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::UnmappedObjectAdaptor

SYNOPSIS

  my $uoa = $database_adaptor->get_UnmappedObjectAdaptor();

  my $missed = @{ $uoa->fetch_all_by_type('xref') };

DESCRIPTION

Unmapped ObjectAdaptor - An adaptor responsible for the creation, editing, retrieval of Unmapped Objects. These being the Objects that where not mapped in a specific process i.e. xref, cDNA, Markers.

METHODS

new

  Arg [1]    : list of args @args
               Superclass constructor arguments
  Example    : none
  Description: Constructor which just initializes internal cache structures
  Returntype : Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor
  Exceptions : none
  Caller     : implementing subclass constructors
  Status     : At Risk

list_dbIDs

  Arg [1]    : none
  Example    : @unmapped_object_ids = @{$unmapped_object_adaptor->list_dbIDs()};
  Description: Gets an array of internal ids for all unmapped_objects in the current db
  Returntype : list of ints
  Exceptions : none
  Caller     : ?
  Status     : Stable

list_unmapped_reasons

  Arg [1]    : none
  Example    : @unmapped_object_reason+ids = 
                   @{$unmapped_object_adaptor->list_unmapped_reasons()};
  Description: Gets an array of internal ids for all unmapped_objects in the current db
  Returntype : list of ints
  Exceptions : none
  Caller     : ?
  Status     : Stable

store

  Arg [1]    : list of Bio::EnsEMBL::UnmappedObjects @uo
               the unmapped objects to store in the database
  Example    : $ou_adaptor->store(@uo);
  Description: Stores a list of unmapped objects in the database
  Returntype : none
  Exceptions : thrown if no Analysis, or no list of objects to store. 
  Caller     : general
  Status     : Stable

fetch_all_by_type

  Arg [1]  : string type. The type of unmapped objects
  Example  : @unmapped_object = @{$uoa->fetch_all_by_type('xref')};
  Description : Retrieves all the unmapped object for a particular
                type. e.g. 'xref','cDNA', 'marker'
  Returntype  : Array ref of Bio::EnsEMBL::UnmappedObject
  Exceptions  : none
  Caller      : general
  Status      : At Risk

fetch_all_by_analysis

  Arg [1]  : Bio:EnsEMBL::Analysis object
  Arg [2]  : (optional) string database name
  Example  : @unmapped_object = @{$uoa->fetch_all_by_analysis($analysis)};
  Description : Retrieves all the unmapped object for a particular
                analysis type with the the option of a particular
                database type.
  Returntype  : array ref of Bio::EnsEMBL::UnmappedObject
  Exceptions  : thorws if first argument is not an anaylisi object
  Caller      : general
  Status      : At Risk

fetch_by_identifier

  Arg [1]  : string type. The type of unmapped objects
  Arg [2]  : (optional) string database name
  Example  : @unmapped_object = @{$uoa->fetch_by_identifier('Q123345')};
  Description : Retrieves the unmapped object for a particular
                identifier/accession
  Returntype  : array ref of Bio::EnsEMBL::UnmappedObject
  Exceptions  : none
  Caller      : general
  Status      : At Risk

fetch_all_by_object_type_id

  Arg [1]  : string - The object type of the ensembl object e.g. Gene
  Arg [2]  : int    - The internal dbID of the ensembl object
  Example  : my @unmapped_objects = @{$uoa->fetch_all_by_object_type_id('Gene', 12341)};
  Description : Retrieves the unmapped objects for a particular ensembl object
                This is a base method which should be called by wrapper methods
                defining the correct object type e.g. $uoa->fetch_all_by_Gene($gene)
  Returntype  : array ref of Bio::EnsEMBL::UnmappedObject objects
  Exceptions  : Throws if arguments are not defined
  Caller      : general
  Status      : At Risk