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::TranscriptSupportingFeatureAdaptor - Retrieves supporting features from the database.

SYNOPSIS

  $supporting_feature_adaptor =
    $database_adaptor->get_TranscriptSupportingFeatureAdaptor;

  @supporting_feats =
    @{ $supporting_feat_adaptor->fetch_all_by_Transcript($transcript) };

METHODS

fetch_all_by_Transcript

  Arg [1]    : Bio::EnsEMBL::Transcript $transcript 
               The transcript to fetch supporting features for
  Arg [2]    : String (optional)
               Feature type to filter upon (either 'dna_align_feature' or 'protein_align_feature')
  Example    : @sfs = @{$supporting_feat_adaptor->fetch_all_by_Transcript($transcript)};
                           @sfs = @{$supporting_feat_adaptor->fetch_all_by_Transcript($transcript, $feature_type)};     
  Description: Retrieves supporting features (evidence) for a given transcript. 
  Returntype : list of Bio::EnsEMBL::BaseAlignFeatures in the same coordinate
               system as the $transcript argument
  Exceptions : warning if $transcript is not in the database (i.e. dbID not defined)
               throw if a retrieved or requested supporting feature is of unknown type 
  Caller     : Bio::EnsEMBL::Transcript
  Status     : Stable

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