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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NAME

  Bio::EnsEMBL::DBSQL::BiotypeAdaptor - An adaptor which performs database
  interaction relating to the storage and retrieval of Biotypes

SYNOPSIS

  my $biotype = $db_adaptor->fetch_by_name_object_type('protein_coding', 'gene');

DESCRIPTION

    This adaptor provides a means to retrieve and store information related
    to Biotypes.  Primarily this involves the retrieval or storage of
    Bio::EnsEMBL::Biotype objects from a database.

    See Bio::EnsEMBL::Biotype for details of the Biotype class.

METHODS

_tables

  Arg [1]    : none
  Description: PROTECTED implementation of superclass abstract method.
               Returns the names, aliases of the tables to use for queries.
  Returntype : list of arrays of strings
  Exceptions : none

_columns

  Arg [1]    : none
  Example    : none
  Description: PROTECTED implementation of superclass abstract method.
               Returns a list of columns to use for queries.
  Returntype : list of strings
  Exceptions : none

_objs_from_sth

  Arg [1]    : StatementHandle $sth
  Example    : none
  Description: PROTECTED implementation of abstract superclass method.
               responsible for the creation of ProteinFeatures
  Returntype : arrayref of Bio::EnsEMBL::Biotype objects
  Exceptions : none

fetch_by_name_object_type

  Arg [1]    : String $name
               The name of the biotype to retrieve
  Arg [2]    : String $object_type
               The object type of the biotype to retrieve (gene or transcript)
  Example    : $biotype = $biotype_adaptor->fetch_by_name_object_type('mRNA', 'gene');
  Description: Retrieves a biotype object from the database via its combined key (name, object_type).
               If the Biotype requested does not exist in the database, a new Biotype object is
               created with the provided name and object_type to be returned.
  Returntype : Bio::EnsEMBL::Biotype
  Exceptions : none

fetch_all_by_object_type

  Arg [1]    : String $object_type
               The object_type of the biotypes to retrieve (gene or transcript).
  Example    : $biotypes = $biotype_adaptor->fetch_all_by_object_type('gene');
  Description: Retrieves an array reference of biotype objects from the database.
  Returntype : arrayref of Bio::EnsEMBL::Biotype objects or empty arrayref
  Warning    : If empty arrayref is to be returned
  Exceptions : none

fetch_all_by_name

  Arg [1]    : String $name
               The name of the biotype to retrieve
  Arg [2]    : (optional) String $object_type
               The object_type of the biotypes to retrieve (gene or transcript).
  Example    : $biotypes = $biotype_adaptor->fetch_all_by_name('lincRNA');
  Description: Retrieves an array reference of biotype objects from the database.
  Returntype : arrayref of Bio::EnsEMBL::Biotype objects or empty arrayref
  Warning    : If empty arrayref is to be returned
  Exceptions : none

fetch_all_by_group_object_db_type

  Arg [1]    : String $biotype_group
               The group of the biotypes to retrieve
  Arg [2]    : String $object_type
               The object type of the biotypes to retrieve (gene or transcript)
  Arg [3]    : (optional) String $db_type
               The db_type of the biotypes to retrieve. If not provided defaults to 'core'.
  Example    : $biotype = $biotype_adaptor->fetch_all_by_group_object_db_type('coding', 'gene');
  Description: Retrieves an array reference of biotype objects from the database of the provided
               biotype_group and object_type and core db_type.
  Returntype : arrayref of Bio::EnsEMBL::Biotype objects or empty arrayref
  Warning    : If empty arrayref is to be returned
  Exceptions : none