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Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::DumpAllHomologiesOrthoXML Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::DumpAllHomologiesOrthoXML:

List of all members.


Class Summary

Description

This Analysis/RunnableDB is designed to dump all the homologies of a database
in a single file, with the OrthoXML format
It requires one parameter:

  • compara_db: connection parameters to the Compara database
The following parameters are optional:

  • tree_type: [string] restriction on which trees should be dumped (see the corresponding field in the gene_tree_root table)
  • possible_ortho: [boolean] (default 0) whether or not low confidence duplications should be treated as speciations
  • file: [string] output file to dump (otherwise: standard output)
 

Synopsis

standaloneJob.pl Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::DumpAllHomologiesOrthoXML
  -compara_db 'mysql://ensro:@compara4:3306/mp12_compara_nctrees_66c'

Definition at line 31 of file DumpAllHomologiesOrthoXML.pm.

Available Methods

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

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:
click to view
public Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::DumpAllHomologiesOrthoXML::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:
click to view
public Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::DumpAllHomologiesOrthoXML::param_defaults ( )

Undocumented method

Code:
click to view

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

public Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::DumpAllHomologiesOrthoXML::run ( )

Undocumented method

Code:
click to view

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

public Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::DumpAllHomologiesOrthoXML::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: