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Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Mercator Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Mercator:

List of all members.


Class Summary

Synopsis

Description

Wrapper around Bio::EnsEMBL::Analysis::Runnable::Mercator
Create Pecan jobs
Supported keys:
    'genome_db_ids' => <list of genome_db_ids>
        The genome_db_ids for the Pecan method link species set
    'mlss_id' => <number>
        The id of the pecan method link species set. Used to retreive the genome_db_ids
        if not set by 'genome_db_ids'
     'input_dir' => <directory_path>
        Location of input files
     'output_dir' => <directory_path>
        Location to write output files
     'method_link_type' => <type>
        Synteny method link type 
        eg "method_link_type" => "SYNTENY"
 

Definition at line 39 of file Mercator.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 Arrayref store_synteny ()
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:
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public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Mercator::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::MercatorPecan::Mercator::run ( )

Undocumented method

Code:
click to view

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

public Arrayref Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Mercator::store_synteny ( )
  Arg[1]      : hashref $run_ids2synteny_and_constraints (unused)
  Example     : $self->store_synteny();
  Description : This method will store the syntenies defined by Mercator
                into the compara DB. The MethodLinkSpecieSet for these
                syntenies is created and stored if needed at this point.
                The IDs for the new Bio::EnsEMBL::Compara::SyntenyRegion
                objects are returned in an arrayref.
  ReturnType  : arrayref of integer
  Exceptions  :
  Status      : stable
 
Code:
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public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Mercator::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:
  • Bio/EnsEMBL/Compara/RunnableDB/MercatorPecan/Mercator.pm