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"
17 #include "sharedrabundvector.h"
18 #include "inputdata.h"
20 //**********************************************************************************************************************
21 class GetSharedOTUCommand : public Command {
25 GetSharedOTUCommand(string);
26 GetSharedOTUCommand();
27 ~GetSharedOTUCommand() {}
29 vector<string> setParameters();
30 string getCommandName() { return "get.sharedseqs"; }
31 string getCommandCategory() { return "OTU-Based Approaches"; }
32 string getRequiredCommand() { return "none"; }
34 string getHelpString();
35 string getOutputPattern(string);
36 string getCitation() { return "http://www.mothur.org/wiki/Get.sharedseqs"; }
37 string getDescription() { return "identifies sequences that are either unique or shared by specific groups"; }
40 void help() { m->mothurOut(getHelpString()); }
49 string fastafile, label, groups, listfile, groupfile, sharedfile, output, userGroups, outputDir, format;
50 bool abort, allLines, unique;
51 vector<string> Groups;
52 map<string, string> groupFinder;
53 map<string, string>::iterator it;
54 vector<Sequence> seqs;
55 vector<string> outputNames;
57 int process(ListVector*);
58 int process(vector<SharedRAbundVector*>&);
62 //**********************************************************************************************************************