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

List of all members.


Class Summary

Definition at line 14 of file StableIdMapper.pm.

Available Methods

public Bio::EnsEMBL::Analysis analysis ()
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 DESTROY ()
public fetch_input ()
public go_figure_compara_dba ()
public go_figure_dbc ()
public void info ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public new ()
public An new_without_hive ()
public Array output ()
public param ()
public param_defaults ()
public param_substitute ()
public parameters ()
public Bio::EnsEMBL::Hive::Queen queen ()
public run ()
public void run_without_hive ()
public Arrayref runnable ()
public Array stack_trace ()
public String stack_trace_dump ()
public strict_hash_format ()
public void throw ()
public Depend try ()
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::StableIdMapper::fetch_input ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

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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public An Bio::EnsEMBL::Compara::RunnableDB::StableIdMapper::new_without_hive ( )
  
  Arg [DB_ADAPTOR] : DBAdaptor pointing to current Compara DB 
  Arg [TYPE] : The type of mapping to perform (f and t only supported)
  Arg [RELEASE] : The release of the current database
  Arg [PREV_RELEASE] : The release we are mapping IDs from
  Arg [PREV_RELEASE_DB] : DBAdaptor or HASH of the connection details 
                          to the prevous release database
  Arg [MASTER_DB] : DBAdaptor or HASH of the connection details to the 
                    master database instance
  Returntype  : An instance of this class
  Description : Builds an instance of this runnable to be used outside of a 
                hive process 
  Exceptions  : If DBAdaptor is not a Compara DBAdaptor
  Status      : Beta
 
Code:
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public Bio::EnsEMBL::Compara::RunnableDB::StableIdMapper::run ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

public void Bio::EnsEMBL::Compara::RunnableDB::StableIdMapper::run_without_hive ( )
  
  Returntype  : None
  Description : Runs the three stages of the hive process in one continous
                call.
  Exceptions  : Lots possible from bad identifier mappings
  Status      : Beta
 
Code:
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public Bio::EnsEMBL::Compara::RunnableDB::StableIdMapper::write_output ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::Hive::Process.


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