Raw content of Bio::EnsEMBL::Mapper::Coordinate
<![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::Mapper::Coordinate
=head1 SYNOPSIS
=head1 DESCRIPTION
Representation of a mapped region in a sequence; returned from Mapper.pm
when the target region maps on to valid sequence.
=head1 METHODS
=cut
package Bio::EnsEMBL::Mapper::Coordinate;
use strict;
=head2 new
Arg [1] char|int id of object in mapped region
Arg [2] int start of region
Arg [3] int end of region
Arg [4] int strand if region
Arg [5] Bio::EnsEMBL::CoordSystem coordsytem of the region
Function creates a new Coordinate object
Returntype Bio::EnsEMBL::Mapper::Coordinate
Exceptions none
Status Stable
=cut
sub new {
my ( $proto, $id, $start, $end, $strand, $coord_system ) = @_;
my $class = ref($proto) || $proto;
return
bless( { 'id' => $id,
'start' => $start,
'end' => $end,
'strand' => $strand,
'coord_system' => $coord_system
},
$class );
}
=head2 start
Arg 1 int $start
start coordinate of object in mapped region
Function getter/setter method
Returntype int
Exceptions none
Caller Bio::EnsEMBL::Mapper::Coordinate
Status Stable
=cut
sub start {
my ( $self, $value ) = @_;
if ( defined($value) ) {
$self->{'start'} = $value;
}
return $self->{'start'};
}
=head2 end
Arg 1 int $end
end coordinate of object in mapped region
Function getter/setter method
Returntype int
Exceptions none
Caller Bio::EnsEMBL::Mapper::Coordinate
Status Stable
=cut
sub end {
my ( $self, $value ) = @_;
if ( defined($value) ) {
$self->{'end'} = $value;
}
return $self->{'end'};
}
=head2 strand
Arg 1 int $strand
strand of object in mapped region
Function getter/setter method
Returntype int
Exceptions none
Caller Bio::EnsEMBL::Mapper::Coordinate
Status Stable
=cut
sub strand {
my ( $self, $value ) = @_;
if ( defined($value) ) {
$self->{'strand'} = $value;
}
return $self->{'strand'};
}
=head2 id
Arg 1 char|int $id
id of object in mapped region
e.g. seq_region_id / seq_region_name
Function getter/setter method
Returntype char|int
Exceptions none
Caller Bio::EnsEMBL::Mapper::Coordinate
Status Stable
=cut
sub id {
my ( $self, $value ) = @_;
if ( defined($value) ) {
$self->{'id'} = $value;
}
return $self->{'id'};
}
=head2 coord_system
Arg 1 Bio::EnsEMBL::CoordSystem
Function getter/setter method
Returntype Bio::EnsEMBL::CoordSystem
Exceptions none
Caller Bio::EnsEMBL::Mapper::Coordinate
Status Stable
=cut
sub coord_system {
my ( $self, $value ) = @_;
if ( defined($value) ) {
$self->{'coord_system'} = $value;
}
return $self->{'coord_system'};
}
=head2 length
Function getter method
Returntype int
Exceptions none
Caller ?
Status Stable
=cut
sub length {
my ($self) = @_;
return $self->{'end'} - $self->{'start'} + 1;
}
1;
]]>