Bio::EnsEMBL::Funcgen::DBSQL ProbeFeatureAdaptor
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Summary
Bio::EnsEMBL::DBSQL::Funcgen::ProbeFeatureAdaptor - A database adaptor for fetching and
storing ProbeFeature objects.
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor
Bio::EnsEMBL::Funcgen::DBSQL::BaseFeatureAdaptor
Bio::EnsEMBL::Funcgen::ProbeFeature
Bio::EnsEMBL::Utils::Exception qw ( throw warning )
strict
warnings
Inherit
Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor Bio::EnsEMBL::Funcgen::DBSQL::BaseFeatureAdaptor
Synopsis
my $ofa = $db->get_ProbeFeatureAdaptor();
my $features = $ofa->fetch_all_by_Probe($probe);
$features = $ofa->fetch_all_by_Slice_arrayname($slice, 'Array-1', 'Array-2');
Description
The ProbeFeatureAdaptor is a database adaptor for storing and retrieving
ProbeFeature objects.
Methods
_columnsDescriptionCode
_default_where_clauseDescriptionCode
_final_clauseDescriptionCode
_new_fastDescriptionCode
_objs_from_sthDescriptionCode
_tablesDescriptionCode
delete_featuresDescriptionCode
fetch_all_by_ProbeDescriptionCode
fetch_all_by_Probe_idDescriptionCode
fetch_all_by_Slice_ArrayDescriptionCode
fetch_all_by_Slice_ArraysDescriptionCode
fetch_all_by_Slice_ExperimentalChipsDescriptionCode
fetch_all_by_Slice_arraynameDescriptionCode
fetch_all_by_probesetDescriptionCode
list_dbIDsDescriptionCode
reassign_feature_to_probe
No description
Code
storeDescriptionCode
Methods description
_columnscode    nextTop
  Args       : 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 : At Risk
_default_where_clausecodeprevnextTop
  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
_final_clausecodeprevnextTop
  Args       : None
Example : None
Description: PROTECTED implementation of superclass abstract method.
Returns an ORDER BY clause. Sorting by probe_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
_new_fastcodeprevnextTop
  Args       : Hashref to be passed to ProbeFeature->new_fast()
Example : None
Description: Construct an ProbeFeature object using quick and dirty new_fast.
Returntype : Bio::EnsEMBL::Funcgen::ProbeFeature
Exceptions : None
Caller : _objs_from_sth
Status : Medium Risk
_objs_from_sthcodeprevnextTop
  Arg [1]    : DBI statement handle object
Example : None
Description: PROTECTED implementation of superclass abstract method.
Creates ProbeFeature objects from an executed DBI statement
handle.
Returntype : Listref of Bio::EnsEMBL::ProbeFeature objects
Exceptions : None
Caller : Internal
Status : At Risk
_tablescodeprevnextTop
  Args       : None
Example : None
Description: PROTECTED implementation of superclass abstract method.
Returns the names and aliases of the tables to use for queries.
Returntype : List of listrefs of strings
Exceptions : None
Caller : Internal
Status : At Risk
delete_featurescodeprevnextTop
  Arg[0]     : ARRAYREF - feature dbIDs to reassign
Example : $pfa->delete_feature(\@fids);
Description: Deletes feature with given probe_feature_ids
Returntype : None
Exceptions : Throws if not arg defines
Caller : Importer
Status : At Risk
fetch_all_by_ProbecodeprevnextTop
  Arg [1]    : Bio::EnsEMBL::Funcgen::Probe
Example : my $features = $ofa->fetch_all_by_Probe($probe);
Description: Fetchs all features that a given probe creates.
Returntype : Listref of Bio::EnsEMBL::PasteFeature objects
Exceptions : Throws if argument is not a stored Probe object
Caller : Probe->get_all_ProbeFeatures()
Status : At Risk
fetch_all_by_Probe_idcodeprevnextTop
  Arg [1]    : int - Probe dbID
Example : my @features = @{$ofa->fetch_all_by_Probe_id($pid)};
Description: Fetchs all features that a given probe creates.
Returntype : Listref of Bio::EnsEMBL::PasteFeature objects
Exceptions : Throws if argument not defined
Caller : Probe->get_all_ProbeFeatures()
Status : At Risk
fetch_all_by_Slice_ArraycodeprevnextTop
  Arg [1]    : Bio::EnsEMBL::Slice
Arg [2] : Bio::EnsEMBL::Funcgen::Array
Example : my $slice = $sa->fetch_by_region('chromosome', '1');
my $features = $pfa->fetch_all_by_Slice_Array($slice, $exp);
Description: Retrieves a list of features on a given slice that are created
by probes from the given Array.
Returntype : Listref of Bio::EnsEMBL::Funcgen::ProbeFeature objects
Exceptions : Throws if no array name is provided
Caller :
Status : At Risk
fetch_all_by_Slice_ArrayscodeprevnextTop
  Arg [1]    : Bio::EnsEMBL::Slice
Arg [2] : ARRAYREF of Bio::EnsEMBL::Funcgen::Array objects
Arg [3] : HASHREF - optional params hash e.g. {logic_name => 'AFFY_ProbeTranscriptAlign'}
Example : my $slice = $sa->fetch_by_region('chromosome', '1');
my $features = $pfa->fetch_all_by_Slice_Array($slice, $exp);
Description: Retrieves a list of features on a given slice that are created
by probes from the given Array.
Returntype : Listref of Bio::EnsEMBL::Funcgen::ProbeFeature objects
Exceptions : Throws if ARRAYREF if arrays is not provided
Caller :
Status : At Risk
fetch_all_by_Slice_ExperimentalChipscodeprevnextTop
  Arg [1]    : Bio::EnsEMBL::Slice
Arg [2...] : listref of Bio::EnsEMBL::Funcgen::ExperimentalChip objects
Example : my $slice = $sa->fetch_by_region('chromosome', '1');
my $features = $ofa->fetch_by_Slice_arrayname($slice, $exp);
Description: Retrieves a list of features on a given slice that are created
by probes from the given ExperimentalChip.
Returntype : Listref of Bio::EnsEMBL::Funcgen::ProbeFeature objects
Exceptions : Throws if no array name is provided
Caller :
Status : At Risk
fetch_all_by_Slice_arraynamecodeprevnextTop
  Arg [1]    : Bio::EnsEMBL::Slice
Arg [2...] : List of strings - array name(s)
Example : my $slice = $sa->fetch_by_region('chromosome', '1');
my $features = $ofa->fetch_by_Slice_arrayname($slice, '');
Description: Retrieves a list of features on a given slice that are created
by probes from the specified arrays.
Returntype : Listref of Bio::EnsEMBL::Funcgen::ProbeFeature objects
Exceptions : Throws if no array name is provided
Caller : Slice->get_all_ProbesFeatures()
Status : At Risk
fetch_all_by_probesetcodeprevnextTop
  Arg [1]    : string - probeset
Example : my $features = $ofa->fetch_all_by_probeset('Set-1');
Description: Fetchs all features that a given probeset creates.
Returntype : Listref of Bio::EnsEMBL::ProbeFeature objects
Exceptions : Throws if no probeset argument
Caller : General
Status : At Risk
list_dbIDscodeprevnextTop
  Args       : None
Example : my @feature_ids = @{$ofa->list_dbIDs()};
Description: Gets an array of internal IDs for all ProbeFeature objects in
the current database.
Returntype : List of ints
Exceptions : None
Caller : ?
Status : Medium Risk
storecodeprevnextTop
  Args       : List of Bio::EnsEMBL::Funcgen::ProbeFeature objects
Example : $ofa->store(@features);
Description: Stores given ProbeFeature objects in the database. Should only
be called once per feature because no checks are made for
duplicates. Sets dbID and adaptor on the objects that it stores.
Returntype : None
Exceptions : Throws if a list of ProbeFeature objects is not provided or if
an analysis is not attached to any of the objects
Caller : General
Status : At Risk
Methods code
_columnsdescriptionprevnextTop
sub _columns {
	my $self = shift;
	
