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
47
|
//
// removedistscommand.h
// Mothur
//
// Created by Sarah Westcott on 1/29/13.
// Copyright (c) 2013 Schloss Lab. All rights reserved.
//
#ifndef Mothur_removedistscommand_h
#define Mothur_removedistscommand_h
#include "command.hpp"
class RemoveDistsCommand : public Command {
public:
RemoveDistsCommand(string);
~RemoveDistsCommand(){}
vector<string> setParameters();
string getCommandName() { return "remove.dists"; }
string getCommandCategory() { return "General"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Remove.dists"; }
string getDescription() { return "removes distances from a phylip or column file related to groups or sequences listed in an accnos file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
unordered_set<string> names;
string accnosfile, phylipfile, columnfile;
bool abort;
vector<string> outputNames;
int readPhylip();
int readColumn();
};
#endif
|
