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

List of all members.


Class Summary

Synopsis

This RunnableDB module is part of the DumpMultiAlign pipeline.

Description

This RunnableDB module runs DumpMultiAlign jobs. It creates emf2maf jobs if
necessary and compression jobs
 

Definition at line 19 of file DumpMultiAlign.pm.

Available Methods

protected _healthcheck ()
protected _write_gab_file ()
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 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 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

protected Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::DumpMultiAlign::_healthcheck ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::DumpMultiAlign::_write_gab_file ( )

Undocumented method

Code:
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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::DumpMultiAlign::DumpMultiAlign::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 Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::DumpMultiAlign::run ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::DumpMultiAlign::strict_hash_format ( )
    Description : Implements strict_hash_format() interface method of Bio::EnsEMBL::Hive::Process that is used to set the strictness level of the parameters' parser.
                  Here we return 0 in order to indicate that neither input_id() nor parameters() is required to contain a hash.
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

public Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::DumpMultiAlign::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: