getlineagecommand.h

   1 #ifndef GETLINEAGECOMMAND_H
   2 #define GETLINEAGECOMMAND_H
   3
   4 /*
   5  *  getlineagecommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 9/24/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14
  15 class GetLineageCommand : public Command {
  16
  17         public:
  18
  19                 GetLineageCommand(string);
  20                 ~GetLineageCommand(){};
  21                 int execute();
  22                 void help();
  23
  24         private:
  25                 set<string> names;
  26                 vector<string> outputNames;
  27                 string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
  28                 bool abort, dups;
  29
  30                 int readFasta();
  31                 int readName();
  32                 int readGroup();
  33                 int readAlign();
  34                 int readList();
  35                 int readTax();
  36                 string removeConfidences(string);
  37 };
  38
  39 #endif
  40