Raw content of Bio::EnsEMBL::CoordSystem
<![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::CoordSystem
=head1 SYNOPSIS
my $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
my $csa = $db->get_CoordSystemAdaptor();
#
# Get all coord systems in the database:
#
foreach my $cs ( @{ $csa->fetch_all() } ) {
my $str = join ':', $cs->name(), $cs->version(), $cs->dbID();
print "$str\n";
}
=head1 DESCRIPTION
This is a simple object which contains a few coordinate system attributes:
name, internal identifier, version. A coordinate system is uniquely defined
by its name and version. A version of a coordinate system applies to all
sequences within a coordinate system. This should not be confused with
individual sequence versions.
Take for example the Human assembly. The version 'NCBI33' applies to
to all chromosomes in the NCBI33 assembly (that is the entire 'chromosome'
coordinate system). The 'clone' coordinate system in the same database would
have no version however. Although the clone sequences have their own sequence
versions, there is no version which applies to the entire set of clones.
Coordinate system objects are immutable. Their name and version, and other
attributes may not be altered after they are created.
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::CoordSystem;
use Bio::EnsEMBL::Storable;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Storable);
=head2 new
Arg [..] : List of named arguments:
-NAME - The name of the coordinate system
-VERSION - (optional) The version of the coordinate system.
Note that if the version passed in is undefined,
it will be set to the empty string in the
resulting CoordSystem object.
-RANK - The rank of the coordinate system. The highest
level coordinate system should have rank 1, the
second highest rank 2 and so on. An example of
a high level coordinate system is 'chromosome' an
example of a lower level coordinate system is
'clone'.
-TOP_LEVEL - (optional) Sets whether this is a top-level coord
system. Default = 0. This should only be set to
true if you are creating an artificial toplevel
coordsystem by the name of 'toplevel'
-SEQUENCE_LEVEL - (optional) Sets whether this is a sequence
level coordinate system. Default = 0
-DEFAULT - (optional)
Whether this is the default version of the
coordinate systems of this name. Default = 0
-DBID - (optional) The internal identifier of this
coordinate system
-ADAPTOR - (optional) The adaptor which provides database
interaction for this object
Example : $cs = Bio::EnsEMBL::CoordSystem->new(-NAME => 'chromosome',
-VERSION => 'NCBI33',
-RANK => 1,
-DBID => 1,
-ADAPTOR => adaptor,
-DEFAULT => 1,
-SEQUENCE_LEVEL => 0);
Description: Creates a new CoordSystem object representing a coordinate
system.
Returntype : Bio::EnsEMBL::CoordSystem
Exceptions : none
Caller : general
Status : Stable
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
my ($name,$version, $top_level, $sequence_level, $default, $rank) =
rearrange(['NAME','VERSION','TOP_LEVEL', 'SEQUENCE_LEVEL',
'DEFAULT', 'RANK'], @_);
throw('The NAME argument is required') if(!$name);
$version = '' if(!defined($version));
$top_level = ($top_level) ? 1 : 0;
$sequence_level = ($sequence_level) ? 1 : 0;
$default = ($default) ? 1 : 0;
$rank ||= 0;
if($top_level) {
if($rank) {
throw('RANK argument must be 0 if TOP_LEVEL is 1');
}
if($name) {
if($name ne 'toplevel') {
throw('The NAME argument must be "toplevel" if TOP_LEVEL is 1')
}
} else {
$name = 'toplevel';
}
if($sequence_level) {
throw("SEQUENCE_LEVEL argument must be 0 if TOP_LEVEL is 1");
}
$default = 0;
} else {
if(!$rank) {
throw("RANK argument must be non-zero if not toplevel CoordSystem");
}
if($name eq 'toplevel') {
throw("Cannot name coord system 'toplevel' unless TOP_LEVEL is 1");
}
}
if($rank !~ /^\d+$/) {
throw('The RANK argument must be a positive integer');
}
$self->{'version'} = $version;
$self->{'name'} = $name;
$self->{'top_level'} = $top_level;
$self->{'sequence_level'} = $sequence_level;
$self->{'default'} = $default;
$self->{'rank'} = $rank;
return $self;
}
=head2 name
Arg [1] : (optional) string $name
Example : print $coord_system->name();
Description: Getter for the name of this coordinate system
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub name {
my $self = shift;
return $self->{'name'};
}
=head2 version
Arg [1] : none
Example : print $coord->version();
Description: Getter for the version of this coordinate system. This
will return an empty string if no version is defined for this
coordinate system.
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub version {
my $self = shift;
return $self->{'version'};
}
=head2 species
Arg [1] : none
Example : print $coord->species();
Description: Shortcut method to get the species this CoordSystem refers to.
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub species {
my $self = shift;
return $self->adaptor->db->species;
}
=head2 equals
Arg [1] : Bio::EnsEMBL::CoordSystem $cs
The coord system to compare to for equality.
Example : if($coord_sys->equals($other_coord_sys)) { ... }
Description: Compares 2 coordinate systems and returns true if they are
equivalent. The definition of equivalent is sharing the same
name and version.
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub equals {
my $self = shift;
my $cs = shift;
if(!$cs || !ref($cs) || !$cs->isa('Bio::EnsEMBL::CoordSystem')) {
if ($cs->isa('Bio::EnsEMBL::ExternalData::DAS::CoordSystem')) {
return $cs->equals($self);
}
throw('Argument must be a CoordSystem');
}
if($self->{'version'} eq $cs->version() && $self->{'name'} eq $cs->name()) {
return 1;
}
return 0;
}
=head2 is_top_level
Arg [1] : none
Example : if($coord_sys->is_top_level()) { ... }
Description: Returns true if this is the toplevel pseudo coordinate system.
The toplevel coordinate system is not a real coordinate system
which is stored in the database, but it is a placeholder that
can be used to request transformations or retrievals to/from
the highest defined coordinate system in a given region.
Returntype : 0 or 1
Exceptions : none
Caller : general
Status : Stable
=cut
sub is_top_level {
my $self = shift;
return $self->{'top_level'};
}
=head2 is_sequence_level
Arg [1] : none
Example : if($coord_sys->is_sequence_level()) { ... }
Description: Returns true if this is a sequence level coordinate system
Returntype : 0 or 1
Exceptions : none
Caller : general
Status : Stable
=cut
sub is_sequence_level {
my $self = shift;
return $self->{'sequence_level'};
}
=head2 is_default
Arg [1] : none
Example : if($coord_sys->is_default()) { ... }
Description: Returns true if this coordinate system is the default
version of the coordinate system of this name.
Returntype : 0 or 1
Exceptions : none
Caller : general
Status : Stable
=cut
sub is_default {
my $self = shift;
return $self->{'default'};
}
=head2 rank
Arg [1] : none
Example : if($cs1->rank() < $cs2->rank()) {
print $cs1->name(), " is a higher level coord system than",
$cs2->name(), "\n";
}
Description: Returns the rank of this coordinate system. A lower number
is a higher coordinate system. The highest level coordinate
system has a rank of 1 (e.g. 'chromosome'). The toplevel
pseudo coordinate system has a rank of 0.
Returntype : int
Exceptions : none
Caller : general
Status : Stable
=cut
sub rank {
my $self = shift;
return $self->{'rank'};
}
1;
]]>