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::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