——————————=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
Questions may also be sent to the Ensembl help desk at
=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;
$Bio::EnsEMBL::Mapper::Coordinate::VERSION
=
'112.0_52'
;
# TRIAL
$Bio::EnsEMBL::Mapper::Coordinate::VERSION
=
'112.052'
;
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
,
$rank
) =
@_
;
my
$class
=
ref
(
$proto
) ||
$proto
;
return
bless
( {
'id'
=>
$id
,
'start'
=>
$start
,
'end'
=>
$end
,
'strand'
=>
$strand
,
'coord_system'
=>
$coord_system
,
'rank'
=>
$rank
|| 0
},
$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
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 name
Arg 1 char name
name of object in mapped region
e.g. seq_region_name
Function getter/setter method
Returntype char
Exceptions none
Caller Bio::EnsEMBL::Mapper::Coordinate
Status Stable
=cut
sub
name {
my
(
$self
,
$value
) =
@_
;
if
(
defined
(
$value
) ) {
$self
->{
'name'
} =
$value
;
}
return
$self
->{
'name'
};
}
=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;
}
sub
rank {
my
(
$self
,
$value
) =
@_
;
if
(
defined
(
$value
) ) {
$self
->{
'rank'
} =
$value
;
}
return
$self
->{
'rank'
};
}
1;