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Bio::EnsEMBL::Compara::DBSQL::SpeciesTreeAdaptor Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::DBSQL::SpeciesTreeAdaptor:

List of all members.


Class Summary

Synopsis

    my $species_tree = $compara_dba-\>get_SpeciesTreeAdaptor-\>create_species_tree();                                         # include all available species from genome_db by default

    my $species_tree = $compara_dba-\>get_SpeciesTreeAdaptor-\>create_species_tree( -species_set_id =\> 12345 );               # only use the species from given species_set

    my $species_tree = $compara_dba-\>get_SpeciesTreeAdaptor-\>create_species_tree( -param1 =\> value1, -param2 =\> value2 );   # more complex scenarios

Description

    This is not strictly a DBSQL adaptor, because there is no corresponding DB-persistent object type.
    This module encapsulates functionality to create/manipulate species trees in the form of subroutines
    ( and so the code should be easier to reuse than that in ensembl-compara/scripts/tree ).
 

Definition at line 24 of file SpeciesTreeAdaptor.pm.

Available Methods

protected _columns ()
protected _default_where_clause ()
protected _final_clause ()
protected _left_join ()
protected _list_dbIDs ()
protected _objs_from_sth ()
protected _straight_join ()
protected _tables ()
public Listref bind_param_generic_fetch ()
public create_species_tree ()
public
Bio::EnsEMBL::DBSQL::DBAdaptor 
db ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public dump_data ()
public fetch_all ()
public Listref fetch_all_by_dbID_list ()
public Bio::EnsEMBL::Feature fetch_by_dbID ()
public Listref generic_fetch ()
public get_dumped_data ()
public Boolean is_multispecies ()
public Scalar last_insert_id ()
public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
new ()
public DBI::StatementHandle prepare ()
public prune_tree ()
public Int species_id ()

Method Documentation

public Bio::EnsEMBL::Compara::DBSQL::SpeciesTreeAdaptor::create_species_tree ( )
    Create a taxonomy tree from original NCBI taxonomy tree by only using a subset of taxa (provided either as a list or species_set or all_genome_dbs)
 
Code:
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public Bio::EnsEMBL::Compara::DBSQL::SpeciesTreeAdaptor::prune_tree ( )
    Only retain the leaves that belong to the species_set
 
Code:
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The documentation for this class was generated from the following file: