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Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::RFAMClassify Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::RFAMClassify:

List of all members.


Class Summary

Synopsis

my $db           = Bio::EnsEMBL::Compara::DBAdaptor-\>new($locator);
my $rfamclassify = Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::RFAMClassify-\>new
  (
   -db         =\> $db,
   -input_id   =\> $input_id,
   -analysis   =\> $analysis
  );

$rfamclassify-\>fetch_input(); #reads from DB
$rfamclassify-\>run();
$rfamclassify-\>output();
$rfamclassify-\>write_output(); #writes to DB

Description

This Analysis/RunnableDB is designed to take the descriptions of each
ncrna member and classify them into the respective cluster according
to their RFAM id. It also takes into account information from mirBase.
 

Definition at line 39 of file RFAMClassify.pm.

Available Methods

public Bio::EnsEMBL::Analysis analysis ()
public build_hash_cms ()
public build_hash_models ()
public catch ()
public void check_if_exit_cleanly ()
public compara_dba ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
data_dbc ()
public dataflow_clusters ()
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 go_figure_compara_dba ()
public go_figure_dbc ()
public void info ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public load_mirbase_families ()
public load_names_model_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 run_rfamclassify ()
public Arrayref runnable ()
public Array stack_trace ()
public String stack_trace_dump ()
public strict_hash_format ()
public tag_assembly_coverage_depth ()
public void throw ()
public Depend try ()
public Int verbose ()
public warning ()
public worker ()
public worker_temp_directory ()
public write_output ()

Method Documentation

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::RFAMClassify::build_hash_cms ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::RFAMClassify::build_hash_models ( )

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::ncRNAtrees::RFAMClassify::dataflow_clusters ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::RFAMClassify::fetch_input ( )

Undocumented method

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

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.
 
Code:
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public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::RFAMClassify::load_mirbase_families ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::RFAMClassify::load_names_model_id ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::RFAMClassify::run ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::RFAMClassify::run_rfamclassify ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::RFAMClassify::tag_assembly_coverage_depth ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::RFAMClassify::write_output ( )

Undocumented method

Code:
click to view

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


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