Archive Ensembl HomeArchive Ensembl Home
Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref Class Reference

List of all members.

Class Summary


This object serves two functions. In the first instance it is a 
RunnableDB instance to be used in a Hive pipeline and therefore 
inherits from Hive's Process object. A second set of methods is provided 
with the suffix without_hive which allows you to use this object 
outside of a Hive pipeline.
The Runnable is here to bring together a ProjectionEngine with the
GenomeDB instances it will work with and have it interact with a 
ProjectionEngine writer (which can be a database or a file). See the
fetch_input() method for information on the parameters the module
responds and to new_without_hive() for information on how to use
the module outside of hive.

Definition at line 33 of file

Available Methods

protected _build_engine ()
protected _target_filename ()
protected _writer ()
public fetch_input ()
public file ()
new_without_hive ()
public projection_engine ()
public projections ()
public run ()
public run_without_hive ()
public target_genome_db ()
public write_dba ()
public write_output ()

Method Documentation

protected Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref::_build_engine ( )

Undocumented method

click to view
protected Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref::_target_filename ( )
If file is a file name we will return that. If it was a directory we will 
return a automatically generated name (sourcename_to_targetname.txt)
click to view
protected Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref::_writer ( )
Returns the writer instance depending on what was given during construction.
click to view
public Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref::fetch_input ( )
Expect to see the following params:
=over 8
=item source_genome_db_id - Required GenomeDB ID
=item target_genome_db_id - Required GenomeDB ID
=item projection_engine_class - Required String which is the package of the engine to use
=item method_link - Optional but should be the method_link class of the types of Homologies to get
=item write_to_db - Boolean which if on will start writing results to a core DB
=item core_db - String which should be a URL of the core DB to write to IF the one available via the Registry is read-only
=item write_to_file - Boolean which if on will start writing results to a file
=item file - String indicating a directory to write to (auto generated file name) or a target file name. We do not automatically create directories
=item engine_params - Give optional parameters to the engine if required
=item source - The source of the DBEntries to use; specify the source_name as used in member
click to view
public Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref::file ( )
The file or directory to write to.
click to view
public Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref::new_without_hive ( )
  Arg [PROJECTION_ENGINE]       : (ProjectionEngine) The projection engine to use to transfer terms 
  Arg [TARGET_GENOME_DB]        : (GenomeDB)  GenomeDB to project terms to
  Arg [WRITE_DBA]               : (DBAdaptor) Required if not given -FILE; used to 
  Arg [FILE]                    : (String) Location of pipeline output; if given a directory it will generate a file name
  Example    : See synopsis
  Description: Non-hive version of the object construction to be used with scripts
  Returntype : Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref
  Exceptions : if PROJECTION_ENGINE was not given and was not a valid object. 
               Also if we had no GenomeDBs given
  Caller     : general
click to view
public Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref::projection_engine ( )
The engine used to transfer terms.
click to view
public Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref::projections ( )
The projections we have projected; an ArrayRef of Projection objects
click to view
public Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref::run ( )
Gets the engine, runs it & sets the output into projections
click to view
public Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref::run_without_hive ( )
Performs the run() and write_output() calls in one method.
click to view
public Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref::target_genome_db ( )
The GenomeDB instance used to project terms to
click to view
public Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref::write_dba ( )
A DBAdaptor instance which can write to a core DBAdaptor; assumed to be the
same as the target GenomeDB.
click to view
public Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref::write_output ( )
Takes the output pushed into projections and sends them into the specified
sources according to the options given.
click to view

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