1 #ifndef GETSHAREDOTUCOMMAND_H
2 #define GETSHAREDOTUCOMMAND_H
5 * getsharedotucommand.h
8 * Created by westcott on 9/22/09.
9 * Copyright 2009 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "listvector.hpp"
15 #include "sequence.hpp"
18 //**********************************************************************************************************************
19 class GetSharedOTUCommand : public Command {
23 GetSharedOTUCommand(string);
24 GetSharedOTUCommand();
25 ~GetSharedOTUCommand() {}
27 vector<string> setParameters();
28 string getCommandName() { return "get.sharedseqs"; }
29 string getCommandCategory() { return "OTU-Based Approaches"; }
30 string getRequiredCommand() { return "none"; }
31 string getOutputFileNameTag(string, string);
32 string getHelpString();
33 string getCitation() { return "http://www.mothur.org/wiki/Get.sharedseqs"; }
34 string getDescription() { return "identifies sequences that are either unique or shared by specific groups"; }
37 void help() { m->mothurOut(getHelpString()); }
46 string fastafile, label, groups, listfile, groupfile, output, userGroups, outputDir, format;
47 bool abort, allLines, unique;
48 vector<string> Groups;
49 map<string, string> groupFinder;
50 map<string, string>::iterator it;
51 vector<Sequence> seqs;
52 vector<string> outputNames;
54 int process(ListVector*);
57 //**********************************************************************************************************************