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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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