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Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing:

List of all members.


Class Summary

Synopsis

Abstract base class of AlignmentChains and AlignmentNets

Description

 

Definition at line 19 of file AlignmentProcessing.pm.

Available Methods

protected _write_output ()
public Bio::EnsEMBL::Analysis analysis ()
public catch ()
public void check_if_exit_cleanly ()
public cleanse_output ()
public compara_cigars_from_daf_cigar ()
public compara_dba ()
public convert_output ()
public daf_cigar_from_compara_cigars ()
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 delete_alignments ()
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 output ()
public param ()
public param_defaults ()
public param_substitute ()
public parameters ()
public Bio::EnsEMBL::Hive::Queen queen ()
public Array run ()
public Arrayref runnable ()
public sort_chains_by_max_block_score ()
public split_feature ()
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

protected Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::_write_output ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::cleanse_output ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::compara_cigars_from_daf_cigar ( )

Undocumented method

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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
 
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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::convert_output ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::daf_cigar_from_compara_cigars ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::delete_alignments ( )

Undocumented method

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Reimplemented in Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentNets.

public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::fetch_input ( )

Undocumented method

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

Reimplemented in Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentChains, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentNets, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ImportChains, and Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ImportNets.

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.
 
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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::new ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::output ( )

Undocumented method

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

public Array Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::run ( )
  Arg [1]   : Bio::EnsEMBL::Analysis::RunnableDB
  Function  : cycles through all the runnables, calls run and pushes
  their output into the RunnableDBs output array
  Returntype: array ref
  Exceptions: none
  Example   :
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

Reimplemented in Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentNets, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ImportChains, and Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ImportNets.

public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::sort_chains_by_max_block_score ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::split_feature ( )

Undocumented method

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public Boolean Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::write_output ( )
    Title   :   write_output
    Usage   :   $self->write_output()
    Function:   Writes contents of $self->output into $self->db
    Returns :   1
    Args    :   None
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

Reimplemented in Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentChains, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentNets, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ImportChains, and Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ImportNets.


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