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PhasedPMarkov Class Reference

Phased Parcimonious Markov modelling, estimation and simulation. More...

#include <seqpp/PhasedPMarkov.h>

Inheritance diagram for PhasedPMarkov:

PhasedMarkov List of all members.

Public Member Functions

 PhasedPMarkov (const SequenceSet &seqset, short phase, short initial_phase=0, double prior_alpha=-1., double penalty=0., const string &xmlfile=string())
 Constructor 1 from a SequenceSet.
 PhasedPMarkov (const Sequence &seq, short phase, short initial_phase=0, double prior_alpha=-1., double penalty=0., const Translator &trans=Translator(), const string &xmlfile=string())
 Constructor 2 from a Sequence.
 PhasedPMarkov (const string &partitionfile, const SequenceSet &seqset, short phase, short initial_phase=0, double prior_alpha=-1., double penalty=0., const string &xmlfile=string())
 Constructor 3 from a SequenceSet and a Partition -file.
 PhasedPMarkov (const string &partitionfile, const Translator &trans, const Sequence &seq, short phase, short initial_phase=0, double prior_alpha=-1., double penalty=0., const string &xmlfile=string())
 Constructor 4 from a Sequence and a Partition -file.
 PhasedPMarkov (unsigned long **count, short size, short order, short phase, short initial_phase=0, double prior_alpha=-1., double penalty=0., const Translator &trans=Translator(), const string &xmlfile=string())
 Constructor 5 from a coded-word count.
 PhasedPMarkov (const string &partitionfile, const Translator &trans, unsigned long **count, short order, short phase, short initial_phase=0, double prior_alpha=-1., double penalty=0., const string &xmlfile=string())
 Constructor 6 from a coded-word count and a Partition -file.
void estimate (unsigned long **count, bool decal_required, const Translator &trans, Partition &p, short phase, short initial_phase, double prior_alpha, double penalty, const string &xmlfile)
 performs the estimation [used by each constructor]
 ~PhasedPMarkov ()
 Destructor.

Protected Attributes

pmm_tree * _pmmtree
 Parcimonious Context Trees.

Detailed Description

Phased Parcimonious Markov modelling, estimation and simulation.

PhasedPMarkov is a PhasedMarkov object with a different estimation step. This object performs the estimation with the Parcimonious Markov algorithm and then transfoms, once per phase, the parcimonious context tree in a markovian matrix. xml outputs can be activated to save the associated trees.


Constructor & Destructor Documentation

PhasedPMarkov::PhasedPMarkov const SequenceSet seqset,
short  phase,
short  initial_phase = 0,
double  prior_alpha = -1.,
double  penalty = 0.,
const string &  xmlfile = string()
[inline]
 

Constructor 1 from a SequenceSet.

Parameters:
seqset a set of sequences for estimation
phase phase
initial_phase phase of the first element of each sequence
prior_alpha alpha for the a priori law, by default -1. means 1./alphabet_size
penalty penalty on the leaves number, by default 0
xmlfile xmlfile for tree saving (if xml2 activated)

PhasedPMarkov::PhasedPMarkov const Sequence seq,
short  phase,
short  initial_phase = 0,
double  prior_alpha = -1.,
double  penalty = 0.,
const Translator trans = Translator(),
const string &  xmlfile = string()
[inline]
 

Constructor 2 from a Sequence.

Parameters:
seq sequence for estimation
phase phase
initial_phase phase of the first element of each sequence
prior_alpha alpha for the a priori law, by default -1. means 1./alphabet_size
penalty penalty on the leaves number, by default 0
trans a Translator is required only for the xml saving
xmlfile xmlfile for tree saving (if xml2 activated)

PhasedPMarkov::PhasedPMarkov const string &  partitionfile,
const SequenceSet seqset,
short  phase,
short  initial_phase = 0,
double  prior_alpha = -1.,
double  penalty = 0.,
const string &  xmlfile = string()
[inline]
 

Constructor 3 from a SequenceSet and a Partition -file.

Parameters:
partitionfile file containing a selected partition, when default overall partition is too heavy
seqset a set of sequences for estimation
phase phase
initial_phase phase of the first element of each sequence
prior_alpha alpha for the a priori law, by default -1. means 1./alphabet_size
penalty penalty on the leaves number, by default 0
xmlfile xmlfile for tree saving (if xml2 activated)
Exple of partitionfile (grouped tokens, separed with a "|", beware the spaces) with 4 partitions
     a c | g t
     a c | g | t
     a | c | g | t
     c g t | a

PhasedPMarkov::PhasedPMarkov const string &  partitionfile,
const Translator trans,
const Sequence seq,
short  phase,
short  initial_phase = 0,
double  prior_alpha = -1.,
double  penalty = 0.,
const string &  xmlfile = string()
[inline]
 

Constructor 4 from a Sequence and a Partition -file.

Parameters:
partitionfile file containing a selected partition, when default overall partition is too heavy
trans a Translator is required for the partition reading
seq sequence for estimation
phase phase
initial_phase phase of the first element of each sequence
prior_alpha alpha for the a priori law, by default -1. means 1./alphabet_size
penalty penalty on the leaves number, by default 0
xmlfile xmlfile for tree saving (if xml2 activated)
Exple of partitionfile (grouped tokens, separed with a "|", beware the spaces) with 4 partitions
    a c | g t
    a c | g | t
    a | c | g | t
    c g t | a

PhasedPMarkov::PhasedPMarkov unsigned long **  count,
short  size,
short  order,
short  phase,
short  initial_phase = 0,
double  prior_alpha = -1.,
double  penalty = 0.,
const Translator trans = Translator(),
const string &  xmlfile = string()
[inline]
 

Constructor 5 from a coded-word count.

Parameters:
count count of all the coded word(base size) of size order+1 for each phase, for estimation
size alphabet size
order markovian order associated to the word count
phase phase
initial_phase phase of the first element of each sequence
prior_alpha alpha for the a priori law, by default -1. means 1./alphabet_size
penalty penalty on the leaves number, by default 0
trans a Translator is required only for the xml saving
xmlfile xmlfile for tree saving (if xml2 activated)

PhasedPMarkov::PhasedPMarkov const string &  partitionfile,
const Translator trans,
unsigned long **  count,
short  order,
short  phase,
short  initial_phase = 0,
double  prior_alpha = -1.,
double  penalty = 0.,
const string &  xmlfile = string()
[inline]
 

Constructor 6 from a coded-word count and a Partition -file.

Parameters:
partitionfile file containing a selected partition, when default overall partition is too heavy
trans a Translator is required for the partition reading
count count of all the coded word(base size) of size order+1 for each phase, for estimation
order markovian order associated to the word count
phase phase
initial_phase phase of the first element of each sequence
prior_alpha alpha for the a priori law, by default -1. means 1./alphabet_size
penalty penalty on the leaves number, by default 0
xmlfile xmlfile for tree saving (if xml2 activated)
Exple of partitionfile (grouped tokens, separed with a "|", beware the spaces) with 4 partitions
    a c | g t
    a c | g | t
    a | c | g | t
    c g t | a


The documentation for this class was generated from the following file:



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