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Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML:

List of all members.


Class Summary

Description

This Analysis/RunnableDB is designed to take ProteinTree as input
This must already have a multiple alignment run on it. It uses that alignment
as input into the NJTREE PHYML program which then generates a phylogenetic tree
input_id/parameters format eg: "{'protein_tree_id'=\>1234}"
    protein_tree_id : use 'id' to fetch a cluster from the ProteinTree
 

Synopsis

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

Definition at line 42 of file NJTREE_PHYML.pm.

Available Methods

protected _slurp ()
protected _store_tree_tags ()
public Bio::EnsEMBL::Analysis analysis ()
public Bio::EnsEMBL::Analysis analysis ()
public analyze_genepairlink ()
public ancient_residual_test ()
public catch ()
public catch ()
public check_for_split_genes ()
public check_homology_consistency ()
public void check_if_exit_cleanly ()
public void check_if_exit_cleanly ()
public compara_dba ()
public compara_dba ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
data_dbc ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
data_dbc ()
public dataflow_output_id ()
public dataflow_output_id ()
public
Bio::EnsEMBL::Hive::DBSQL::DBAdaptor 
db ()
public
Bio::EnsEMBL::Hive::DBSQL::DBAdaptor 
db ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public Int debug ()
public Int debug ()
public delete_old_homologies ()
public delete_old_homologies_old ()
public delete_old_orthotree_tags ()
public void deprecate ()
public void deprecate ()
public DESTROY ()
public direct_ortholog_test ()
public display_link_analysis ()
public dumpTreeMultipleAlignmentToWorkdir ()
public duplication_confidence_score ()
public fetch_input ()
public genepairlink_check_dups ()
public genepairlink_fetch_homology ()
public generate_attribute_arguments ()
public get_ancestor_species_hash ()
public get_ancestor_taxon_level ()
public get_matrix_hash ()
public get_species_tree_file ()
public get_species_tree_string ()
public go_figure_compara_dba ()
public go_figure_compara_dba ()
public go_figure_dbc ()
public go_figure_dbc ()
public void info ()
public void info ()
public input_id ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public inspecies_paralog_test ()
public load_species_tree_from_string ()
public new ()
public new ()
public one2many_ortholog_test ()
public Array output ()
public Array output ()
public outspecies_test ()
public param ()
public param ()
public param_defaults ()
public param_substitute ()
public param_substitute ()
public parameters ()
public parameters ()
public parse_newick_into_proteintree ()
public Bio::EnsEMBL::Hive::Queen queen ()
public Bio::EnsEMBL::Hive::Queen queen ()
public run ()
public run_analysis ()
public run_njtree_phyml ()
public Arrayref runnable ()
public Arrayref runnable ()
public Array stack_trace ()
public Array stack_trace ()
public String stack_trace_dump ()
public String stack_trace_dump ()
public store_gene_link_as_homology ()
public store_homologies ()
public store_proteintree ()
public store_tags ()
public strict_hash_format ()
public strict_hash_format ()
public void throw ()
public void throw ()
public Depend try ()
public Depend try ()
public Int verbose ()
public Int verbose ()
public warning ()
public warning ()
public worker ()
public worker ()
public worker_temp_directory ()
public worker_temp_directory ()
public write_output ()

Method Documentation

protected Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::_slurp ( ) [inherited]

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML::_store_tree_tags ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::analyze_genepairlink ( ) [inherited]

Undocumented method

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::ancient_residual_test ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML::check_for_split_genes ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::check_homology_consistency ( ) [inherited]

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::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::ProteinTrees::OrthoTree::delete_old_homologies ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::delete_old_homologies_old ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::delete_old_orthotree_tags ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML::DESTROY ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree.

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::direct_ortholog_test ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::display_link_analysis ( ) [inherited]

Undocumented method

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML::dumpTreeMultipleAlignmentToWorkdir ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::duplication_confidence_score ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML::fetch_input ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree.

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::genepairlink_check_dups ( ) [inherited]

Undocumented method

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::genepairlink_fetch_homology ( ) [inherited]

Undocumented method

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::generate_attribute_arguments ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::get_ancestor_species_hash ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::get_ancestor_taxon_level ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::get_matrix_hash ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML::get_species_tree_file ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::get_species_tree_string ( ) [inherited]

Undocumented method

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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::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::ProteinTrees::OrthoTree::inspecies_paralog_test ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::load_species_tree_from_string ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::one2many_ortholog_test ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::outspecies_test ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML::param_defaults ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree.

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML::parse_newick_into_proteintree ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML::run ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree.

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::run_analysis ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML::run_njtree_phyml ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::store_gene_link_as_homology ( ) [inherited]

Undocumented method

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::store_homologies ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML::store_proteintree ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML::store_tags ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML::write_output ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree.


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