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

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.
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

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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 | ( | ) |
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 | ( | ) |
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 | ( | ) |
The documentation for this class was generated from the following file:
- Bio/EnsEMBL/Compara/RunnableDB/ncRNAtrees/CAFESpeciesTree.pm