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Bio::EnsEMBL::Compara::Production::Projection::GOAProjectionEngine Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::Production::Projection::GOAProjectionEngine:

List of all members.


Class Summary

Description

This is an extension of the ProjectionEngine object which provides methods
for filtering according to rules discussed with the GOA team at the EBI.
 

Definition at line 18 of file GOAProjectionEngine.pm.

Available Methods

protected _dbentry_predicate_builder ()
protected _dbentry_types_builder ()
protected _decode_homology ()
protected _decode_member ()
protected _filter_dbentry ()
protected _get_homologies ()
protected _get_mlss ()
protected _homologies ()
protected _homology_predicate_builder ()
protected _log_builder ()
protected _method_link_type_builder ()
protected _transfer_dbentry_by_targets ()
protected _valid_sources ()
public Projection build_projection ()
public dba ()
public dbentry_predicate ()
public dbentry_source_object ()
public dbentry_types ()
public excluded_terms ()
public genome_db ()
public homology_predicate ()
public log ()
public method_link_type ()
public new ()
public
Bio::EnsEMBL::Compara::Production::Projection::Projection 
project ()
public source ()

Method Documentation

protected Bio::EnsEMBL::Compara::Production::Projection::GOAProjectionEngine::_dbentry_predicate_builder ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine.

protected Bio::EnsEMBL::Compara::Production::Projection::GOAProjectionEngine::_dbentry_types_builder ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine::_decode_homology ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::Compara::Production::Projection::GOAProjectionEngine::_decode_member ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine::_filter_dbentry ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine::_get_homologies ( ) [inherited]

Undocumented method

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Reimplemented in Bio::EnsEMBL::Compara::Production::Projection::DisplayXrefProjectionEngine.

protected Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine::_get_mlss ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine::_homologies ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::Compara::Production::Projection::GOAProjectionEngine::_homology_predicate_builder ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine.

protected Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine::_log_builder ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine::_method_link_type_builder ( ) [inherited]

Undocumented method

protected Bio::EnsEMBL::Compara::Production::Projection::GOAProjectionEngine::_transfer_dbentry_by_targets ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine.

protected Bio::EnsEMBL::Compara::Production::Projection::GOAProjectionEngine::_valid_sources ( )

Undocumented method

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public Projection Bio::EnsEMBL::Compara::Production::Projection::GOAProjectionEngine::build_projection ( )
  Arg[1]      : Member; source member of projection
  Arg[2]      : Member; target member of projection
  Arg[3]      : Source attribute
  Arg[4]      : Target attribute
  Arg[5]      : DBEntry projected
  Arg[6]      : The homology used for projection
  Description : Provides an abstraction to building a projection from a 
                set of elements.
  Returntype  : Projection object. Can be null & the current projection code
                will ignore it
 
Code:
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Reimplemented from Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine.

public Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine::dba ( ) [inherited]
  Description : Getter. Compara adaptor to get homologies from
 
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public Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine::dbentry_predicate ( ) [inherited]
  Description : Getter. Predicate used to filter out DBEntry instances
  Can be customised by overriding _dbentry_predicate_builder().
 
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public Bio::EnsEMBL::Compara::Production::Projection::GOAProjectionEngine::dbentry_source_object ( )
Override of the method from the super engine which uses the FakeXrefHolder
object to get Xrefs quickly. The class returned responds to the
get_all_DBEntries() subroutine call returning all of those Translation
based DBEntry objects.
The method looks at the type of member given which will instruct the level
we perform projections at i.e. ENSEMBLGENE or ENSEMBLPEP
 
Code:
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Reimplemented from Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine.

public Bio::EnsEMBL::Compara::Production::Projection::GOAProjectionEngine::dbentry_types ( )
  Description : Getter. Percentage identity in the source
  Can be customised by overriding _dbentry_types_builder(). Defaults to
  an arrayref containing GO by default.
 
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public Bio::EnsEMBL::Compara::Production::Projection::GOAProjectionEngine::excluded_terms ( )
Used to remove terms from the projected items which are deemed as not-useful.
This defaults to GO:0005515 (protein binding)
 
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public Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine::genome_db ( ) [inherited]
  Description : Getter. GenomeDB to use as the source of the homologies
 
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public Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine::homology_predicate ( ) [inherited]
  Description : Getter. Predicate used to filter out Homology instances
  Can be customised by overriding _homology_predicate_builder().
 
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public Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine::log ( ) [inherited]
  Description : Getter. Logger instance
 
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public Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine::method_link_type ( ) [inherited]
  Description : Getter. Method link to get homologies from
  Can be customised by overriding _method_link_type_builder(). Defaults to
  ENSEMBL_ORTHOLOGUES.
 
public Bio::EnsEMBL::Compara::Production::Projection::GOAProjectionEngine::new ( )
  Arg[-dbentry_types] : The DBEntry database name to use. Defaults to GO
  Arg[-source]: String; defines the level to use for finding xrefs to project
                which should be assigned to the SOURCE_NAME used in MEMBER
  Description : New method used for a new instance of the given object. 
                Required fields are indicated accordingly. Fields are specified
                using the Arguments syntax (case insensitive).
 
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Reimplemented from Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine.

public Bio::EnsEMBL::Compara::Production::Projection::Projection Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine::project ( ) [inherited]
  Arg[0]      : GenomeDB object which is used as the projection target
  Description : Workhorse subroutine which loops through homologies and filters
                through those and DBEntry objects using Data::Predicate
                objects. See class description for more information on the
                filtering process.
  Returntype  : Bio::EnsEMBL::Compara::Production::Projection::Projection
  Exceptions  : If we cannot contact the target databases
 
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Reimplemented in Bio::EnsEMBL::Compara::Production::Projection::DisplayXrefProjectionEngine.

public Bio::EnsEMBL::Compara::Production::Projection::GOAProjectionEngine::source ( )
  Description : Getter. Source used to define the level we use to get DBEntries
  from
 
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The documentation for this class was generated from the following file: