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Bio-EnsEMBL-112.0_52
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/ Bio::EnsEMBL::CoordSystem

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

http://www.apache.org/licenses/LICENSE-2.0

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NAME

Bio::EnsEMBL::CoordSystem

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";
}

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.

METHODS

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
             -ALIAS_TO  - (optional) Sets an alias for a coordsystem. If set 
                          it should only be set to 'chromosome'
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

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

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

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

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

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 : 1 or 0
Exceptions : none
Caller     : general
Status     : Stable

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 : 1 or 0
Exceptions : none
Caller     : general
Status     : Stable

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 : 1 or 0
Exceptions : none
Caller     : general
Status     : Stable

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

alias_to

Arg [1]    : string
Example    : $coord->alias_to('chromosome');
Description: Getter/Setter for the alias of this coordinate system.
Returntype : Bio::EnsEMBL::CoordSystem
Exceptions : none
Caller     : general
Status     : Stable