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

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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