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

List of all members.


Class Summary

Synopsis

  my $db      = Bio::EnsEMBL::DBAdaptor-\>new($locator);
  my $genscan = Bio::EnsEMBL::Compara::Production::GenomicAlign::AlignmentNets-\>new (
                                                    -db      =\> $db,
                                                    -input_id   =\> $input_id
                                                    -analysis   =\> $analysis );
  $genscan-\>fetch_input();
  $genscan-\>run();
  $genscan-\>write_output(); #writes to DB

Description

Given an compara MethodLinkSpeciesSet identifer, and a reference genomic
slice identifer, fetches the GenomicAlignBlocks from the given compara
database, infers chains from the group identifiers, and then forms
an alignment net from the chains and writes the result
back to the database.
This module (at least for now) relies heavily on Jim Kent\'s Axt tools.
 

Definition at line 36 of file AlignmentNets.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 Nothing 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 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 write_output ()

Method Documentation

protected Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::_write_output ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::cleanse_output ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::compara_cigars_from_daf_cigar ( ) [inherited]

Undocumented method

Code:
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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
 
Code:
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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::convert_output ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::daf_cigar_from_compara_cigars ( ) [inherited]

Undocumented method

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

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing.

public Nothing Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentNets::fetch_input ( )
    Title   :   fetch_input
    Usage   :   $self->fetch_input
    Function:   
    Returns :   nothing
    Args    :   none
 
Code:
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Reimplemented from Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing.

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 ( ) [inherited]

Undocumented method

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

public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::output ( ) [inherited]

Undocumented method

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

public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentNets::run ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing.

public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::sort_chains_by_max_block_score ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing::split_feature ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentNets::write_output ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing.


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