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                 vector<string> getRequiredParameters();
  39                 vector<string> getValidParameters();
  40                 vector<string> getRequiredFiles();
  41                 map<string, vector<string> > getOutputFiles() { return outputTypes; }
  42                 int execute();
  43                 void help();
  44
  45         private:
  46                 vector<int> structMap;
  47                 string mapfile, fastafile, outputDir;
  48                 bool abort;
  49                 int seqLength, haderror;
  50                 vector<string> outputNames;
  51                 map<string, vector<string> > outputTypes;
  52
  53                 void readMap();
  54                 statData getStats(string sequence);
  55 };
  56
  57 /**************************************************************************************************/
  58 #endif
  59