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 getOutputFileNameTag(string, string);
  27         string getHelpString();
  28                 string getCitation() { return "http://www.mothur.org/wiki/Get.lineage"; }
  29                 string getDescription()         { return "gets sequences from a list, fasta, name, group, alignreport or taxonomy file from a given taxonomy or set of taxonomies"; }
  30
  31
  32                 int execute();
  33                 void help() { m->mothurOut(getHelpString()); }
  34
  35
  36         private:
  37                 set<string> names;
  38                 vector<string> outputNames, listOfTaxons;
  39                 string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
  40                 bool abort, dups;
  41
  42                 int readFasta();
  43                 int readName();
  44                 int readGroup();
  45                 int readAlign();
  46                 int readList();
  47                 int readTax();
  48                 vector< map<string, float> > getTaxons(string);
  49 };
  50
  51 #endif
  52