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Bio::EnsEMBL::Compara::Production::EPOanchors::TrimAnchorAlign Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::Production::EPOanchors::TrimAnchorAlign:

List of all members.


Class Summary

Definition at line 13 of file TrimAnchorAlign.pm.

Available Methods

protected Boolean _dump_fasta ()
public Bio::EnsEMBL::Analysis analysis ()
public anchor_id ()
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 fetch_input ()
public get_best_trimming_position ()
public get_params ()
public get_trimmed_anchor_aligns ()
public go_figure_dbc ()
public void info ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public input_method_link_species_set_id ()
public new ()
public Array output ()
public output_method_link_species_set_id ()
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 Boolean Bio::EnsEMBL::Compara::Production::EPOanchors::TrimAnchorAlign::_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    :
 
Code:
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public Bio::EnsEMBL::Compara::Production::EPOanchors::TrimAnchorAlign::anchor_id ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::EPOanchors::TrimAnchorAlign::fetch_input ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::Production::EPOanchors::TrimAnchorAlign::get_best_trimming_position ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::EPOanchors::TrimAnchorAlign::get_params ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::EPOanchors::TrimAnchorAlign::get_trimmed_anchor_aligns ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::EPOanchors::TrimAnchorAlign::input_method_link_species_set_id ( )

Undocumented method

public Bio::EnsEMBL::Compara::Production::EPOanchors::TrimAnchorAlign::output_method_link_species_set_id ( )

Undocumented method

public Bio::EnsEMBL::Compara::Production::EPOanchors::TrimAnchorAlign::run ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::Production::EPOanchors::TrimAnchorAlign::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: