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                 ~GetLineageCommand(){}
  22
  23                 vector<string> setParameters();
  24                 string getCommandName()                 { return "get.lineage";                         }
  25                 string getCommandCategory()             { return "Phylotype Analysis";          }
  26                 string getHelpString();
  27                 string getCitation() { return "http://www.mothur.org/wiki/Get.lineage"; }
  28
  29                 int execute();
  30                 void help() { m->mothurOut(getHelpString()); }
  31
  32
  33         private:
  34                 set<string> names;
  35                 vector<string> outputNames, listOfTaxons;
  36                 string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
  37                 bool abort, dups;
  38
  39                 int readFasta();
  40                 int readName();
  41                 int readGroup();
  42                 int readAlign();
  43                 int readList();
  44                 int readTax();
  45                 string removeConfidences(string);
  46                 vector< map<string, float> > getTaxons(string);
  47 };
  48
  49 #endif
  50