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

List of all members.


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 ()

Method Documentation

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

Undocumented method

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

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::check_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::ncRNAtrees::CAFESpeciesTree::ensembl_timetree_mya_to_distance_to_parent ( )

Undocumented method

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public void Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::fetch_input ( )
    Title     : fetch_input
    Usage     : $self->fetch_input
    Function  : Fetches input data from database
    Returns   : none
    Args      : none
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

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

Undocumented method

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

Undocumented method

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

Undocumented method

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

Undocumented method

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

Undocumented method

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

Undocumented method

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

Undocumented method

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

Undocumented method

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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.
 
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public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree::include_distance_to_parent ( )

Undocumented method

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

Undocumented method

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

Undocumented method

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

Undocumented method

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

Undocumented method

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

Undocumented method

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

Undocumented method

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

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

Undocumented method

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

Undocumented method

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

Undocumented method

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

Undocumented method

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

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

Undocumented method

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

Undocumented method

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

Undocumented method

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


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