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

List of all members.


Class Summary

Definition at line 15 of file Pecan.pm.

Available Methods

protected _build_tree_string ()
protected Boolean _dump_fasta ()
protected _hard_trim_gab ()
protected Listref _load_DnaFragRegions ()
protected _run_ortheus ()
protected _trim_gab_left ()
protected _trim_gab_right ()
protected
Bio::EnsEMBL::Compara::NestedSet 
_update_tree ()
protected _write_gerp_dataflow ()
protected _write_output ()
public add_species_order ()
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 void fetch_input ()
public get_species_tree ()
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 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::MercatorPecan::Pecan::_build_tree_string ( )
  Arg [1]    : -none-
  Example    : $self->_build_tree_string();
  Description: This method sets the tree_string using the orginal
               species tree and the set of DnaFragRegions. The
               tree is edited by the _update_tree method which
               resort the DnaFragRegions (see _update_tree elsewwhere
               in this document)
  Returntype : -none-
  Exception  :
  Warning    :
 
Code:
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protected Boolean Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Pecan::_dump_fasta ( )
  Arg [1]    : -none-
  Example    : $self->_dump_fasta();
  Description: Dumps FASTA files in the order given by the tree
               string (needed by Pecan). Resulting file names are
               stored using the fasta_files getter/setter
  Returntype : 1
  Exception  :
  Warning    :
 
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protected Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Pecan::_hard_trim_gab ( )

Undocumented method

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protected Listref Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Pecan::_load_DnaFragRegions ( )
  Arg [1]    : int syteny_region_id
  Example    : $self->_load_DnaFragRegions();
  Description: Gets the list of DnaFragRegions for this
               syteny_region_id. Resulting DnaFragRegions are
               stored using the dnafrag_regions getter/setter.
  Returntype : listref of Bio::EnsEMBL::Compara::DnaFragRegion objects
  Exception  :
  Warning    :
 
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protected Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Pecan::_run_ortheus ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Pecan::_trim_gab_left ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Pecan::_trim_gab_right ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::NestedSet Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Pecan::_update_tree ( )
  Arg [1]    : Bio::EnsEMBL::Compara::NestedSet $tree_root
  Example    : $self->_update_nodes_names($tree);
  Description: This method updates the tree by removing or
               duplicating the leaves according to the orginal
               tree and the set of DnaFragRegions. The tree nodes
               will be renamed seq1, seq2, seq3 and so on and the
               DnaFragRegions will be resorted in order to match
               the names of the nodes (the first DnaFragRegion will
               correspond to seq1, the second to seq2 and so on).
  Returntype : Bio::EnsEMBL::Compara::NestedSet (a tree)
  Exception  :
  Warning    :
 
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protected Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Pecan::_write_gerp_dataflow ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Pecan::_write_output ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Pecan::add_species_order ( )

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 void Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Pecan::fetch_input ( )
    Title   :   fetch_input
    Usage   :   $self->fetch_input
    Function:   Fetches input data for repeatmasker from the database
    Returns :   none
    Args    :   none
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Pecan::get_species_tree ( )

Undocumented method

Code:
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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::MercatorPecan::Pecan::run ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Pecan::write_output ( )

Undocumented method

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


The documentation for this class was generated from the following file:
  • Bio/EnsEMBL/Compara/RunnableDB/MercatorPecan/Pecan.pm