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Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::DeleteAlignment Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::DeleteAlignment:

List of all members.


Class Summary

Synopsis

Description

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

Definition at line 21 of file DeleteAlignment.pm.

Available Methods

public Bio::EnsEMBL::Analysis analysis ()
public catch ()
public void check_if_exit_cleanly ()
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 deleteAlignment ()
public void deprecate ()
public DESTROY ()
public void fetch_input ()
public get_params ()
public go_figure_dbc ()
public void info ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public method_link_species_set_id ()
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::Production::GenomicAlignBlock::DeleteAlignment::deleteAlignment ( )

Undocumented method

Code:
click to view
public void Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::DeleteAlignment::fetch_input ( )
    Title   :   fetch_input
    Usage   :   $self->fetch_input
    Function:   Fetches input data for gerp from the database
    Returns :   none
    Args    :   none
 
Code:
click to view

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

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::DeleteAlignment::get_params ( )

Undocumented method

Code:
click to view
public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::DeleteAlignment::method_link_species_set_id ( )

Undocumented method

public void Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::DeleteAlignment::run ( )
    Title   :   run
    Usage   :   $self->run
    Function:   Run gerp
    Returns :   none
    Args    :   none
 
Code:
click to view

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

public Boolean Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::DeleteAlignment::write_output ( )
    Title   :   write_output
    Usage   :   $self->write_output
    Function:   Write results to the database
    Returns :   1
    Args    :   none
 
Code:
click to view

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


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