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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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     http://www.apache.org/licenses/LICENSE-2.0

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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