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
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
|
//
// classifysvmsharedcommand.h
// Mothur
//
// Created by Joshua Lynch on 6/28/2013.
// Copyright (c) 2013 Schloss Lab. All rights reserved.
//
// This class is based on ClassifySharedCommand
//
#ifndef __Mothur__classifysvmsharedcommand__
#define __Mothur__classifysvmsharedcommand__
#include "command.hpp"
#include "inputdata.h"
#include "svm.hpp"
#include "designmap.h"
class ClassifySvmSharedCommand : public Command {
public:
ClassifySvmSharedCommand(string);
~ClassifySvmSharedCommand() = default;;
vector<string> setParameters();
string getCommandName() { return "classify.svm"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Classify.svm\n"; }
string getDescription() { return "implements the support vector machine machine learning algorithm to identify OTUs that can be used to differentiate between various groups of samples"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
void readSharedAndDesignFiles(const string&, const string&, LabeledObservationVector&, FeatureVector&);
void readSharedRAbundVectors(vector<SharedRAbundVector*>&, DesignMap&, LabeledObservationVector&, FeatureVector&, vector<string>);
vector<double>& getSmocList() { return smocList; }
const KernelParameterRangeMap& getKernelParameterRangeMap() { return kernelParameterRangeMap; }
private:
bool abort;
vector<string> outputNames, Groups;
string sharedfile, designfile;
set<string> labels;
bool allLines;
int processors;
bool useTiming;
DesignMap designMap;
// mode is either "rfe" or "classify"
string mode;
int evaluationFoldCount;
int trainingFoldCount;
vector<double> smocList;
KernelParameterRangeMap kernelParameterRangeMap;
string transformName;
int verbosity;
double stdthreshold;
void processSharedAndDesignData(vector<SharedRAbundVector*> lookup, vector<string>);
void trainSharedAndDesignData(vector<SharedRAbundVector*> lookup, vector<string>);
void getParameterValue(int& target, string pstring, int defaultvalue) {
if (pstring == "not found" or pstring == "") {
target = defaultvalue;
}
else {
util.mothurConvert(pstring, target);
}
}
};
#endif /* defined(__Mothur__classifysvmsharedcommand__) */
|
