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

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NAME

Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor

SYNOPSIS

  use Bio::EnsEMBL::Registry;

  Bio::EnsEMBL::Registry->load_registry_from_db(
    -host => 'ensembldb.ensembl.org',
    -user => 'anonymous'
  );

  $pfa = Bio::EnsEMBL::Registry->get_adaptor( "human", "core",
    "proteinfeature" );

  my @prot_feats = @{ $pfa->fetch_all_by_translation_id(1231) };

  my $prot_feat = $pfa->fetch_by_dbID(523);

METHODS

fetch_all_by_translation_id

  Arg [1]    : int $transl
               the internal id of the translation corresponding to protein 
               whose features are desired 
  Example    : @prot_feats =
                  @{ $prot_feat_adaptor->fetch_by_translation_id(1234) };
  Description: Gets all protein features present on a peptide using the
               translations internal identifier.  This method will return
               an unsorted list of all protein_feature types.  The feature
               types may be distinguished using the logic name attribute of
               the attached analysis objects.   
  Returntype : listref of Bio::EnsEMBL::ProteinFeatures
  Exceptions : none
  Caller     : ?
  Status     : Stable

fetch_all_by_logic_name

  Arg [1]    : string $logic_name
               the logic name of the type of features to obtain
  Example    : $fs = $a->fetch_all_by_logic_name('foobar');
  Description: Returns a listref of features created from the database.
               only features with an analysis of type $logic_name will
               be returned.  If the logic name is invalid (not in the
               analysis table), a reference to an empty list will be
               returned.
  Returntype : listref of Bio::EnsEMBL::ProteinFeatures
  Exceptions : thrown if no $logic_name
  Caller     : General
  Status     : Stable

fetch_by_dbID

  Arg [1]    : int $protfeat_id
               the unique database identifier of the protein feature to obtain
  Example    : my $feature = $prot_feat_adaptor->fetch_by_dbID();
  Description: Obtains a protein feature object via its unique id
  Returntype : Bio::EnsEMBL::ProteinFeauture
  Exceptions : none
  Caller     : ?
  Status     : Stable

store

  Arg [1]    : Bio::EnsEMBL::ProteinFeature $feature
               The feature to be stored
  Arg [2]    : int $translation_id
            
  Example    : $protein_feature_adaptor->store($protein_feature);
  Description: Stores a protein feature in the database
  Returntype : int - the new internal identifier of the stored protein feature
  Exceptions : thrown if arg is not a Bio::EnsEMBL:
  Caller     : none
  Status     : Stable

fetch_all_by_uniprot_acc

  Arg [1]    : string uniprot accession
               The uniprot accession of the features to obtain
  Arg [2]    : (optional) string $logic_name
               The analysis logic name of the type of features to
               obtain. Default is 'gifts_import'
  Example    : @feats =
                 @{ $adaptor->fetch_all_by_uniprot_acc( 'P20366',
                   'gifts_import' ); }
  Description: Returns a listref of features created from the
               database which correspond to the given uniprot accession.  If
               logic name is defined, only features with an analysis
               of type $logic_name will be returned. Defaults to 'gifts_import'
  Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
  Exceptions : thrown if uniprot_acc is not defined
  Caller     : general
  Status     : Stable