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Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::ImportAlignment Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::ImportAlignment:

List of all members.


Class Summary

Synopsis

Description

This module imports a specified alignment. This is used in the low coverage genome alignment pipeline for importing the high coverage alignment which is used to build the low coverage genomes on.
 

Definition at line 18 of file ImportAlignment.pm.

Available Methods

public Bio::EnsEMBL::Analysis analysis ()
public catch ()
public void check_if_exit_cleanly ()
public compara_dba ()
public copy_data ()
public copy_data_in_text_mode ()
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 void fetch_input ()
public go_figure_compara_dba ()
public go_figure_dbc ()
public importAlignment ()
public importAlignment_quick ()
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 void 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 Boolean 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::EpoLowCoverage::ImportAlignment::copy_data ( )
  Arg[1]      : Bio::EnsEMBL::Compara::DBSQL::DBAdaptor $from_dba
  Arg[2]      : Bio::EnsEMBL::Compara::DBSQL::DBAdaptor $to_dba
  Arg[3]      : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $this_mlss
  Arg[4]      : string $table
  Arg[5]      : string $sql_query
  Description : copy data in this table using this SQL query.
  Returns     :
  Exceptions  : throw if argument test fails
 
Code:
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public Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::ImportAlignment::copy_data_in_text_mode ( )
  Arg[1]      : Bio::EnsEMBL::Compara::DBSQL::DBAdaptor $from_dba
  Arg[2]      : Bio::EnsEMBL::Compara::DBSQL::DBAdaptor $to_dba
  Arg[3]      : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $this_mlss
  Arg[4]      : string $table
  Arg[5]      : string $sql_query
  Description : copy data in this table using this SQL query.
  Returns     :
  Exceptions  : throw if argument test fails
 
Code:
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public void Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::ImportAlignment::fetch_input ( )
    Title   :   fetch_input
    Usage   :   $self->fetch_input
    Function:   Fetches input data for gerp from the database
    Returns :   none
    Args    :   none
 
Code:
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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::EpoLowCoverage::ImportAlignment::importAlignment ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::ImportAlignment::importAlignment_quick ( )

Undocumented method

Code:
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public void Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::ImportAlignment::run ( )
    Title   :   run
    Usage   :   $self->run
    Function:   Run gerp
    Returns :   none
    Args    :   none
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

public Boolean Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::ImportAlignment::write_output ( )
    Title   :   write_output
    Usage   :   $self->write_output
    Function:   Write results to the database
    Returns :   1
    Args    :   none
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.


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