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Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDisplayXrefWriter Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDisplayXrefWriter:

List of all members.


Class Summary

Description

This class will write the results of the given projections to a 
database given at construction by setting the target Display Xref and 
description if required.
 

Definition at line 16 of file ProjectedDisplayXrefWriter.pm.

Available Methods

protected _dbname_to_original_type ()
protected _dbname_to_original_type_builder ()
protected _descriptions_builder ()
protected _process_description ()
protected _process_entry ()
protected _type_and_object ()
protected _update_status ()
public dba ()
public descriptions ()
public new ()
public projections ()
public write ()
public write_projection ()

Method Documentation

protected Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDisplayXrefWriter::_dbname_to_original_type ( )
  Arg[1]      : DBAdaptor; should point to the source of the Hash (normally
                the source)
  Description : Getter. Returns what type of object to link the
 
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protected Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDisplayXrefWriter::_dbname_to_original_type_builder ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDisplayXrefWriter::_descriptions_builder ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDisplayXrefWriter::_process_description ( )
Copies the description from a source to a target gene if allowed
 
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protected Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDisplayXrefWriter::_process_entry ( )
Sets up an Xref to be persisted back to the target core database for 
later processing.
 
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protected Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDisplayXrefWriter::_type_and_object ( )
Performs the lookup of what the original entry was located on and then
returns the object the DBEntry should be attached to and the type of
object it is. We also allow for the mapping of those which are marked as
HGNC*transcript or Gene to go to the correct object
 
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protected Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDisplayXrefWriter::_update_status ( )
Assigns everything to KNOWN_BY_PROJECTION for the given gene and transcripts
 
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public Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDisplayXrefWriter::dba ( )
  Description : Getter. Should be a write enabled connection
 
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public Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDisplayXrefWriter::descriptions ( )
  Description : Getter. Returns if we want to propagate the descriptions or not
 
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public Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDisplayXrefWriter::new ( )
  Arg[-dba]           : required; Assumed to be a DBA which we can write to
  Arg[-descriptions]  : If set to true will force the transfer of descriptions
                        and not just the display xref. 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).
 
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Reimplemented from Bio::EnsEMBL::Compara::Production::Projection::Writer::BaseWriter.

public Bio::EnsEMBL::Compara::Production::Projection::Writer::BaseWriter::projections ( ) [inherited]
  Description : Getter.
 
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public Bio::EnsEMBL::Compara::Production::Projection::Writer::BaseWriter::write ( ) [inherited]
The subroutine we call in order to write projection data out
 
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public Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDisplayXrefWriter::write_projection ( )
Re-assigns the attacted DBEntry from the list of projections to the
core database which was given to this object during construction. This method
also stores the newly assigned DBEntry.
 
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Reimplemented from Bio::EnsEMBL::Compara::Production::Projection::Writer::BaseWriter.


The documentation for this class was generated from the following file: