bpp-core  2.2.0
FullHmmTransitionMatrix.cpp
Go to the documentation of this file.
1 //
2 // File: FullHmmTransitionMatrix.cpp
3 // Created by: Laurent Guéguen
4 // Created on: samedi 21 septembre 2013, à 14h 43
5 //
6 
7 /*
8 Copyright or © or Copr. Bio++Development Team, (November 16, 2004)
9 
10 This software is a computer program whose purpose is to provide classes
11 for phylogenetic data analysis.
12 
13 This software is governed by the CeCILL license under French law and
14 abiding by the rules of distribution of free software. You can use,
15 modify and/ or redistribute the software under the terms of the CeCILL
16 license as circulated by CEA, CNRS and INRIA at the following URL
17 "http://www.cecill.info".
18 
19 As a counterpart to the access to the source code and rights to copy,
20 modify and redistribute granted by the license, users are provided only
21 with a limited warranty and the software's author, the holder of the
22 economic rights, and the successive licensors have only limited
23 liability.
24 
25 In this respect, the user's attention is drawn to the risks associated
26 with loading, using, modifying and/or developing or reproducing the
27 software by the user in light of its specific status of free software,
28 that may mean that it is complicated to manipulate, and that also
29 therefore means that it is reserved for developers and experienced
30 professionals having in-depth computer knowledge. Users are therefore
31 encouraged to load and test the software's suitability as regards their
32 requirements in conditions enabling the security of their systems and/or
33 data to be ensured and, more generally, to use and operate it in the
34 same conditions as regards security.
35 
36 The fact that you are presently reading this means that you have had
37 knowledge of the CeCILL license and that you accept its terms.
38 */
39 
41 
42 #include "../../Text/TextTools.h"
43 
44 #include "../Matrix/MatrixTools.h"
45 #include "../VectorTools.h"
46 
47 using namespace bpp;
48 using namespace std;
49 
52  AbstractParametrizable(prefix),
53  vSimplex_()
54 {
55  size_t size=(size_t)getNumberOfStates();
56 
57  for (size_t i=0; i<size; i++)
58  {
59  vSimplex_.push_back(Simplex(size,1));
60  ParameterList pl=vSimplex_[i].getParameters();
61  for (size_t j=0; j<pl.size(); j++)
62  {
63  Parameter* p=pl[j].clone();
64  p->setName(TextTools::toString(i+1)+"."+p->getName());
65  addParameter_(p);
66  }
67  }
68 }
69 
73  vSimplex_(hptm.vSimplex_)
74 {
75 }
76 
78 {
80  AbstractParametrizable::operator=(hptm);
81 
82  return *this;
83 }
84 
86 {
87  if (mat.getNumberOfRows()!=vSimplex_.size())
88  throw BadSizeException("FullHmmTransitionMatrix::setTransitionProbabilities: Wrong number of rows in given Matrix", mat.getNumberOfRows(), vSimplex_.size());
89 
90  ParameterList pl;
91 
92  for (size_t i=0; i<mat.getNumberOfRows();i++)
93  {
94  vSimplex_[i].setFrequencies(mat.row(i));
95  ParameterList pls=vSimplex_[i].getParameters();
96  for (size_t j=0; j<pls.size(); j++)
97  {
98  Parameter* p=pls[j].clone();
99  p->setName(TextTools::toString(i+1)+"."+p->getName());
100  pl.addParameter(p);
101  }
102  }
103 
105 }
106 
107 
109  {
110  if (!upToDate_){
111  for (size_t i=0; i<vSimplex_.size(); i++)
112  for (size_t j=0; j<vSimplex_[i].dimension(); j++)
113  pij_(i,j)=vSimplex_[i].prob(j);
114  upToDate_=true;
115  }
116 
117  return pij_;
118  }
119 
120 const std::vector<double>& FullHmmTransitionMatrix::getEquilibriumFrequencies() const
121 {
122  size_t salph=getNumberOfStates();
123 
124  if (!upToDate_){
125  pij_=getPij();
126 
128 
129  for (size_t i = 0; i < salph; i++)
130  eqFreq_[i] = tmpmat_(0,i);
131 
132  upToDate_=true;
133  }
134 
135  return eqFreq_;
136 }
137 
139 {
140  size_t salph=getNumberOfStates();
141 
142  for (size_t i=0; i< salph; i++)
143  {
144  ParameterList pl=vSimplex_[i].getParameters();
145 
146  for (size_t j=0; j<pl.size(); j++)
147  pl[j].setValue(getParameterValue(TextTools::toString(i+1)+"."+pl[j].getName()));
148 
149  vSimplex_[i].matchParametersValues(pl);
150  }
151 
152  upToDate_=false;
153 }
154 
155 
Hidden states alphabet.
The matrix template interface.
Definition: Matrix.h:58
FullHmmTransitionMatrix & operator=(const FullHmmTransitionMatrix &hptm)
void fireParameterChanged(const ParameterList &parameters)
Notify the class when one or several parameters have changed.
This class allows to perform a correspondence analysis.
A partial implementation of the Parametrizable interface.
const Matrix< double > & getPij() const
Get all transition probabilities as a matrix.
size_t size() const
Definition: ParameterList.h:90
STL namespace.
This class is designed to facilitate the manipulation of parameters.
Definition: Parameter.h:135
Describe the transition probabilities between hidden states of a Hidden Markov Model.
A Simplex object, used to define sets of probabilities that sum 1.
Definition: Simplex.h:100
static std::string toString(T t)
General template method to convert to a string.
Definition: TextTools.h:189
The parameter list object.
Definition: ParameterList.h:61
Wrong size exception class.
Definition: Exceptions.h:334
Partial implementation of HmmTransitionMatrix.
ParameterList * clone() const
Create a copy of this object and send a pointer to it.
Definition: ParameterList.h:82
bool matchParametersValues(const ParameterList &parameters)
Update the parameters from parameters.
static void pow(const Matrix &A, size_t p, Matrix &O)
Compute the power of a given matrix.
Definition: MatrixTools.h:355
virtual const std::string & getName() const
Get the name of this parameter.
Definition: Parameter.h:234
void addParameter_(Parameter *parameter)
virtual void setName(const std::string &name)
Set the name of this parameter.
Definition: Parameter.h:208
virtual void addParameter(const Parameter &param)
Add a new parameter at the end of the list.
virtual std::vector< Scalar > row(size_t i) const =0
FullHmmTransitionMatrix(const HmmStateAlphabet *alph, const std::string &prefix="")
void setTransitionProbabilities(const Matrix< double > &mat)
Set the matrix of the transition probabilities.
virtual size_t getNumberOfRows() const =0
AbstractHmmTransitionMatrix & operator=(const AbstractHmmTransitionMatrix &hptm)
const std::vector< double > & getEquilibriumFrequencies() const
double getParameterValue(const std::string &name) const
Get the value for parameter of name &#39;name&#39;.