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Version 4.0.0 |
#include <seqpp/PMarkov.h>
Inheritance diagram for PMarkov:
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. |
This is a special case of a phased Parcimonious Markov [PhasedPMarkov] model when only one phase is considered, and also a Markov object.
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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.
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Contributors : M.Baudry, P.Y.Bourguignon, M.Hoebeke, V.Miele, P.Nicolas, G.Nuel, H.Richard, D.Robelin |