1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
|
//
// makeclrcommand.hpp
// Mothur
//
// Created by Sarah Westcott on 1/20/20.
// Copyright © 2020 Schloss Lab. All rights reserved.
//
#ifndef makeclrcommand_hpp
#define makeclrcommand_hpp
#include "command.hpp"
#include "inputdata.h"
class MakeCLRCommand : public Command {
public:
MakeCLRCommand(string);
~MakeCLRCommand() = default;
vector<string> setParameters();
string getCommandName() { return "make.clr"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Make.clr"; }
string getDescription() { return "create a log centered ratio file from a shared file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, allLines;
set<string> labels; //holds labels to be used
string groups, label, sharedfile, zeroReplacement;
vector<string> Groups, outputNames;
double zeroReplacementValue;
void process(SharedRAbundVectors*&, ofstream&, bool&);
};
#endif /* makeclrcommand_hpp */
|
