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Changes to seq.error so that an alignment is not necessary
[mothur.git] / systemcommand.h
1 #ifndef SYSTEMCOMMAND_H
2 #define SYSTEMCOMMAND_H
3
4 /*
5  *  systemcommand.h
6  *  Mothur
7  *
8  *  Created by Sarah Westcott on 7/8/09.
9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10  *
11  */
12
13 #include "command.hpp"
14
15
16 class SystemCommand : public Command {
17         
18         public:
19         
20                 SystemCommand(string);  
21                 SystemCommand() { setParameters(); abort = true; calledHelp = true; }
22                 ~SystemCommand(){}
23         
24                 vector<string> setParameters();
25                 string getCommandName()                 { return "system";              }
26                 string getCommandCategory()             { return "General";             }
27         string getHelpString(); 
28         string getOutputPattern(string){ return ""; }   
29                 string getCitation() { return "http://www.mothur.org/wiki/System"; }
30                 string getDescription()         { return "execute system commands from within mothur"; }
31
32                 int execute(); 
33                 void help() { m->mothurOut(getHelpString()); }  
34         
35         private:
36                 string command;
37                 bool abort;
38                 vector<string> outputNames;
39                 
40                 
41 };
42
43 #endif
44