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1 #ifndef SHAREDCOMMAND_H
2 #define SHAREDCOMMAND_H
3 /*
4  *  sharedcommand.h
5  *  Dotur
6  *
7  *  Created by Sarah Westcott on 1/2/09.
8  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
9  *
10  */
11
12 #include "command.hpp"
13 #include "sharedlistvector.h"
14 #include "inputdata.h"
15 #include "shared.h"
16 #include "readotu.h"
17
18 /* The shared() command:
19         The shared command can only be executed after a successful read.shared command.  
20         The shared command parses a .list file and separates it into groups.  
21         It outputs a .shared file containing the OTU information for each group.  
22         There are no shared command parameters.  The shared command should be in the following format: shared(). */
23
24
25 class GlobalData;
26
27 class SharedCommand : public Command {
28         
29 public:
30         SharedCommand();        
31         ~SharedCommand();
32         int execute();  
33         void help() {}
34         
35 private:
36         void printSharedData();
37         GlobalData* globaldata;
38         ReadOTUFile* read;
39         SharedListVector* SharedList;
40         InputData* input;
41         Shared* shared;
42         map<string, SharedRAbundVector*>::iterator it;
43         //vector<SharedRAbundVector*> lookup;
44         ofstream out;
45         string filename;
46
47 };
48
49 #endif