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::DnaAlignFeatureAdaptor - Adaptor for DnaAlignFeatures

SYNOPSIS

  $dafa = $registry->get_adaptor( 'Human', 'Core', 'DnaAlignFeature' );

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

  $dafa->store(@features);

DESCRIPTION

This is an adaptor responsible for the retrieval and storage of DnaDnaAlignFeatures from the database. This adaptor inherits most of its functionality from the BaseAlignFeatureAdaptor and BaseFeatureAdaptor superclasses.

METHODS

_tables

  Args       : none
  Example    : @tabs = $self->_tables
  Description: PROTECTED implementation of the abstract method inherited from
               BaseFeatureAdaptor.  Returns list of [tablename, alias] pairs
  Returntype : list of listrefs of strings
  Exceptions : none
  Caller     : Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::generic_fetch
  Status     : Stable

_columns

  Args       : none
  Example    : @columns = $self->_columns
  Description: PROTECTED implementation of abstract superclass method.  
               Returns a list of columns that are needed for object creation.
  Returntype : list of strings
  Exceptions : none
  Caller     : Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::generic_fetch
  Status     : Stable

store

  Arg [1]    : list of Bio::EnsEMBL::DnaAlignFeatures @feats
               the features to store in the database
  Example    : $dna_align_feature_adaptor->store(@features);
  Description: Stores a list of DnaAlignFeatures 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 associate 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

remove

  Arg [1]    : A feature $feature 
  Example    : $feature_adaptor->remove($feature);
  Description: This removes a feature from the database.  The table the
               feature is removed from is defined by the abstract method
               _tablename, and the primary key of the table is assumed
               to be _tablename() . '_id'.  The feature argument must 
               be an object implementing the dbID method, and for the
               feature to be removed from the database a dbID value must
               be returned.
  Returntype : none
  Exceptions : thrown if $feature arg does not implement dbID(), or if
               $feature->dbID is not a true value
  Caller     : general
  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::DnaDnaAlignFeatures
  Exceptions : none
  Caller     : Bio::EnsEMBL::BaseFeatureAdaptor::generic_fetch
  Status     : Stable

list_dbIDs

  Arg [1]    : none
  Example    : @feature_ids = @{$dna_align_feature_adaptor->list_dbIDs()};
  Description: Gets an array of internal ids for all dna align 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