LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

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CONTACT

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NAME

Bio::EnsEMBL::DBSQL::MergedAdaptor

SYNOPSIS

  # load all available adaptors of the given type for the species
  my $merged_adaptor = Bio::EnsEMBL::DBSQL::MergedAdaptor->new(
    -species => "human",
    -type    => "gene"
  );

  # only load adaptors from the given groups of the given type for the species
  my $merged_adaptor = Bio::EnsEMBL::DBSQL::MergedAdaptor->new(
    -species => "human",
    -type    => "gene",
    -groups  => ['core','otherfeatures']
  );

DESCRIPTION

The MergedAdaptor object is merely a list of adaptors. AUTOLOAD is used to call a subroutine on each adaptor and merge the results. This object structure allows you to treat a set of adaptors as a logical single entity. The end result is that disparate database source data sets are accessible through a single adaptor call.

This code will convert single object return calls into ArrayRef returning calls and so is only safe to use with the fetch_all_XXX or get_all_XXX methods.

METHODS

new

  Arg [SPECIES]: String species name to get adaptors for
  Arg [TYPE]   : String type to get adaptors for
  Arg [GROUPS] : (optional) ArrayRef of groups to load
  Example      : my $adaptor = Bio::EnsEMBL::DBSQL::MergedAdaptor->new(
                    -species=> 'human', -type =>'Population', -groups => ['Sanger','Ensembl']);
                 my $alL_adaptor = Bio::EnsEMBL::DBSQL::MergedAdaptor->new(
                    -species=> 'human', -type =>'Population');
  Description: Creates a new MergedAdaptor.
  Returntype : Bio::EnsEMBL::DBSQL::MergedAdaptor
  Exceptions : throws if species or type not specified
  Caller     : general
  Status     : At Risk
             : Under development

_populate_adaptors

  Arg [1]      : String species name to get adaptors for
  Arg [2]      : String type to get adaptors for
  Arg [3]      : (optional) ArrayRef of groups to load
  Description  : Auto-populates the current MergedAdaptor with the
                 adaptors linked to this species, type and optional set of groups
  Caller       : general
  Status       : At Risk

add_list

  Arg [n]     : Adaptors to add into this instance
  Description : Adds the given adaptors to the internal adaptor list

add_list

  Arg [1]     : Adaptor to add into this instance
  Description : Adds the given adaptor to the internal adaptor list. For
                multiple adaptor addition use C<add_list()>.

can

  Arg [1]     : String method name to be called
  Description : Implementation of UNIVERSAL::can(). We loop through the
                available adaptors and return true if any will respond
                to the given method name
  Returntype  : Boolean indicating if any delegating object will respond to this method

isa

  Arg [1]     : String method name to be called
  Description : Implementation of UNIVERSAL::isa(). We loop through the
                available adaptors and return true if any inherited from
                the given class
  Returntype  : Boolean indicating if any delegating object inherits from the given class

AUTOLOAD

  Description : Internal override of AUTLOAD. The code will detect the requested
                method, loop through all available adaptors and will 
  Returntype  : Boolean indicating if any delegating object inherits from the given class