LICENSE

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::SupportingFeatureAdaptor - Retrieves supporting features from the database.

SYNOPSIS

my $sfa =
  $registry->get_adaptor( 'Human', 'Core', 'SupportingFeature' );

my @supporting_feats = @{ $sfa->fetch_all_by_Exon($exon) };

METHODS

fetch_all_by_Exon

Arg [1]    : Bio::EnsEMBL::Exon $exon 
             The exon to fetch supporting features.
Example    : @sfs =
              @{ $supporting_feat_adaptor->fetch_all_by_Exon($exon) };
Description: Retrieves supporting features (evidence) for a given
             exon.
Returntype : List of Bio::EnsEMBL::BaseAlignFeatures in the same
             coordinate system as the $exon argument
Exceptions : Warning if $exon is not in the database (i.e. dbID
             not defined).
             Throw if a retrieved supporting feature is of unknown
             type.
Caller     : Bio::EnsEMBL::Exon
Status     : Stable

store

Arg [1]    : Int $exonsID
             The dbID of an EnsEMBL exon to associate with
             supporting features.
Arg [2]    : Ref to array of Bio::EnsEMBL::BaseAlignFeature
             (the support)
Example    : $sfa->store($exon_id, \@features);
Description: Stores a set of alignment features and associates an
             EnsEMBL exon with them
Returntype : none
Exceptions : thrown when invalid dbID is passed to this method
Caller     : TranscriptAdaptor
Status     : Stable