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
48
49
|
#ifndef SUMMARYTAXCOMMAND_H
#define SUMMARYTAXCOMMAND_H
/*
* summarytaxcommand.h
* Mothur
*
* Created by westcott on 9/23/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "counttable.h"
/**************************************************************************************************/
class SummaryTaxCommand : public Command {
public:
SummaryTaxCommand(string);
~SummaryTaxCommand(){}
vector<string> setParameters();
string getCommandName() { return "summary.tax"; }
string getCommandCategory() { return "Phylotype Analysis"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Summary.tax"; }
string getDescription() { return "summarize the taxonomies of a set of sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, relabund;
string taxfile, namefile, groupfile, countfile, output;
int printlevel, threshold;
vector<string> outputNames;
map<string, int> nameMap;
string processTaxMap(string);
int findMaxLevel(string);
};
/**************************************************************************************************/
#endif
|
