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         string getHelpString();
  30         string getCitation() { return "http://www.mothur.org/wiki/Phylotype"; }
  31         string getDescription()         { return "cluster your sequences into OTUs based on their classifications"; }
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36 private:
  37         bool abort, allLines;
  38         string taxonomyFileName, label, outputDir, namefile;
  39         set<string> labels; //holds labels to be used
  40         int cutoff;
  41         map<string, string> namemap;
  42         vector<string> outputNames;
  43         map<string, vector<string> > outputTypes;
  44
  45         map<int, int> currentNodes;
  46         map<int, int> parentNodes;
  47         map<int, int>::iterator itCurrent;
  48
  49         int readNamesFile();
  50
  51 };
  52
  53
  54 /*************************************************************************/
  55
  56
  57 #endif
  58
  59
  60