Raw content of Bio::LiveSeq::DNA
<![CDATA[# $Id: DNA.pm,v 1.9 2001/10/22 08:22:51 heikki Exp $
#
# bioperl module for Bio::LiveSeq::DNA
#
# Cared for by Joseph Insana <insana@ebi.ac.uk> <jinsana@gmx.net>
#
# Copyright Joseph Insana
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=head1 NAME
Bio::LiveSeq::DNA - DNA object for LiveSeq
=head1 SYNOPSIS
# documentation needed
=head1 DESCRIPTION
This holds the DNA sequence (or the RNA in the case of cDNA entries)
and is accessed by exons, genes, transcripts... objects
=head1 AUTHOR - Joseph A.L. Insana
Email: Insana@ebi.ac.uk, jinsana@gmx.net
Address:
EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom
=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::LiveSeq::DNA;
$VERSION=1.4;
# Version history:
# Mon Mar 20 19:21:22 GMT 2000 v.1.0 begun
# Tue Mar 21 14:20:30 GMT 2000 v.1.1 new() is now here, not inherited
# Wed Mar 22 19:43:20 GMT 2000 v.1.2 length override
# Thu Jun 22 20:02:39 BST 2000 v 1.3 valid() from SeqI now moved here, as override
# Wed Mar 28 17:01:59 BST 2001 v 1.4 changed croaks into throw
use strict;
use vars qw($VERSION @ISA);
use Bio::LiveSeq::SeqI 3.2; # uses SeqI, inherits from it
@ISA=qw(Bio::LiveSeq::SeqI);
=head2 new
Title : new
Usage : $dna = Bio::LiveSeq::DNA->new(-seq => "atcgaccaatggacctca",
-offset => 3 );
Function: generates a new Bio::LiveSeq::DNA
Returns : reference to a new object of class DNA
Errorcode -1
Args : a string
AND an optional offset to create nucleotide labels (default is 1, i.e.
starting the count of labels from "1") -> do not bother using it ->
it could be used by alternative loaders !EMBL format
NOTE : strand of DNA is set to 1 by default
=cut
sub new {
my ($thing, %args) = @_;
my $class = ref($thing) || $thing;
my (%empty,$obj);
if ($args{-seq}) {
$obj = $thing->string2chain($args{-seq},$args{-offset}); # inherited from ChainI
$obj = bless $obj, $class;
} else {
$obj=\%empty;
$obj = bless $obj, $class;
$obj->throw("$class not initialized properly");
}
$obj->{'alphabet'}='dna'; # set alphabet default
$obj->{'strand'}=1; # set strand default = 1
$obj->{'seq'}=$obj; # set seq field to itself
return $obj;
}
# START method
# it has to be redefined here because default from SeqI accesses field "start"
sub start {
my $self = shift;
return $self->{'begin'}; # the chain's start is called begin
}
# it is overridden to provide faster output
sub length {
my $self=shift;
return $self->chain_length();
}
# it is overridden to provide MUCH faster output
sub valid {
my $self=shift(@_);
return $self->label_exists(@_);
}
1;
]]>