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

List of all members.


Class Summary

Definition at line 14 of file Mlagan.pm.

Available Methods

protected _trim_gab_left ()
protected _trim_gab_right ()
protected _write_gerp_dataflow ()
public Bio::EnsEMBL::Analysis analysis ()
public build_tree_string ()
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 void deprecate ()
public DESTROY ()
public dumpFasta ()
public fasta_files ()
public void fetch_input ()
public get_params ()
public get_species_tree ()
public go_figure_dbc ()
public void info ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public max_block_size ()
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 run ()
public Arrayref runnable ()
public Array stack_trace ()
public String stack_trace_dump ()
public strict_hash_format ()
public synteny_region_id ()
public void throw ()
public tree_string ()
public Depend try ()
public update_node_names ()
public Int verbose ()
public warning ()
public worker ()
public worker_temp_directory ()
public write_output ()

Method Documentation

protected Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mlagan::_trim_gab_left ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mlagan::_trim_gab_right ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mlagan::_write_gerp_dataflow ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mlagan::build_tree_string ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mlagan::dumpFasta ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mlagan::fasta_files ( )

Undocumented method

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public void Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mlagan::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::Production::GenomicAlignBlock::Mlagan::get_params ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mlagan::get_species_tree ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mlagan::max_block_size ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mlagan::method_link_species_set_id ( )

Undocumented method

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

Undocumented method

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

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mlagan::synteny_region_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mlagan::tree_string ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mlagan::update_node_names ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mlagan::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/Production/GenomicAlignBlock/Mlagan.pm