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Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::CheckGenomedbReusability Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::CheckGenomedbReusability:

List of all members.


Class Summary

Description

This Runnable checks whether a certain genome_db data can be reused for the purposes of ProteinTrees pipeline
The format of the input_id follows the format of a Perl hash reference.
Example:
    { 'genome_db_id' => 90 }
supported keys:
    'genome_db_id'  => <number>
        the id of the genome to be checked (main input_id parameter)
    'release'       => <number>
        number of the current release
    'prev_release'  => <number>
        (optional) number of the previous release for reuse purposes (may coincide, may be 2 or more releases behind, etc)
    'registry_dbs'  => <list_of_dbconn_hashes>
        list of hashes with registry connection parameters (tried in succession).
    'reuse_this'    => <0|1>
        (optional) if defined, the code is skipped and this value is passed to the output
    'do_not_reuse_list' => <list_of_species_ids_or_names>
        (optional)  is a 'veto' list of species we definitely do not want to be reused this time

Definition at line 37 of file CheckGenomedbReusability.pm.

Available Methods

public Bio::EnsEMBL::Analysis analysis ()
public Bio::EnsEMBL::DBSQL::DBAdaptor::extract_assembly_name ()
public catch ()
public void check_if_exit_cleanly ()
public check_presence ()
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 hash_all_exons_from_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

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::CheckGenomedbReusability::Bio::EnsEMBL::DBSQL::DBAdaptor::extract_assembly_name ( )
public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::CheckGenomedbReusability::check_presence ( )

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::ProteinTrees::CheckGenomedbReusability::fetch_input ( )

Undocumented method

Code:
click to view

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::ProteinTrees::CheckGenomedbReusability::hash_all_exons_from_dbc ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::CheckGenomedbReusability::run ( )

Undocumented method

Code:
click to view

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

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::CheckGenomedbReusability::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: