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::ProteinAlignFeatureAdaptor - Adaptor for ProteinAlignFeatures

SYNOPSIS

  $pafa =
    $registry->get_adaptor( 'Human', 'Core', 'ProteinAlignFeature' );

  my @features = @{ $pafa->fetch_all_by_Slice($slice) };

  $pafa->store(@features);

METHODS

store

  Arg [1]    : list of Bio::EnsEMBL::DnaPepAlignFeature @feats
  Example    : $protein_align_feature_adaptor->store(@feats);
  Description: stores a list of ProteinAlignFeatures in the database
  Returntype : none
  Exceptions : throw if any of the provided features cannot be stored
               which may occur if:
                 * The feature does not have an associated Slice
                 * The feature does not have an associated analysis
                 * The Slice the feature is associated with is on a seq_region
                   unknown to this database
              A warning is given if:
                 * The feature has already been stored in this db
  Caller     : Pipeline
  Status     : Stable

_objs_from_sth

  Arg [1]    : DBI statement handle $sth
               an exectuted DBI statement handle generated by selecting 
               the columns specified by _columns() from the table specified 
               by _table()
  Example    : @dna_dna_align_feats = $self->_obj_from_hashref
  Description: PROTECTED implementation of superclass abstract method. 
               Creates DnaDnaAlignFeature objects from a DBI hashref
  Returntype : listref of Bio::EnsEMBL::ProteinAlignFeatures
  Exceptions : none
  Caller     : Bio::EnsEMBL::BaseFeatureAdaptor::generic_fetch
  Status     : Stable

list_dbIDs

  Arg [1]    : none
  Example    : @feature_ids = @{$protein_align_feature_adaptor->list_dbIDs()};
  Description: Gets an array of internal ids for all protein align 
               features in the current db
  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
  Returntype : listref of ints
  Exceptions : none
  Caller     : ?
  Status     : Stable