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Version 4.0.0 |
#include <seqpp/PhasedPMarkov.h>
Inheritance diagram for PhasedPMarkov:
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. |
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.
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Constructor 1 from a SequenceSet.
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Constructor 2 from a Sequence.
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Constructor 3 from a SequenceSet and a Partition -file.
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Constructor 4 from a Sequence and a Partition -file.
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Constructor 5 from a coded-word count.
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Constructor 6 from a coded-word count and a Partition -file.
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Contributors : M.Baudry, P.Y.Bourguignon, M.Hoebeke, V.Miele, P.Nicolas, G.Nuel, H.Richard, D.Robelin |