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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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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