Raw content of Bio::Seq::LargeSeq
<![CDATA[# $Id: LargeSeq.pm,v 1.11 2002/10/22 07:38:40 lapp Exp $
#
# BioPerl module for Bio::Seq::LargeSeq
#
# Cared for by Ewan Birney, Jason Stajich
#
# Copyright Ewan Birney, Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Seq::LargeSeq - SeqI compliant object that stores sequence as files in /tmp
=head1 SYNOPSIS
# normal primary seq usage
=head1 DESCRIPTION
This object stores a sequence as a series of files in a temporary
directory. The aim is to allow someone the ability to store very large
sequences (eg, E<gt> 100MBases) in a file system without running out of memory
(eg, on a 64 MB real memory machine!).
Of course, to actually make use of this functionality, the programs
which use this object B<must> not call $primary_seq-E<gt>seq otherwise the
entire sequence will come out into memory and probably paste your
machine. However, calls $primary_seq-E<gt>subseq(10,100) will cause only
90 characters to be brought into real memory.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://www.bioperl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Ewan Birney
Email birney@ebi.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Seq::LargeSeq;
use vars qw($AUTOLOAD @ISA);
use strict;
# Object preamble - inherits from Bio::Root::Objecttest 8,
use Bio::Seq::LargePrimarySeq;
use Bio::Seq;
@ISA = qw(Bio::Seq);
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($pseq) = $self->_rearrange([qw(PRIMARYSEQ)], @args);
if( ! defined $pseq ) {
$pseq = new Bio::Seq::LargePrimarySeq(@args);
}
$self->primary_seq($pseq);
return $self;
}
=head2 trunc
Title : trunc
Usage : $subseq = $myseq->trunc(10,100);
Function: Provides a truncation of a sequence,
Example :
Returns : a fresh Bio::SeqI object
Args :
=cut
sub trunc {
my ($self, $s, $e) = @_;
return new Bio::Seq::LargeSeq(
'-display_id' => $self->display_id,
'-accession_number' => $self->accession_number,
'-desc' => $self->desc,
'-alphabet' => $self->alphabet,
-primaryseq =>
$self->primary_seq->trunc($s,$e));
}
=head2 Bio::Seq::LargePrimarySeq methods
=cut
=head2 add_sequence_as_string
Title : add_sequence_as_string
Usage : $seq->add_sequence_as_string("CATGAT");
Function: Appends additional residues to an existing LargePrimarySeq object.
This allows one to build up a large sequence without storing
entire object in memory.
Returns : Current length of sequence
Args : string to append
=cut
sub add_sequence_as_string {
my ($self,$str) = @_;
return $self->primary_seq->add_sequence_as_string($str);
}
1;
]]>