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 "globaldata.hpp"
19 //**********************************************************************************************************************
20 class GetSharedOTUCommand : public Command {
24 GetSharedOTUCommand(string);
25 GetSharedOTUCommand();
26 ~GetSharedOTUCommand();
27 vector<string> getRequiredParameters();
28 vector<string> getValidParameters();
29 vector<string> getRequiredFiles();
30 map<string, vector<string> > getOutputFiles() { return outputTypes; }
36 GlobalData* globaldata;
41 string fastafile, label, groups, listfile, groupfile, output, userGroups, outputDir;
42 bool abort, allLines, unique;
43 vector<string> Groups;
44 map<string, string> groupFinder;
45 map<string, string>::iterator it;
46 vector<Sequence> seqs;
47 vector<string> outputNames;
48 map<string, vector<string> > outputTypes;
50 int process(ListVector*);
53 //**********************************************************************************************************************