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Bio::EnsEMBL::Compara::RunnableDB::ObjectFactory Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::ObjectFactory:

List of all members.


Class Summary

Description

This is a Compara-specific generic job factory that:
    1) creates an object adaptor
    2) runs a fetch_all_by... method on that adaptor (which returns a list of objects)
    3) flows each object into a job using a given getter-to-column mapping
It also serves as a good simple example of a Compara job factory:
    1) Inherits main factory functionality from Hive::RunnableDB::JobFactory
    2) Inherits Compara-specific functionality (like $self->compara_dba ) from Compara::RunnableDB::BaseRunnable
    3) Only defines fetch_input() method that takes specific parameters, uses API to fetch data and sets the $self->param('inputlist') in the end.
 

Definition at line 19 of file ObjectFactory.pm.

Available Methods

protected _fisher_yates_shuffle_in_place ()
protected _get_rows_from_list ()
protected _get_rows_from_open ()
protected _get_rows_from_query ()
protected _substitute_minibatched_rows ()
protected _substitute_rows ()
public Bio::EnsEMBL::Analysis analysis ()
public catch ()
public catch ()
public void check_if_exit_cleanly ()
public compara_dba ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
data_dbc ()
public dataflow_output_id ()
public
Bio::EnsEMBL::Hive::DBSQL::DBAdaptor 
db ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public Int debug ()
public void deprecate ()
public void deprecate ()
public DESTROY ()
public fetch_input ()
public go_figure_compara_dba ()
public go_figure_dbc ()
public void info ()
public void info ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public new ()
public Array output ()
public param ()
public param_defaults ()
public param_substitute ()
public parameters ()
public Bio::EnsEMBL::Hive::Queen queen ()
public run ()
public Arrayref runnable ()
public Array stack_trace ()
public Array stack_trace ()
public String stack_trace_dump ()
public String stack_trace_dump ()
public strict_hash_format ()
public void throw ()
public void throw ()
public Depend try ()
public Depend try ()
public Int verbose ()
public Int verbose ()
public warning ()
public worker ()
public worker_temp_directory ()
public write_output ()

Method Documentation

public Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable::compara_dba ( ) [inherited]
    Description: this is an intelligent setter/getter of a Compara DBA. Resorts to magic in order to figure out how to connect.
    Example 1:   my $family_adaptor = $self->compara_dba()->get_FamilyAdaptor();    # implicit initialization and hashing
    Example 2:   my $external_foo_adaptor = $self->compara_dba( $self->param('db_conn') )->get_FooAdaptor();    # explicit initialization and hashing
 
Code:
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public Bio::EnsEMBL::Compara::RunnableDB::ObjectFactory::fetch_input ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Hive::RunnableDB::JobFactory.

public Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable::go_figure_compara_dba ( ) [inherited]
    Description: this is a method that tries lots of different ways to find connection parameters
                 from a given object/hash and returns a Compara DBA. Does not hash anything, just does the detective magic.
 
Code:
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The documentation for this class was generated from the following file: