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fixed rf memory issue in constructure
[mothur.git] / getrelabundcommand.h
1 #ifndef GETRELABUNDCOMMAND_H
2 #define GETRELABUNDCOMMAND_H
3
4 /*
5  *  getrelabundcommand.h
6  *  Mothur
7  *
8  *  Created by westcott on 6/21/10.
9  *  Copyright 2010 Schloss Lab. All rights reserved.
10  *
11  */
12  
13 #include "command.hpp"
14 #include "inputdata.h"
15 #include "sharedrabundvector.h"
16
17
18 class GetRelAbundCommand : public Command {
19
20 public:
21         GetRelAbundCommand(string);
22         GetRelAbundCommand();
23         ~GetRelAbundCommand(){}
24         
25         vector<string> setParameters();
26         string getCommandName()                 { return "get.relabund";                        }
27         string getCommandCategory()             { return "OTU-Based Approaches";        }
28         string getOutputFileNameTag(string, string);
29         string getHelpString(); 
30         string getCitation() { return "http://www.mothur.org/wiki/Get.relabund"; }
31         string getDescription()         { return "calculates the relative abundance of each OTU in a sample"; }
32
33         
34         int execute(); 
35         void help() { m->mothurOut(getHelpString()); }  
36         
37 private:
38         InputData* input;
39         vector<SharedRAbundVector*> lookup;
40         
41         bool abort, allLines, pickedGroups;
42         set<string> labels; //holds labels to be used
43         string groups, label, outputDir, scale, sharedfile;
44         vector<string> Groups, outputNames;
45         
46         int getRelAbundance(vector<SharedRAbundVector*>&, ofstream&);
47
48 };
49
50 #endif
51