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PMarkov Class Reference

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

#include <seqpp/PMarkov.h>

Inheritance diagram for PMarkov:

Markov PhasedMarkov List of all members.

Public Member Functions

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

Protected Attributes

pmm_tree * _pmmtree
 Parcimonious Context Tree.

Detailed Description

Parcimonious Markov modelling, estimation and simulation.

This is a special case of a phased Parcimonious Markov [PhasedPMarkov] model when only one phase is considered, and also a Markov object.

Constructor & Destructor Documentation

PMarkov::PMarkov (  const SequenceSet &  seqset,
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
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)

PMarkov::PMarkov (  const Sequence &  seq,
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
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)

PMarkov::PMarkov (  const string &  partitionfile,
const SequenceSet &  seqset,
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
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

PMarkov::PMarkov (  const string &  partitionfile,
const Translator &  trans,
const Sequence &  seq,
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
seq sequence for estimation
trans a Translator is required for the partition reading
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

PMarkov::PMarkov (  unsigned long *  count,
short  size,
short  order,
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
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)

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

Constructor 6 from a coded-word count.

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
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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