Bio::EnsEMBL::DBSQL AffyFeatureAdaptor
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Summary
Bio::EnsEMBL::DBSQL::AffyFeatureAdaptor - A database adaptor for fetching and
storing AffyFeature objects.
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::AffyFeature
Bio::EnsEMBL::DBSQL::OligoFeatureAdaptor
Inherit
Bio::EnsEMBL::DBSQL::OligoFeatureAdaptor
Synopsis
  my $afa = $db->get_AffyFeatureAdaptor();
my $features = $afa->fetch_all_by_AffyProbe($probe); $features = $afa->fetch_all_by_Slice_arrayname( $slice, 'Affy-1', 'Affy-2' );
Description
The AffyFeatureAdaptor is a database adaptor for storing and retrieving
AffyFeature objects.
Methods
_default_where_clauseDescriptionCode
_new_fastDescriptionCode
fetch_all_by_AffyProbeDescriptionCode
list_dbIDsDescriptionCode
Methods description
_default_where_clausecode    nextTop
  Args       : None
Example : None
Description: PROTECTED implementation of superclass abstract method.
Returns an additional table joining constraint to use for
queries.
Returntype : List of strings
Exceptions : None
Caller : Internal
Status : Medium Risk
_new_fastcodeprevnextTop
  Args       : Hashref to be passed to AffyFeature->new_fast()
Example : None
Description: Construct an AffyFeature object using quick and dirty new_fast.
Returntype : Bio::EnsEMBL::AffyFeature
Exceptions : None
Caller : _objs_from_sth
Status : Medium Risk
fetch_all_by_AffyProbecodeprevnextTop
  Arg [1]    : Bio::EnsEMBL::AffyProbe
Example : my $features = $afa->fetch_all_by_AffyProbe($probe);
Description: Fetchs all features that a given probe creates.
Returntype : Listref of Bio::EnsEMBL::AffyFeature objects
Exceptions : None
Caller : AffyProbe->get_all_AffyFeatures()
Status : Medium Risk
list_dbIDscodeprevnextTop
  Args       : None
Example : my @feature_ids = @{$afa->list_dbIDs()};
Description: Gets an array of internal IDs for all AffyFeature objects
in the current database. NOTE: In a multi-species
database, this method will return the dbIDs of all
AffyFeature objects, not just the ones associated with
the current species.
Returntype : List of ints
Exceptions : None
Caller : ?
Status : Medium Risk
Methods code
_default_where_clausedescriptionprevnextTop
sub _default_where_clause {
	my $self = shift;
	
	return "
		    of.oligo_probe_id = op.oligo_probe_id
		AND op.oligo_array_id = oa.oligo_array_id
		AND oa.type='AFFY'
	";
}
_new_fastdescriptionprevnextTop
sub _new_fast {
	my $self = shift;
	
	my $hash_ref = shift;
	return Bio::EnsEMBL::AffyFeature->new_fast($hash_ref);
}
fetch_all_by_AffyProbedescriptionprevnextTop
sub fetch_all_by_AffyProbe {
	my $self  = shift;
	my $probe = shift;
	
	return $self->fetch_all_by_Probe($probe);
}
list_dbIDsdescriptionprevnextTop
sub list_dbIDs {
	my $self = shift;
	
	#return $self->_list_dbIDs('oligo_feature');
# Can't use _list_dbIDs because only want OligoProbe objects on arrays of type AFFY
my @out; # FIXME: This SQL will not work as expected on multi-species
# databases. It needs to be anchored in a coord_system entry
# coord_system.species_id = $self->species_id(). /ak4@2008-07-15
my $sql = " SELECT DISTINCT of.oligo_feature_id FROM oligo_feature of, oligo_probe op, oligo_array oa WHERE of.oligo_probe_id=op.oligo_probe_id AND op.oligo_array_id=oa.oligo_array_id AND oa.type='AFFY' "; my $sth = $self->prepare($sql); $sth->execute; while (my ($id) = $sth->fetchrow() ) { push @out, $id; } $sth->finish; return\@ out; } 1;
}
General documentation
LICENSETop
  Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license. For license details, please see /info/about/code_licence.html
CONTACTTop
  Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at <helpdesk@ensembl.org>.