Partition Class Reference

Dealer of alphabet partitions. More...

#include <seqpp/Partition.h>

List of all members.

Public Member Functions
	Partition ()
	empty constructor
	Partition (short alphabet_size)
	constructor with integrated creation of the set of partitions
	Partition (const Translator &alphabet, const string &pfile)
	Constructor from a file containing the partitions or the list of synonymous tokens.
	Partition (const Partition &part)
	copy constructor
	~Partition ()
	destructor
Partition &	operator= (Partition &part)
	oeprator =
const vector< vector< short > > &	list_possible_elements ()
	initialize the list_possible_elements of possible tokens'subset in a partition and return it
const vector< vector< short > > &	synonymous () const
	returns the synonymous list
const vector< int > &	nbpartition_with_nbelement () const
	return the number of partition per number of elements
const vector< int > &	compute_nbpartition_with_nbelement ()
	compute and return the number of partition per number of elements, if no cutoff method previously called
long	tell_nbposs () const
	returns the number of possible tokens'subset in a partition
short	tell_size () const
	returns the size of the space to partition
bool	create_default ()
	create the default motif if it not exists
int	motifdefault () const
	return the index of the default motif
bool	motifdefault_skip () const
	true if the default motif is added to _list_possib at the end, false if it already exists
long	tell_cardinal () const
	cardinal of the partition
const_iterator	begin () const
	first possibility of the partition
const_iterator	end () const
	end of list of possibilities (not a possibility)

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Detailed Description

Dealer of alphabet partitions.

Let a partition of an alphabet be a set of tokens'subset, i.e. a division of the alphabet into subset. The Partition object gives 2 possibilities:

• to compute the overall set of possible partitions (automatically generated) given the alphabet

• to compute the overall set of possible partitions (automatically generated) given a synonymous pseud-alphabet: by declaring synonymous tokens, it is possible to group tokens as a single predictor so that the number of partitions is lower.
  In this case, a configuration file with the top key word "#Synonymous", containing the lists of synonymous tokens, is required.
  Exple:

  #Synonymous
  a t
  g c
  

• to input a selected set of partitions. In this case, in a configuration file after a "#Partition" on the first line, each partition is represented as a list of tokens'subset delimited by a "|", each subset being composed with tokens of the alphabet separed by space
  Exple:

  #Partition
  a | g | c | t
  a g | c | t
  a c t | g
  

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Constructor & Destructor Documentation

Partition::Partition

(

short

alphabet_size

)

[inline]

constructor with integrated creation of the set of partitions

Parameters:

alphabet_size

size of the alphabet

Partition::Partition	(	const Translator &	alphabet,
		const string &	pfile
	)			[inline]

Constructor from a file containing the partitions or the list of synonymous tokens.

Parameters:

	alphabet	a link to a Translator object required for the file reading
	pfile	partitions file -> 1st possibility: after a "#Partition" on the first line, each partition is represented as a list of tokens'subset delimited by a "|", each subset being composed with tokens of the alphabet separed by space Example: #Partition a g | c t -> 2nd possibility: after a "#Synonymous" on the first line, tokens are grouped (separed by spaces) into synonymous classes on each line Example: #Synonymous a t g c

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

• Partition.h