Bio::EnsEMBL::CoordSystem Class Reference
Inheritance diagram for Bio::EnsEMBL::CoordSystem:
Class Summary
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.
Definition at line 40 of file CoordSystem.pm.
Available Methods | |
| public Bio::EnsEMBL::DBSQL::BaseAdaptor | adaptor () |
| public Int | dbID () |
| public String | equals () |
| public | get_all_DAS_Features () |
| public | is_default () |
| public | is_sequence_level () |
| public Boolean | is_stored () |
| public | is_top_level () |
| public String | name () |
| public Bio::EnsEMBL::CoordSystem | new () |
| public Int | rank () |
| public String | species () |
| public String | version () |
Method Documentation
| public Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::Storable::adaptor | ( | ) | [inherited] |
Arg [1] : Bio::EnsEMBL::DBSQL::BaseAdaptor $adaptor Example : none Description: get/set for this objects Adaptor Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor Exceptions : none Caller : general, set from adaptor on store Status : Stable
Code:
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| public Int Bio::EnsEMBL::Storable::dbID | ( | ) | [inherited] |
Arg [1] : int $dbID Example : none Description: getter/setter for the database internal id Returntype : int Exceptions : none Caller : general, set from adaptor on store Status : Stable
Code:
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Reimplemented in Bio::EnsEMBL::Map::Ditag, and Bio::EnsEMBL::Map::DitagFeature.
| public String Bio::EnsEMBL::CoordSystem::equals | ( | ) |
Arg [1] : Bio::EnsEMBL::CoordSystem $cs The coord system to compare to for equality. Example : if($coord_sys->equals($other_coord_sys)) { ... } Description: Compares 2 coordinate systems and returns true if they are equivalent. The definition of equivalent is sharing the same name and version. Returntype : string Exceptions : none Caller : general Status : Stable
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| public Bio::EnsEMBL::Storable::get_all_DAS_Features | ( | ) | [inherited] |
Undocumented method
Code:
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Reimplemented in Bio::EnsEMBL::Gene, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Translation.
| public Bio::EnsEMBL::CoordSystem::is_default | ( | ) |
Arg [1] : none Example : if($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
Code:
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| public Bio::EnsEMBL::CoordSystem::is_sequence_level | ( | ) |
Arg [1] : none Example : if($coord_sys->is_sequence_level()) { ... } Description: Returns true if this is a sequence level coordinate system Returntype : 0 or 1 Exceptions : none Caller : general Status : Stable
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| public Boolean Bio::EnsEMBL::Storable::is_stored | ( | ) | [inherited] |
Arg [1] : Bio::EnsEMBL::DBSQL::DBConnection : or Bio::EnsEMBL::DBSQL::DBAdaptor Example : do_something if($object->is_stored($db)); Description: Returns true if this object is stored in the provided database. This works under the assumption that if the adaptor and dbID are set and the database of the adaptor shares the port, dbname and hostname with the provided database, this object is stored in that database. Returntype : 1 or 0 Exceptions : throw if dbID is set but adaptor is not throw if adaptor is set but dbID is not throw if incorrect argument is passed Caller : store methods Status : Stable
Code:
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| public Bio::EnsEMBL::CoordSystem::is_top_level | ( | ) |
Arg [1] : none Example : if($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
Code:
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| public String Bio::EnsEMBL::CoordSystem::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
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| public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::CoordSystem::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 : $cs = Bio::EnsEMBL::CoordSystem->new(-NAME => 'chromosome',
-VERSION => 'NCBI33',
-RANK => 1,
-DBID => 1,
-ADAPTOR => adaptor,
-DEFAULT => 1,
-SEQUENCE_LEVEL => 0);
Description: Creates a new CoordSystem object representing a coordinate
system.
Returntype : Bio::EnsEMBL::CoordSystem
Exceptions : none
Caller : general
Status : StableCode:
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Reimplemented from Bio::EnsEMBL::Storable.
| public Int Bio::EnsEMBL::CoordSystem::rank | ( | ) |
Arg [1] : none Example : if($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
Code:
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| public String Bio::EnsEMBL::CoordSystem::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
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| public String Bio::EnsEMBL::CoordSystem::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
Code:
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The documentation for this class was generated from the following file:
- Bio/EnsEMBL/CoordSystem.pm