Raw content of Bio::EnsEMBL::Map::Ditag
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::Map::Ditag
=head1 SYNOPSIS
my $feature = Bio::EnsEMBL::Map::Ditag->new(
-dbID => $tag_id,
-name => $name,
-type => $type,
-tag_count => $tag_count,
-sequence => $sequence,
-adaptor => $dbAdaptor
);
=head1 DESCRIPTION
Represents an unmapped ditag object in the EnsEMBL database.
Corresponds to original tag containing the full sequence. This can be
a single piece of sequence like CAGE tags or a ditag with concatenated
sequence from 5' and 3' end like GIS or GSC tags.
=head1 METHODS
=cut
package Bio::EnsEMBL::Map::Ditag;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Storable;
use Bio::EnsEMBL::Utils::Exception qw( throw );
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
@ISA = qw(Bio::EnsEMBL::Storable);
=head2 new
Arg [1] : (optional) int $dbID
Arg [2] : (optional) string name
Arg [3] : (optional) string type
Arg [4] : (optional) int tag_count
Arg [5] : (optional) string sequence
Arg [6] : (optional) Bio::EnsEMBL::Map::DBSQL::DitagAdaptor $adaptor
Description: Creates a new ditag
Returntype : Bio::EnsEMBL::Map::Ditag
Exceptions : none
Caller : general
=cut
sub new {
my ($caller, @args) = @_;
my ($dbID, $name, $type, $tag_count, $sequence, $adaptor) = rearrange(
[ 'DBID', 'NAME', 'TYPE', 'TAG_COUNT', 'SEQUENCE', 'ADAPTOR' ], @args);
my $class = ref($caller) || $caller;
if(!$name or !$type or !$sequence) {
throw('Missing information for Ditag object:
Bio::EnsEMBL::Map::Ditag->new (
-dbID => $tag_id,
-name => $name,
-type => $type,
-tag_count => $tag_count,
-sequence => $sequence,
-adaptor => $dbAdaptor
);');
}
if(!$tag_count){ $tag_count = 0; }
if(!($sequence =~ /^[ATCGN]+$/i)){
throw('ditag sequence contains non-standard characters: '.$sequence);
}
my $self = bless( {'dbID' => $dbID,
'name' => $name,
'type' => $type,
'tag_count' => $tag_count,
'sequence' => $sequence,
'adaptor' => $adaptor,
}, $class);
return $self;
}
=head2 name
Arg [1] : (optional) string $type
Example : $type = $ditag->name;
Description: Getter/Setter for the name of a ditag
Returntype : text
Caller : general
=cut
sub name {
my $self = shift;
if(@_) {
$self->{'name'} = shift;
}
return $self->{'name'};
}
=head2 dbID
Arg [1] : (optional) int id
Example : $ditag_id = $ditag->dbID;
Description: Getter/Setter for the dbID of a ditag
Returntype : int
Caller : general
=cut
sub dbID {
my $self = shift;
if(@_) {
$self->{'dbID'} = shift;
}
return $self->{'dbID'};
}
=head2 type
Arg [1] : (optional) string $type
Example : $type = $ditag->type;
Description: Getter/Setter for the type of a ditag
Returntype : text
Caller : general
=cut
sub type {
my $self = shift;
if(@_) {
$self->{'type'} = shift;
}
return $self->{'type'};
}
=head2 tag_count
Arg [1] : (optional) string $tag_count
Example : $type = $ditag->tag_count;
Description: Getter/Setter for the tag_count of a ditag
Returntype : int
Caller : general
=cut
sub tag_count {
my $self = shift;
if(@_) {
$self->{'tag_count'} = shift;
}
return $self->{'tag_count'};
}
=head2 sequence
Arg [1] : (optional) string $sequence
Example : $sequence = $ditag->sequence;
Description: Getter/Setter for the sequence of a ditag
Returntype : text
Caller : general
=cut
sub sequence {
my $self = shift;
if(@_) {
$self->{'sequence'} = shift;
}
return $self->{'sequence'};
}
=head2 get_ditagFeatures
Arg : none
Example : @features = @{$ditag->get_ditagFeatures};
Description: Fetch ditag_features created from this ditag
Returntype : listref of Bio::EnsEMBL::Map::DitagFeature
Caller : general
=cut
sub get_ditagFeatures {
my $self = shift;
return $self->adaptor->db->get_adaptor("ditagFeature")
->fetch_all_by_ditagID($self->dbID);
}
1;
]]>