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::Utils::RNAProductTypeMapper - Utility class for mapping between RNA-product types used in the Ensembl database and respective Perl API classes.

DESCRIPTION

The purpose of this class is to hide from the users the mappings between classes representing various mature RNA products (e.g. generic, miRNA, circRNA etc.) and their respective identifiers in the Ensembl database. In principle there should be no need for users to call the mapper directly; it is invoked internally whenever such mappings are needed (e.g. in RNAProduct constructor or in RNAProductAdaptor).

Note that the type_code<->class_name mappings are hardcoded here, specifically in the constructor, instead of being fetched from the database. This is so that it is not possible for someone to trigger construction of arbitrary objects by having modified class names stored in the database.

SYNOPSIS

  my $rpt_mapper = Bio::EnsEMBL::Utils::RNAProductTypeMapper->new();

  my $class_name = $rpt_mapper->type_code_to_class( 'generic' );
  my $type_code = $rpt_mapper->class_to_type_code( 'Bio::EnsEMBL::MicroRNA' );

mapper

  Example    : my $mapper = Bio::EnsEMBL::Utils::RNAProductTypeMapper->mapper();
  Description: Retrieves an instance of RNAProductTypeMapper from its module,
               reusing an existing one should it exist.
  Returntype : Bio::EnsEMBL::Utils::RNAProductTypeMapper
  Exceptions : none
  Caller     : internal
  Status     : Stable

new

  Example    : my $mapper = Bio::EnsEMBL::Utils::RNAProductTypeMapper->new();
  Description: Constructor.  Creates a new RNAProductTypeMapper object.
               Not particularly useful for end users because all
               RNAProductTypeMapper objects are identical; use mapper()
               instead.
  Returntype : Bio::EnsEMBL::Utils::RNAProductTypeMapper
  Exceptions : none
  Caller     : internal
  Status     : Stable

class_attribute_cache_map

  Arg [1]    : string $class_name - fully qualified RNA-product class name
  Example    : my $attr_cache_map
                 = $mapper->class_attribute_cache_map( 'Bio::EnsEMBL::MicroRNA' );
  Description: For the given name of a class representing a mature RNA
               product, returns the map indicating which local members variables
               should be synchronised with which Attributes.
  Returntype : hashref
  Exceptions : throw if the class does not represent known RNA-product type
  Caller     : internal
  Status     : Stable

class_to_type_code

  Arg [1]    : string $class_name - fully qualified RNA-product class name
  Example    : my $type_code
                 = $mapper->class_to_type_code( 'Bio::EnsEMBL::MicroRNA' );
  Description: For the given name of a class representing a mature RNA
               product, returns the type code used to represent it in the
               Ensembl database.
  Returntype : string
  Exceptions : throw if the class does not represent known RNA-product type
  Caller     : internal
  Status     : Stable

type_code_to_class

  Arg [1]    : string $type_code - type code of RNA product
  Example    : my $class_name = $mapper->class_to_type_code( 1 );
  Description: For the type code representing a mature RNA product in the
               Ensembl database, return its API class name
  Returntype : string
  Exceptions : throw if the code does not represent known RNA-product type
  Caller     : internal
  Status     : Stable

_generate_reverse_map

  Description: PRIVATE generates class_name->type_code map from the
               type_code->class_name one.
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable