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
50
51
52
|
#ifndef Mothur_classifytreecommand_h
#define Mothur_classifytreecommand_h
//
// classifytreecommand.h
// Mothur
//
// Created by Sarah Westcott on 2/20/12.
// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
#include "command.hpp"
#include "readtree.h"
#include "treemap.h"
#include "counttable.h"
class ClassifyTreeCommand : public Command {
public:
ClassifyTreeCommand(string);
~ClassifyTreeCommand(){}
vector<string> setParameters();
string getCommandName() { return "classify.tree"; }
string getCommandCategory() { return "Phylotype Analysis"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Classify.tree"; }
string getDescription() { return "Find the consensus taxonomy for the descendant of each tree node"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string treefile, taxonomyfile, groupfile, namefile, countfile, output;
bool abort;
vector<string> outputNames;
int numUniquesInName, cutoff;
map<string, string> nameMap;
map<string, int> nameCount;
map<string, string> taxMap;
CountTable* ct;
int getClassifications(Tree*&);
map<string, set<string> > getDescendantList(Tree*&, int, map<int, map<string, set<string> > >);
string getTaxonomy(set<string>, int&);
};
#endif
|
