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

List of all members.


Class Summary

Description

This class will write the results of the given projections to a 
database given at construction.
 

Definition at line 16 of file ProjectedDBEntryWriter.pm.

Available Methods

protected _add_analysis ()
protected _process_entry ()
protected _to_ensembl_object ()
public Bio::EnsEMBL::Analysis analysis ()
public dba ()
public
Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDBEntryWriter 
new ()
public projections ()
public write ()
public write_projection ()

Method Documentation

protected Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDBEntryWriter::_add_analysis ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDBEntryWriter::_process_entry ( )
Performs processing which at the moment is concerned with 
processing the Entry if it is an OntologyXref
All entries are setup with a linkage type of IEA, info type of PROJECTION
and a text description showing what species the linkage was from and
the stable ID of the source object.
 
Code:
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protected Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDBEntryWriter::_to_ensembl_object ( )
Maps a member object to its Ensembl core object and returns the expected type
for the DBEntryAdaptor to correctly write the xref back
 
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public Bio::EnsEMBL::Analysis Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDBEntryWriter::analysis ( )
  Description : Getter for the analysis to write  
  Returntype  : Bio::EnsEMBL::Analysis or undef
  Exceptions  : None
  Status      : Stable
 
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public Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDBEntryWriter::dba ( )
  Description : Getter. Should be a write enabled connection
 
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public Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDBEntryWriter Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDBEntryWriter::new ( )
  Arg[-DBA]       : Bio::EnsEMBL::DBSQL::DBAdaptor; Assumed to be a DBA which 
                    can be written to. Required argument 
  Arg[-ANALYSIS]  : Bio::EnsEMBL::Analysis; analysis used to link DBEntries to
  Returntype      : Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDBEntryWriter
  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).
  Exceptions      : If the DBAdaptor was not defined 
  Status          : Stable
 
Code:
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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::ProjectedDBEntryWriter::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.
 
Code:
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Reimplemented from Bio::EnsEMBL::Compara::Production::Projection::Writer::BaseWriter.


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