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
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
|
//
// File: test_models.cpp
// Created by: Julien Dutheil
// Created on: Tue Jan 22 22:18 2013
//
/*
Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
This software is a computer program whose purpose is to provide classes
for numerical calculus. This file is part of the Bio++ project.
This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can use,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".
As a counterpart to the access to the source code and rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty and the software's author, the holder of the
economic rights, and the successive licensors have only limited
liability.
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
*/
#include <Bpp/Phyl/Model/Nucleotide/GTR.h>
#include <Bpp/Phyl/Model/Codon/YN98.h>
#include <Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h>
#include <Bpp/Seq/Alphabet/AlphabetTools.h>
#include <Bpp/Seq/Alphabet/CodonAlphabet.h>
#include <Bpp/Seq/GeneticCode/StandardGeneticCode.h>
#include <Bpp/Numeric/Function/Functions.h>
#include <Bpp/Numeric/Function/ReparametrizationFunctionWrapper.h>
#include <Bpp/Numeric/ParameterList.h>
#include <Bpp/Numeric/AbstractParametrizable.h>
#include <Bpp/Numeric/Random/RandomTools.h>
#include <iostream>
using namespace bpp;
using namespace std;
class DummyFunction:
public virtual Function,
public AbstractParametrizable
{
public:
DummyFunction(const SubstitutionModel& model):
AbstractParametrizable("")
{
addParameters_(model.getParameters());
}
DummyFunction* clone() const { return new DummyFunction(*this); }
void setParameters(const ParameterList& pl) {
matchParametersValues(pl);
}
double getValue() const { return 0; }
void fireParameterChanged(const bpp::ParameterList&) {}
};
bool testModel(SubstitutionModel& model) {
ParameterList pl = model.getParameters();
DummyFunction df(model);
ReparametrizationFunctionWrapper redf(&df, pl, false);
//Try to modify randomly each parameter and check that the new parameter apply correctly:
for (unsigned int i = 0; i < 10; ++i) {
//Get random parameters (unconstrained):
ParameterList pl2 = redf.getParameters();
for (size_t j = 0; j < pl.size(); ++j) {
double value = (RandomTools::flipCoin() ? 1. : -1) * RandomTools::giveRandomNumberBetweenZeroAndEntry(1);
pl2[j].setValue(value);
}
//Apply unconstrained parameters:
redf.setParameters(pl2);
//Retrieve transformed parameters:
pl2 = df.getParameters();
//pl2.printParameters(cout);
//Now apply the new parameters and retrieve them again:
model.matchParametersValues(pl2);
ParameterList pl3 = model.getParameters();
//Compare the two lists:
for (size_t j = 0; j < pl.size(); ++j) {
if (abs(pl2[j].getValue() - pl3[j].getValue()) > 0.0000001) {
cerr << "ERROR for parameter " << pl2[j].getName() << ": " << pl2[j].getValue() << "<>" << pl3[j].getValue() << endl;
return false;
}
}
}
return true;
}
int main() {
//Nucleotide models:
GTR gtr(&AlphabetTools::DNA_ALPHABET);
if (!testModel(gtr)) return 1;
//Codon models:
StandardGeneticCode gc(&AlphabetTools::DNA_ALPHABET);
const CodonAlphabet* codonAlphabet = new CodonAlphabet(&AlphabetTools::DNA_ALPHABET);
FrequenciesSet* fset = CodonFrequenciesSet::getFrequenciesSetForCodons(CodonFrequenciesSet::F3X4, &gc);
YN98 yn98(&gc, fset);
if (!testModel(yn98)) return 1;
delete codonAlphabet;
return 0;
}
|
