ensembl-hive
2.6
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Public Member Functions | |
public Bio::EnsEMBL::CoordSystem | new () |
public String | name () |
public String | version () |
public String | species () |
public String | equals () |
public Boolean | is_top_level () |
public Boolean | is_sequence_level () |
public Boolean | is_default () |
public Int | rank () |
public Bio::EnsEMBL::CoordSystem | alias_to () |
Public Member Functions inherited from Bio::EnsEMBL::Storable | |
public Bio::EnsEMBL::Storable | new () |
public Instance | new_fast () |
public Int | dbID () |
public Bio::EnsEMBL::DBSQL::BaseAdaptor | adaptor () |
public Boolean | is_stored () |
public | get_all_DAS_Features () |
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.
public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::CoordSystem::alias_to | ( | ) |
Arg [1] : string Example :
Description: Getter/Setter for the alias of this coordinate system. Returntype : Bio::EnsEMBL::CoordSystem Exceptions : none Caller : general Status : Stable
public String Bio::EnsEMBL::CoordSystem::equals | ( | ) |
Arg [1] : Bio::EnsEMBL::CoordSystem $cs The coord system to compare to for equality. Example :
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
public Boolean Bio::EnsEMBL::CoordSystem::is_default | ( | ) |
Arg [1] : none Example :
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
public Boolean Bio::EnsEMBL::CoordSystem::is_sequence_level | ( | ) |
Arg [1] : none Example :
Description: Returns true if this is a sequence level coordinate system Returntype : 1 or 0 Exceptions : none Caller : general Status : Stable
public Boolean Bio::EnsEMBL::CoordSystem::is_top_level | ( | ) |
Arg [1] : none Example :
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
public String Bio::EnsEMBL::CoordSystem::name | ( | ) |
Arg [1] : (optional) string $name Example :
Description: Getter for the name of this coordinate system Returntype : string Exceptions : none Caller : general Status : Stable
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 -ALIAS_TO - (optional) Sets an alias for a coordsystem. If set it should only be set to 'chromosome' Example :
Description: Creates a new CoordSystem object representing a coordinate system. Returntype : Bio::EnsEMBL::CoordSystem Exceptions : none Caller : general Status : Stable
public Int Bio::EnsEMBL::CoordSystem::rank | ( | ) |
Arg [1] : none Example :
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
public String Bio::EnsEMBL::CoordSystem::species | ( | ) |
Arg [1] : none Example :
Description: Shortcut method to get the species this CoordSystem refers to. Returntype : string Exceptions : none Caller : general Status : Stable
public String Bio::EnsEMBL::CoordSystem::version | ( | ) |
Arg [1] : none Example :
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