Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree Class Reference

Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree:

List of all members.

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Class Summary

Synopsis

Description

This RunnableDB builds a CAFE-compliant species tree (binary & ultrametric with time units).

Definition at line 18 of file CAFESpeciesTree.pm.

Available Methods
protected	_binarize ()
public Bio::EnsEMBL::Analysis	analysis ()
public	binarize ()
public	catch ()
public void	check_if_exit_cleanly ()
public	check_tree ()
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	ensembl_timetree_mya_to_distance_to_parent ()
public void	fetch_input ()
public	fix_ensembl_timetree_mya ()
public	fix_path ()
public	fix_zeros ()
public	fix_zeros_1 ()
public	get_longest_path ()
public	get_species_tree_string ()
public	get_taxon_id_from_dbID ()
public	get_tree_from_db ()
public	go_figure_compara_dba ()
public	go_figure_dbc ()
public	include_distance_to_parent ()
public	include_names ()
public void	info ()
public	input_id ()
public Bio::EnsEMBL::Hive::AnalysisJob	input_job ()
public	is_binary ()
public	is_in ()
public	is_ultrametric ()
public	mya_to_dtp_1path ()
public	new ()
public Array	output ()
public	param ()
public	param_defaults ()
public	param_substitute ()
public	parameters ()
public	path_length ()
public	prune_tree ()
public Bio::EnsEMBL::Hive::Queen	queen ()
public	remove_nodes ()
public	run ()
public Arrayref	runnable ()
public	siblings ()
public Array	stack_trace ()
public String	stack_trace_dump ()
public	strict_hash_format ()
public void	throw ()
public Depend	try ()
public	ultrametrize ()
public Int	verbose ()
public	warning ()
public	worker ()
public	worker_temp_directory ()
public	write_output ()

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Method Documentation

protected Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::_binarize

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Undocumented method

Code:

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::binarize

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Undocumented method

Code:

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::check_tree

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Undocumented method

Code:

public Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable::compara_dba

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[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:

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::ensembl_timetree_mya_to_distance_to_parent

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Undocumented method

Code:

public void Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::fetch_input

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    Title     : fetch_input
    Usage     : $self->fetch_input
    Function  : Fetches input data from database
    Returns   : none
    Args      : none

Code:

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

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::fix_ensembl_timetree_mya

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Undocumented method

Code:

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::fix_path

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Undocumented method

Code:

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::fix_zeros

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Undocumented method

Code:

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::fix_zeros_1

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Undocumented method

Code:

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::get_longest_path

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Undocumented method

Code:

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::get_species_tree_string

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Undocumented method

Code:

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::get_taxon_id_from_dbID

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Undocumented method

Code:

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::get_tree_from_db

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Undocumented method

Code:

public Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable::go_figure_compara_dba

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[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:

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::include_distance_to_parent

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Undocumented method

Code:

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::include_names

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Undocumented method

Code:

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::is_binary

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Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::is_in

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Undocumented method

Code:

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::is_ultrametric

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Undocumented method

Code:

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::mya_to_dtp_1path

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Undocumented method

Code:

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::param_defaults

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Undocumented method

Code:

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

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::path_length

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Undocumented method

Code:

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::prune_tree

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Undocumented method

Code:

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::remove_nodes

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Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::run

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Undocumented method

Code:

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

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::siblings

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Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::ultrametrize

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Undocumented method

Code:

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::write_output

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Undocumented method

Code:

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

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

• Bio/EnsEMBL/Compara/RunnableDB/ncRNAtrees/CAFESpeciesTree.pm