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Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref Class Reference

List of all members.


Class Summary

Description

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 ProjectOntologyXref.pm.

Available Methods

protected _build_engine ()
protected _target_filename ()
protected _writer ()
public fetch_input ()
public file ()
public
Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref 
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

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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)
 
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protected Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref::_writer ( )
Returns the writer instance depending on what was given during construction.
 
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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
=back
 
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public Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref::file ( )
The file or directory to write to.
 
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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
 
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public Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref::projection_engine ( )
The engine used to transfer terms.
 
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public Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref::projections ( )
The projections we have projected; an ArrayRef of Projection objects
 
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public Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref::run ( )
Gets the engine, runs it & sets the output into projections
 
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public Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref::run_without_hive ( )
Performs the run() and write_output() calls in one method.
 
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public Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref::target_genome_db ( )
The GenomeDB instance used to project terms to
 
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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.
 
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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.
 
Code:
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The documentation for this class was generated from the following file: