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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::AssemblyExceptionFeatureAdaptor

SYNOPSIS

my $assembly_exception_feature_adaptor =
  $database_adaptor->get_AssemblyExceptionFeatureAdaptor();

@assembly_exception_features =
  $assembly_exception_feature_adaptor->fetch_all_by_Slice($slice);

DESCRIPTION

Assembly Exception Feature Adaptor - database access for assembly exception features.

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::AssemblyExceptionFeatureAdaptor
Exceptions : none
Caller     : implementing subclass constructors
Status     : Stable

fetch_all

Arg [1]    : none
Example    : my @axfs = @{$axfa->fetch_all()};
Description: Retrieves all assembly exception features which are in the
             database and builds internal caches of the features.
Returntype : reference to list of Bio::EnsEMBL::AssemblyExceptionFeatures
Exceptions : none
Caller     : fetch_by_dbID, fetch_by_Slice
Status     : Stable

fetch_by_dbID

Arg [1]    : int $dbID
Example    : my $axf = $axfa->fetch_by_dbID(3);
Description: Retrieves a single assembly exception feature via its internal
             identifier.  Note that this only retrieves one of the two
             assembly exception features which are represented by a single
             row in the assembly_exception table.
Returntype : Bio::EnsEMBL::AssemblyExceptionFeature
Exceptions : none
Caller     : general
Status     : Stable

fetch_all_by_Slice

Arg [1]    : Bio::EnsEMBL::Slice $slice
Example    : my @axfs = @{$axfa->fetch_all_by_Slice($slice)};
Description: Retrieves all assembly exception features which overlap the
             provided slice.  The returned features will be in coordinate
             system of the slice.
Returntype : reference to list of Bio::EnsEMBL::AssemblyException features
Exceptions : none
Caller     : Feature::get_all_alt_locations, general
Status     : Stable

store

    Arg[1]       : Bio::EnsEMBL::AssemblyException $asx
    Arg[2]       : Bio::EnsEMBL::AssemblyException $asx2

    Example      : $asx = Bio::EnsEMBL::AssemblyExceptionFeature->new(...)
                   $asx2 = Bio::EnsEMBL::AssemblyExceptionFeature->new(...)
                   $asx_seq_region_id = $asx_adaptor->store($asx);
    Description:  This stores a assembly exception feature in the 
                  assembly_exception table and returns the assembly_exception_id.
                  Needs 2 features: one pointing to the Assembly_exception, and the
                  other pointing to the region in the reference that is being mapped to
                  Will check that start, end and type are defined, and the alternate
                  slice is present as well.
    ReturnType:   int
    Exceptions:   throw if assembly exception not defined (needs start, end,
		  type and alternate_slice) of if $asx not a Bio::EnsEMBL::AssemblyException
    Caller:       general
    Status:       Stable

remove

Arg [1]    : $asx Bio::EnsEMBL::AssemblyFeatureException 
Example    : $asx_adaptor->remove($asx);
Description: This removes a assembly exception feature from the database.  
Returntype : none
Exceptions : thrown if $asx arg does not implement dbID(), or if
             $asx->dbID is not a true value
Caller     : general
Status     : Stable