameMap;
  59
  60                 void readMap();
  61                 statData getStats(string sequence);
  62 };
  63
  64 /**************************************************************************************************/
  65 #endif
  66