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

List of all members.


Class Summary

Synopsis

This RunnableDB module is part of the DumpMultiAlign pipeline.

Description

This RunnableDB module generates a general README.{emf} file and a specific README for the multiple alignment being dumped
 

Definition at line 20 of file Readme.pm.

Available Methods

protected _create_specific_epo_low_coverage_readme ()
protected _create_specific_epo_readme ()
protected _create_specific_pecan_readme ()
protected _create_specific_readme ()
protected _get_species_tree ()
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::Readme::_create_specific_epo_low_coverage_readme ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::Readme::_create_specific_epo_readme ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::Readme::_create_specific_pecan_readme ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::Readme::_create_specific_readme ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::Readme::_get_species_tree ( )

Undocumented method

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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
 
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public Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::Readme::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::Readme::run ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::Readme::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::Readme::write_output ( )
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.


The documentation for this class was generated from the following file:
  • Bio/EnsEMBL/Compara/RunnableDB/DumpMultiAlign/Readme.pm