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

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.

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