getgroupscommand.h

   1 #ifndef GETGROUPSCOMMAND_H
   2 #define GETGROUPSCOMMAND_H
   3
   4 /*
   5  *  getgroupscommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 11/10/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15 #include "groupmap.h"
  16
  17 class GetGroupsCommand : public Command {
  18
  19 public:
  20
  21         GetGroupsCommand(string);
  22         GetGroupsCommand();
  23         ~GetGroupsCommand(){}
  24
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "get.groups";                          }
  27         string getCommandCategory()             { return "OTU-Based Approaches";        }
  28         string getHelpString();
  29         string getCitation() { return "http://www.mothur.org/wiki/Get.groups"; }
  30         string getDescription()         { return "gets sequences from a list, fasta, name, group or taxonomy file from a given group or set of groups"; }
  31
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36
  37 private:
  38         set<string> names;
  39         map<string, string> uniqueToRedundant; //if a namefile is given and the first column name is not selected
  40                                                                                    //then the other files need to change the unique name in their file to match.
  41                                                                                    //only add the names that need to be changed to keep the map search quick
  42         string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups, sharedfile;
  43         bool abort;
  44         vector<string> outputNames, Groups;
  45         GroupMap* groupMap;
  46
  47         int readFasta();
  48         int readName();
  49         int readGroup();
  50         void readAccnos();
  51         int readList();
  52         int readTax();
  53         int fillNames();
  54         int readShared();
  55
  56 };
  57
  58 #endif
  59
  60
  61