phylotypecommand.h

   1 #ifndef PHYLOTYPECOMMAND_H
   2 #define PHYLOTYPECOMMAND_H
   3
   4
   5 /*
   6  *  phylotypecommand.h
   7  *  Mothur
   8  *
   9  *  Created by westcott on 11/20/09.
  10  *  Copyright 2009 Schloss Lab. All rights reserved.
  11  *
  12  */
  13
  14 #include "taxonomyequalizer.h"
  15 #include "command.hpp"
  16
  17 /*************************************************************************/
  18
  19 class PhylotypeCommand : public Command {
  20
  21 public:
  22         PhylotypeCommand(string);
  23         PhylotypeCommand();
  24         ~PhylotypeCommand(){}
  25
  26         vector<string> setParameters();
  27         string getCommandName()                 { return "phylotype";           }
  28         string getCommandCategory()             { return "Clustering";          }
  29
  30         string getHelpString();
  31     string getOutputPattern(string);
  32         string getCitation() { return "http://www.mothur.org/wiki/Phylotype"; }
  33         string getDescription()         { return "cluster your sequences into OTUs based on their classifications"; }
  34
  35         int execute();
  36         void help() { m->mothurOut(getHelpString()); }
  37
  38 private:
  39         bool abort, allLines;
  40         string taxonomyFileName, label, outputDir, namefile, countfile;
  41         set<string> labels; //holds labels to be used
  42         int cutoff;
  43         map<string, string> namemap;
  44         vector<string> outputNames;
  45
  46         map<int, int> currentNodes;
  47         map<int, int> parentNodes;
  48         map<int, int>::iterator itCurrent;
  49
  50         int readNamesFile();
  51
  52 };
  53
  54
  55 /*************************************************************************/
  56
  57
  58 #endif
  59
  60
  61