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::SimpleFeatureAdaptor

SYNOPSIS

  my $registry = 'Bio::EnsEMBL::Registry';

  $registry->
    load_registry_from_db( ...

  my $sfa =
    $registry->get_adaptor('homo sapiens', 'core', 'SimpleFeature');

  print ref($sfa), "\n";

  my $sf_aref =
    $sfa->fetch_all;

  print scalar @$sf_aref, "\n";

DESCRIPTION

Simple Feature Adaptor - database access for simple features

METHODS

store

  Arg [1]    : list of Bio::EnsEMBL::SimpleFeatures @sf
               the simple features to store in the database
  Example    : $simple_feature_adaptor->store(@simple_feats);
  Description: Stores a list of simple feature objects in the database
  Returntype : none
  Exceptions : thrown if @sf is not defined, if any of the features do not
               have an attached slice.
               or if any elements of @sf are not Bio::EnsEMBL::SimpleFeatures 
  Caller     : general
  Status     : Stable

_tables

  Arg [1]    : none
  Example    : none
  Description: PROTECTED implementation of superclass abstract method
               returns the names, aliases of the tables to use for queries
  Returntype : list of listrefs of strings
  Exceptions : none
  Caller     : internal
  Status     : Stable

_columns

  Arg [1]    : none
  Example    : none
  Description: PROTECTED implementation of superclass abstract method
               returns a list of columns to use for queries
  Returntype : list of strings
  Exceptions : none
  Caller     : internal
  Status     : Stable

_objs_from_sth

  Arg [1]    : hash reference $hashref
  Example    : none
  Description: PROTECTED implementation of superclass abstract method.
               creates SimpleFeatures from an executed DBI statement handle.
  Returntype : list reference to Bio::EnsEMBL::SimpleFeature objects
  Exceptions : none
  Caller     : internal
  Status     : Stable

list_dbIDs

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