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

List of all members.


Class Summary

Description

This is an extension of the ProjectionEngine object which provides methods
for filtering according to rules originally used in the Ensembl projection
pipeline. This contains the rules for allowing a transfer to occur;
the original pipeline had rules for the formatting of the final
DBEntry so look in the corresponding writer for that information.
 

Definition at line 21 of file DisplayXrefProjectionEngine.pm.

Available Methods

protected _all_sources_builder ()
protected _dbentry_predicate_builder ()
protected _decode_homology ()
protected _filter_dbentry ()
protected _generate_homology_descriptor ()
protected _get_homologies ()
protected _get_mlss ()
protected _homologies ()
protected _homology_descriptor ()
protected _homology_predicate_builder ()
protected _log_builder ()
protected _method_link_type_builder ()
protected _one_to_many_builder ()
protected _species_dbname_map_builder ()
protected _transfer_dbentry_by_targets ()
public all_sources ()
public Projection build_projection ()
public dba ()
public dbentry_predicate ()
public dbentry_source_object ()
public genome_db ()
public homology_predicate ()
public log ()
public method_link_type ()
public new ()
public one_to_many ()
public project ()
public species_dbname_map ()

Method Documentation

protected Bio::EnsEMBL::Compara::Production::Projection::DisplayXrefProjectionEngine::_all_sources_builder ( )

Undocumented method

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

Undocumented method

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

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

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::DisplayXrefProjectionEngine::_generate_homology_descriptor ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::Production::Projection::DisplayXrefProjectionEngine::_get_homologies ( )

Undocumented method

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

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::DisplayXrefProjectionEngine::_homology_descriptor ( )
Used to hold a hash of the following format
  {
    STABLE_ID => {
      current_index => 0,
      total => 3,
      last_projection => ProjectionObj
    },
    STABLE_ID => {
      current_index => 0,
      total => 2,
      last_projection => ProjectionObj
    },
  }
It is used for providing more useful information to display IDs when working
with 1:m relationships. Also allows us to resolve the trickier situation
of rejecting a projection because a more suitable one could appear
 
Code:
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protected Bio::EnsEMBL::Compara::Production::Projection::DisplayXrefProjectionEngine::_homology_predicate_builder ( )

Undocumented method

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

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

Undocumented method

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

Undocumented method

protected Bio::EnsEMBL::Compara::Production::Projection::DisplayXrefProjectionEngine::_one_to_many_builder ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::Production::Projection::DisplayXrefProjectionEngine::_species_dbname_map_builder ( )

Undocumented method

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

Undocumented method

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

public Bio::EnsEMBL::Compara::Production::Projection::DisplayXrefProjectionEngine::all_sources ( )
Returns if we allow all sources to be mapped from
 
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public Projection Bio::EnsEMBL::Compara::Production::Projection::DisplayXrefProjectionEngine::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
 
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::DisplayXrefProjectionEngine::dbentry_source_object ( )
  Arg[1] : Member to get the DBEntry objects for
 
Code:
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Reimplemented from Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine.

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::DisplayXrefProjectionEngine::new ( )
  Arg[-species_dbname_map]    : A hash which maps GenomeDB names to DBNames in
                                a DBEntry if we wish to restrict the source
                                DataSet. Defaults to to H.sap to HGNC & M.mus
                                to MarkerSymbol
  Arg[-all_sources]           : Used to relax the checks for DBName on a DBEntry
                                allowing for any display ID to be projected.
                                Defaults to false
  Arg[-one_to_many]           : Lets the relationships which are not just 
                                1:1 through. Defaults to false
  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).
 
Code:
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Reimplemented from Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine.

public Bio::EnsEMBL::Compara::Production::Projection::DisplayXrefProjectionEngine::one_to_many ( )
Returns if we allow one to many relationships through
 
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public Bio::EnsEMBL::Compara::Production::Projection::DisplayXrefProjectionEngine::project ( )
Override of the default project which does post filtering of the projections
in order to remove any unecessary duplications.
 
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Reimplemented from Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine.

public Bio::EnsEMBL::Compara::Production::Projection::DisplayXrefProjectionEngine::species_dbname_map ( )
Returns the map of Species Name (GenomeDB.Name) to the valud type of 
DBEntry. Value can be an array.
 
Code:
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The documentation for this class was generated from the following file: