Raw content of Bio::EnsEMBL::Funcgen::DBSQL::SetFeatureAdaptor
<![CDATA[#
# Ensembl module for Bio::EnsEMBL::DBSQL::Funcgen::SetFeatureAdaptor
#
# You may distribute this module under the same terms as Perl itself
=head1 NAME
Bio::EnsEMBL::DBSQL::Funcgen::SetFeatureAdaptor - A base database adaptor for SetFeature adaptors.
storing SetFeature objects.
=head1 SYNOPSIS
my $afa = $db->get_SetFeatureAdaptor();
my $features = $afa->fetch_all_by_Slice($slice);
=head1 DESCRIPTION
The SetFeatureAdaptor is a base adaptor for all SetFeature adaptors.
e.g. SetFeature, AnnotatedFeature etc. It provides common methods
across all feature types.
=head1 AUTHOR
This module was created by Nathan Johnson.
This module is part of the Ensembl project: /
=head1 CONTACT
Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::Funcgen::DBSQL::SetFeatureAdaptor;
use Bio::EnsEMBL::Utils::Exception qw( throw warning );
use Bio::EnsEMBL::Funcgen::SetFeature;
use Bio::EnsEMBL::Funcgen::DBSQL::BaseFeatureAdaptor;
use vars qw(@ISA @EXPORT);
@ISA = qw(Bio::EnsEMBL::Funcgen::DBSQL::BaseFeatureAdaptor);
@EXPORT = (@{$DBI::EXPORT_TAGS{'sql_types'}});#required for child adaptor's store and _obj_from_sth methods
=head2 fetch_all_by_FeatureType_FeatureSets
Arg [1] : Bio::EnsEMBL::Slice
Arg [2] : Bio::EnsEMBL::FeatureType
Arg [3] : (optional) hashref - params hash
associated => 1, #Also return feature which have the associated FeatureType
logic_name => 'analysis.logic_name'
Example : my $slice = $sa->fetch_by_region('chromosome', '1');
my $features = $ofa->fetch_all_by_Slice_FeatureType($slice, $ft);
Description: Retrieves a list of features on a given slice, specific for a given FeatureType.
Returntype : Listref of Bio::EnsEMBL::SetFeature objects
Exceptions : Throws if no FeatureType object provided
Caller : General
Status : At Risk
=cut
sub fetch_all_by_FeatureType_FeatureSets {
my ($self, $ftype, $fsets, $params) = @_;
#How do we validate the parameters?
#We can't catch typos as we don't know what might need passing on to other methods
#Set all these so we can use them without exists
$params->{'logic_name'} ||= undef;
$params->{'associated'} ||= undef;
$self->db->is_stored_and_valid('Bio::EnsEMBL::Funcgen::FeatureType', $ftype);
my @fs_ids;
throw('Must provide a list of Bio::EnsEMBL::FeatureSet objects') if scalar(@{$fsets}) == 0;
foreach my $fset (@{$fsets}) {
$self->db->is_stored_and_valid('Bio::EnsEMBL::Funcgen::FeatureSet', $fset);
push (@fs_ids, $fset->dbID());
}
my $fs_ids = join(',', @fs_ids) if scalar(@fs_ids >1);
my ($table_name, $table_syn) = @{$self->_main_table};
my $constraint = $table_syn.'.feature_set_id = fs.feature_set_id AND '.
$table_syn.'.feature_type_id='.$ftype->dbID.' AND '.$table_syn.'.feature_set_id ';
$constraint .= (scalar(@fs_ids) >1) ? "IN ($fs_ids)" : '='.$fs_ids[0];
#We should really pass the params hash on here
$constraint = $self->_logic_name_to_constraint($constraint, $params->{logic_name});
my @features = @{$self->generic_fetch($constraint)};
#This is an interim solution and really needs changing!
#Can we genericise this as a lazy loader function?
#Isn't there already something liek this in core?
if ($params->{'associated'}){
for my $fset(@{$fsets}){
#We want to bring back features from the same set
#We are not bringing back different class of feature i.e. AnnotatedFeatures and ExternalFeatures
#Let's not catch this, but let it silently fail so peaople.
next if $table_name ne lc($fset->type).'_feature';
my $sql = 'SELECT feature_id from associated_feature_type where feature_table="'.$fset->type.'" and feature_type_id='.$ftype->dbID;
my @dbids = map $_ = "@$_", @{$self->dbc->db_handle->selectall_arrayref($sql)};
if(@dbids){
$constraint = " $table_syn.${table_name}_id in (".join(',',@dbids).') ' if @dbids;
push @features, @{$self->generic_fetch($constraint, $params->{logic_name})};
}
}
}
return \@features;
#return $self->generic_fetch($constraint);
}
=head2 fetch_all_by_Feature_associated_feature_types
Arg [1] : Bio::EnsEMBL::SetFeature
Arg [] : (optional) string - analysis logic name
Arg [4] : (optional) hashref - params hash, all entries optional
-logic_name => 'analysis.logic_name'
-include_direct_links => 1, #Also return feature which are linked by Feature->feature_type
Example : my $slice = $sa->fetch_by_region('chromosome', '1');
my $features = $ofa->fetch_all_by_Slice_FeatureType($slice, $ft);
Description: Retrieves a list of all features linked via the associated FeatureTypes of the given Feature in the same FeatureSet
Returntype : Listref of Bio::EnsEMBL::SetFeature objects
Exceptions : Throws if SetFeature not stored and valid
Caller : General
Status : At Risk
=cut
sub fetch_all_by_Feature_associated_feature_types {
my ($self, $feature, $params) = @_;
$self->db->is_stored_and_valid('Bio::EnsEMBL::Funcgen::SetFeature', $feature);
#We always want associated!
#Otherwise it would be just a normal fetch_all_by_FeatureType_FeatureSets query
#Which is more efficient.
#How do we validate the parameters?
#We can't catch typos as we don't know what might need passing on to other methods
#Set all these so we can use them without exists
$params->{'include_direct_links'} ||= undef;
$params->{'logic_name'} ||= undef;
my %dbIDs;#Use a hash to reduce dbID redundancy
my ($table_name, $table_syn) = @{$self->_main_table};
my $fset = $feature->feature_set;
my ($sql, $constraint, @features);
#Direct FeatureType
if($params->{'include_direct_links'}){
#Just grab dbIDs here rather than use generic fetch
$sql = "SELECT ${table_name}_id from $table_name where feature_type_id=".$feature->feature_type->dbID.' and feature_set_id='.$fset->dbID;
#This just sets each value to a key with an undef value
map {$dbIDs{"@$_"} = undef} @{$self->dbc->db_handle->selectall_arrayref($sql)};
}
my @assoc_ftypes = @{$feature->associated_feature_types};
if(@assoc_ftypes){
my $ftype_ids = join(', ', (map $_->dbID, @assoc_ftypes));
#Now we need to restrict the Features based on the FeatureSet of the original Feature, we could make this optional.
$sql = "SELECT feature_id from associated_feature_type aft, $table_name $table_syn where aft.feature_table='".$fset->type."' and aft.feature_type_id in ($ftype_ids) and aft.feature_id=${table_syn}.${table_name}_id and ${table_syn}.feature_set_id=".$fset->dbID;
#This just sets each value to a key with an undef value
map {$dbIDs{"@$_"} = undef} @{$self->dbc->db_handle->selectall_arrayref($sql)};
}
if(keys %dbIDs){
$constraint = " $table_syn.${table_name}_id in (".join(',', keys %dbIDs).')';
push @features, @{$self->generic_fetch($constraint, $params->{logic_name})};
}
return \@features;
}
=head2 fetch_all_by_Slice_FeatureType
Arg [1] : Bio::EnsEMBL::Slice
Arg [2] : Bio::EnsEMBL::FeatureType
Arg [3] : (optional) string - analysis logic name
Example : my $slice = $sa->fetch_by_region('chromosome', '1');
my $features = $ofa->fetch_all_by_Slice_FeatureType($slice, $ft);
Description: Retrieves a list of features on a given slice, specific for a given FeatureType.
Returntype : Listref of Bio::EnsEMBL::SetFeature objects
Exceptions : Throws if no FeatureType object provided
Caller : General
Status : At Risk
=cut
sub fetch_all_by_Slice_FeatureType {
my ($self, $slice, $type, $logic_name) = @_;
$self->db->is_stored_and_valid('Bio::EnsEMBL::Funcgen::FeatureType', $type);
my $ft_id = $type->dbID();
my $constraint = $self->_main_table->[1].".feature_set_id = fs.feature_set_id AND ".
"fs.feature_type_id = '$ft_id'";
$constraint = $self->_logic_name_to_constraint($constraint, $logic_name);
return $self->SUPER::fetch_all_by_Slice_constraint($slice, $constraint);
}
=head2 fetch_all_by_FeatureSets
Arg [1] : Arrayref of Bio::EnsEMBL::FeatureSet objects
Arg [2] : optional - analysis.logic_name
Example : my $features = $set_feature_adaptor->fetch_all_by_FeatureSets(@fsets);
Description: Retrieves a list of features specific for a given list of FeatureSets.
Returntype : Listref of Bio::EnsEMBL::SetFeature objects
Exceptions : Throws if list provided does not contain FeatureSets or if none provided
Caller : General
Status : At Risk
=cut
sub fetch_all_by_FeatureSets {
my ($self, $fsets, $logic_name) = @_;
my @fs_ids;
throw('Must provide a list of Bio::EnsEMBL::FeatureSet objects') if scalar(@{$fsets}) == 0;
foreach my $fset (@{$fsets}) {
throw('Not a FeatureSet object')
if ! (ref($fset) && $fset->isa("Bio::EnsEMBL::Funcgen::FeatureSet"));
push (@fs_ids, $fset->dbID());
}
my $fs_ids = join(',', @fs_ids) if scalar(@fs_ids >1);
my $constraint = $self->_main_table->[1].'.feature_set_id ';
$constraint .= (scalar(@fs_ids) >1) ? "IN ($fs_ids)" : '='.$fs_ids[0];
#could have individual logic_names for each annotated feature here?
$constraint = $self->_logic_name_to_constraint($constraint, $logic_name);
return $self->generic_fetch($constraint);
}
=head2 fetch_all_by_Slice_FeatureSets
Arg [1] : Bio::EnsEMBL::Slice
Arg [2] : Arrayref of Bio::EnsEMBL::FeatureSet objects
Arg [3] : optional - analysis.logic_name
Example : my $slice = $sa->fetch_by_region('chromosome', '1');
my $features = $ofa->fetch_by_Slice_FeatureSets($slice, @fsets);
Description: Retrieves a list of features on a given slice, specific for a given list of FeatureSets.
Returntype : Listref of Bio::EnsEMBL::SetFeature objects
Exceptions : Throws if list provided does not contain FeatureSets or if none provided
Caller : General
Status : At Risk
=cut
sub fetch_all_by_Slice_FeatureSets {
my ($self, $slice, $fsets, $logic_name) = @_;
my @fs_ids;
throw('Must provide a list of Bio::EnsEMBL::FeatureSet objects') if scalar(@{$fsets}) == 0;
foreach my $fset (@{$fsets}) {
throw('Not a FeatureSet object')
if ! ($fset && ref($fset) && $fset->isa("Bio::EnsEMBL::Funcgen::FeatureSet"));
push (@fs_ids, $fset->dbID());
}
my $fs_ids = join(',', @fs_ids) if scalar(@fs_ids >1);
my $constraint = $self->_main_table->[1].'.feature_set_id ';
$constraint .= (scalar(@fs_ids) >1) ? "IN ($fs_ids)" : '='.$fs_ids[0];
#could have individual logic_names for each annotated feature here?
$constraint = $self->_logic_name_to_constraint($constraint, $logic_name);
return $self->SUPER::fetch_all_by_Slice_constraint($slice, $constraint);
}
# Redefine BaseFeatureAdaptor method as analysis now abstracted to feature_set
# Given a logic name and an existing constraint this will
# add an analysis table constraint to the feature. Note that if no
# analysis_id exists in the columns of the primary table then no
# constraint is added at all
# DO WE HAVE TO CALL THIS EXPLICITLY in this adaptor, or will BaseAdaptor use redefined method?
sub _logic_name_to_constraint {
my $self = shift;
my $constraint = shift;
my $logic_name = shift;
return $constraint if (!$logic_name);
my $aa = $self->db->get_AnalysisAdaptor();
my $an = $aa->fetch_by_logic_name($logic_name);
if(! $an) {
#warn or throw?
warn("No analysis associated with logic_name $logic_name");
return undef;
}
my $an_id = $an->dbID();
$constraint .= ' AND' if($constraint);
$constraint .= " fs.analysis_id = $an_id";
return $constraint;
}
=head2 _default_where_clause
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 : At Risk
=cut
sub _default_where_clause {
my $self = shift;
return $self->_main_table->[1].'.feature_set_id = fs.feature_set_id';
}
=head2 _final_clause
Args : None
Example : None
Description: PROTECTED implementation of superclass abstract method.
Returns an ORDER BY clause. Sorting by oligo_feature_id would be
enough to eliminate duplicates, but sorting by location might
make fetching features on a slice faster.
Returntype : String
Exceptions : None
Caller : generic_fetch
Status : At Risk
=cut
sub _final_clause {
my $self = shift;
return ' ORDER BY '.$self->_main_table->[1].'.seq_region_id, '.$self->_main_table->[1].'.seq_region_start';
}
#re-written for non-standard feature table
=head2 fetch_all_by_logic_name
Arg [1] : string $logic_name the logic name of the analysis of features to obtain
Example : $fs = $a->fetch_all_by_logic_name('foobar');
Description : Returns an arrayref of features created from the database. only
features with an analysis of type $logic_name will be returned.
Returntype : arrayref of Bio::EnsEMBL::SetFeatures
Exceptions : thrown if $logic_name not defined
Caller : General
Status : At risk
=cut
sub fetch_all_by_logic_name {
my $self = shift;
my $logic_name = shift || throw( "Need a logic_name" );
my $constraint;
my $an = $self->db->get_AnalysisAdaptor->fetch_by_logic_name($logic_name);
$constraint = ' '.$self->_main_table->[1].'.feature_set_id=fs.feature_set_id and fs.analysis_id = '.$an->dbID() if($an);
return (defined $constraint) ? $self->generic_fetch($constraint) : undef;
}
=head2 store_associated_feature_types
Arg [1] : string $logic_name the logic name of the analysis of features to obtain
Example : $fs = $a->fetch_all_by_logic_name('foobar');
Description : Returns an arrayref of features created from the database. only
features with an analysis of type $logic_name will be returned.
Returntype : arrayref of Bio::EnsEMBL::SetFeatures
Exceptions : thrown if $logic_name not defined
Caller : General
Status : At risk
=cut
sub store_associated_feature_types {
my ($self, $set_feature) = @_;
#Direct access to avoid lazy loading with an unstored SetFeature
my $assoc_ftypes = $set_feature->{'associated_feature_types'};
#Could be undef or empty
return if ! defined $assoc_ftypes || scalar(@$assoc_ftypes) == 0;
my $type = $set_feature->feature_set->type;
my $feature_id = $set_feature->dbID;
my $sql = 'INSERT into associated_feature_type(feature_id, feature_table, feature_type_id) values (?,?,?)';
foreach my $ftype(@$assoc_ftypes){
#We have already tested the class but not whether it is stored
$self->db->is_stored_and_valid('Bio::EnsEMBL::Funcgen::FeatureType', $ftype);
my $sth = $self->prepare($sql);
$sth->bind_param(1, $feature_id, SQL_INTEGER);
$sth->bind_param(2, $type, SQL_VARCHAR);
$sth->bind_param(3, $ftype->dbID, SQL_INTEGER);
$sth->execute();
}
return;
}
=head2 list_dbIDs
Args : None
Example : my @feature_ids = @{$ofa->list_dbIDs()};
Description: Gets an array of internal IDs for all OligoFeature objects in
the current database.
Returntype : List of ints
Exceptions : None
Caller : ?
Status : Medium Risk
=cut
sub list_dbIDs {
my $self = shift;
return $self->_list_dbIDs($self->_main_table->[0]);
}
=head2 _main_table
Example : my $syn = $adaptor->_main_table->[1];
Description: Convenience method to retrieve the main table or main table synonym for this adaptor
Entirely dependent on ensembl convention of always having main table as first element
of tables array.
Returntype : Arrayref
Exceptions : None
Caller : General
Status : At Risk
=cut
sub _main_table{
my $self = shift;
#Need to do this to put it in list context to avoid just returning the last value
my @tables = $self->_tables();
return $tables[0];
}
1;
]]>