SequenceSet Class Reference

Set of Sequence objects. More...

#include <seqpp/SequenceSet.h>

Inheritance diagram for SequenceSet:

List of all members.

Public Member Functions
	SequenceSet ()
	Default constructor.
	SequenceSet (const string &seq_list_file, const string &alpha_file, short order, int nbseq=BUFFERSEQ)
	constructor with a alphabet-needed file
	SequenceSet (const string &seq_list_file, short mode, const string &line2parse, bool case_sensitivity, short order, int nbseq=BUFFERSEQ)
	constructor with a alphabet-needed line2parse

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Detailed Description

Set of Sequence objects.

from :

• a Fasta file (with 1 or more sequences inside separated by a line beginning with a SKIPCHAR) or a Genbank file
  
• or a file containing the name of many Fasta (or a Genbank) sequence files
  

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Constructor & Destructor Documentation

SequenceSet::SequenceSet	(	const string &	seq_list_file,
		const string &	alpha_file,
		short	order,
		int	nbseq = BUFFERSEQ
	)

constructor with a alphabet-needed file

Parameters:

	seq_list_file	file, among the 3 possibilities of files.
	alpha_file	file for initializing the alphabet (see Translator doc)
	order	Markovian order,
	nbseq	number of sequences

References PrimarySequenceSet< Sequence >::_array_seq, PrimaryCount::_coder, PrimaryCount::_coder_in, PrimaryCount::_count, PrimarySequenceSet< Sequence >::_length_max, PrimarySequenceSet< Sequence >::_nb_seq, PrimaryCount::_nbinv, PrimaryCount::_nbvalue, PrimaryCount::_order, PrimarySequenceSet< Sequence >::_total_length, PrimarySequenceSet< Sequence >::_transl, Translator::tell_alphabet_size(), Translator::tell_nb_inv(), and PrimaryCount::tell_nb_value().

SequenceSet::SequenceSet	(	const string &	seq_list_file,
		short	mode,
		const string &	line2parse,
		bool	case_sensitivity,
		short	order,
		int	nbseq = BUFFERSEQ
	)

constructor with a alphabet-needed line2parse

Parameters:

	seq_list_file	file, among the 3 possibilities of files.
	mode	number of char for a token in the alphabet
	line2parse	string for initializing the alphabet (see Translator doc)
	case_sensitivity	true for being case sensitive
	order	Markovian order,
	nbseq	number of sequences

References PrimarySequenceSet< Sequence >::_array_seq, PrimaryCount::_coder, PrimaryCount::_coder_in, PrimaryCount::_count, PrimarySequenceSet< Sequence >::_length_max, PrimarySequenceSet< Sequence >::_nb_seq, PrimaryCount::_nbinv, PrimaryCount::_nbvalue, PrimaryCount::_order, PrimarySequenceSet< Sequence >::_total_length, PrimarySequenceSet< Sequence >::_transl, Translator::tell_alphabet_size(), Translator::tell_nb_inv(), and PrimaryCount::tell_nb_value().

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

• SequenceSet.h
• SequenceSet.cc