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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
Partitionoperator= (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)


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:


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


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



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