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

List of all members.


Class Summary

Definition at line 12 of file Mercator.pm.

Available Methods

public all_hits ()
public Bio::EnsEMBL::Analysis analysis ()
public catch ()
public void check_if_exit_cleanly ()
public cutoff_evalue ()
public cutoff_score ()
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 dumpMercatorFiles ()
public void fetch_input ()
public genome_db_ids ()
public get_params ()
public get_sql_for_peptide_hits ()
public get_table_name_from_dbID ()
public go_figure_dbc ()
public void info ()
public input_dir ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public mavid_constraints ()
public maximum_gap ()
public method_link_species_set ()
public method_link_type ()
public msa_method_link_species_set_id ()
public new ()
public Array output ()
public output_dir ()
public param ()
public param_defaults ()
public param_substitute ()
public parameters ()
public pre_map ()
public Bio::EnsEMBL::Hive::Queen queen ()
public run ()
public Arrayref runnable ()
public Array stack_trace ()
public String stack_trace_dump ()
public Arrayref store_synteny ()
public strict_hash_format ()
public void throw ()
public tree_analysis_data_id ()
public tree_file ()
public Depend try ()
public Int verbose ()
public warning ()
public worker ()
public worker_temp_directory ()
public write_output ()

Method Documentation

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::all_hits ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::cutoff_evalue ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::cutoff_score ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::dumpMercatorFiles ( )

Undocumented method

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public void Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::fetch_input ( )
    Title   :   fetch_input
    Usage   :   $self->fetch_input
    Function:   Fetches input data for repeatmasker from the database
    Returns :   none
    Args    :   none
 
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Reimplemented from Bio::EnsEMBL::Hive::Process.

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::genome_db_ids ( )

Undocumented method

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

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::get_sql_for_peptide_hits ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::get_table_name_from_dbID ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::input_dir ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::mavid_constraints ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::maximum_gap ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::method_link_species_set ( )

Undocumented method

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::method_link_type ( )

Undocumented method

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::msa_method_link_species_set_id ( )

Undocumented method

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::output_dir ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::pre_map ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::run ( )

Undocumented method

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

public Arrayref Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::store_synteny ( )
  Arg[1]      : hashref $run_ids2synteny_and_constraints (unused)
  Example     : $self->store_synteny();
  Description : This method will store the syntenies defined by Mercator
                into the compara DB. The MethodLinkSpecieSet for these
                syntenies is created and stored if needed at this point.
                The IDs for the new Bio::EnsEMBL::Compara::SyntenyRegion
                objects are returned in an arrayref.
  ReturnType  : arrayref of integer
  Exceptions  :
  Status      : stable
 
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::tree_analysis_data_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::tree_file ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator::write_output ( )

Undocumented method

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


The documentation for this class was generated from the following file:
  • Bio/EnsEMBL/Compara/Production/GenomicAlignBlock/Mercator.pm