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

List of all members.


Class Summary

Synopsis

my $db           = Bio::EnsEMBL::Compara::DBAdaptor-\>new($locator);
my $ncfasttree = Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCFastTrees-\>new
  (
   -db         =\> $db,
   -input_id   =\> $input_id,
   -analysis   =\> $analysis
  );
$ncfasttree-\>fetch_input(); #reads from DB
$ncfasttree-\>run();
$ncfasttree-\>output();
$ncfasttree-\>write_output(); #writes to DB

Description

This RunnableDB builds fast phylogenetic trees using RAxML-Light and FastTree2. It is useful in cases where the alignments are too big to build the usual RAxML trees in PrepareSecStructModels and SecStructModelTree.
 

Definition at line 28 of file NCFastTrees.pm.

Available Methods

protected _dumpMultipleAlignmentStructToWorkdir ()
protected _load_and_dump_alignment ()
protected _run_fasttree ()
protected _run_parsimonator ()
protected _run_raxml_light ()
protected _store_newick_into_nc_tree_tag_string ()
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 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 void 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 void write_output ()

Method Documentation

protected Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCFastTrees::_dumpMultipleAlignmentStructToWorkdir ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCFastTrees::_load_and_dump_alignment ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCFastTrees::_run_fasttree ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCFastTrees::_run_parsimonator ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCFastTrees::_run_raxml_light ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCFastTrees::_store_newick_into_nc_tree_tag_string ( )

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 void Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCFastTrees::fetch_input ( )
    Title    : fetch_input
    Usage    : $self->fetch_input
    Function : Fetches input data from the database+
    Returns  : none
    Args     : none
 
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 void Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCFastTrees::run ( )
    Title     : run
    Usage     : $self->run
    Function  : runs something
    Returns   : none
    Args      : none
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

public void Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCFastTrees::write_output ( )
    Title     : write_output
    Usage     : $self->write_output
    Function  : stores something
    Returns   : none
    Args      : none
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.


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