	return qw(
			  pf.probe_feature_id  pf.seq_region_id
			  pf.seq_region_start  pf.seq_region_end
			  pf.seq_region_strand pf.probe_id    
			  pf.analysis_id	   pf.mismatches
			  pf.cigar_line        p.name
			 );
}
_default_where_clausedescriptionprevnextTop
sub _default_where_clause {
	my $self = shift;
	
	return 'pf.probe_id = p.probe_id';# AND p.array_chip_id = ac.array_chip_id';
}
_final_clausedescriptionprevnextTop
sub _final_clause {
	return ' ORDER BY pf.seq_region_id, pf.seq_region_start, pf.probe_feature_id';
}
_new_fastdescriptionprevnextTop
sub _new_fast {
	my $self = shift;
	
	my $hash_ref = shift;
	return Bio::EnsEMBL::Funcgen::ProbeFeature->new_fast($hash_ref);
}
_objs_from_sthdescriptionprevnextTop
sub _objs_from_sth {
	my ($self, $sth, $mapper, $dest_slice) = @_;

	#For EFG this has to use a dest_slice from core/dnaDB whether specified or not.
#So if it not defined then we need to generate one derived from the species_name and schema_build of the feature we're retrieving.
# This code is ugly because caching is used to improve speed
my ($seq_region_id); my $sa = $self->db->get_SliceAdaptor(); $sa = $dest_slice->adaptor->db->get_SliceAdaptor() if($dest_slice);#don't really need this if we're using DNADBSliceAdaptor?
#Some of this in now probably overkill as we'll always be using the DNADB as the slice DB
#Hence it should always be on the same coord system, unless we're projecting
my $aa = $self->db->get_AnalysisAdaptor(); my @features; my (%analysis_hash, %slice_hash, %sr_name_hash, %sr_cs_hash); my ( $probe_feature_id, $efg_seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand, $mismatches, $probe_id, $analysis_id, $probe_name, $cigar_line, ); $sth->bind_columns(\$ probe_feature_id,\$ efg_seq_region_id,\$ seq_region_start,\$ seq_region_end,\$ seq_region_strand,\$ probe_id,\$ analysis_id,\$ mismatches,\$ cigar_line,\$ probe_name ); my ($asm_cs, $cmp_cs, $asm_cs_name, $asm_cs_vers ,$cmp_cs_name, $cmp_cs_vers); if ($mapper) { $asm_cs = $mapper->assembled_CoordSystem(); $cmp_cs = $mapper->component_CoordSystem(); $asm_cs_name = $asm_cs->name(); $asm_cs_vers = $asm_cs->version(); $cmp_cs_name = $cmp_cs->name(); $cmp_cs_vers = $cmp_cs->version(); } my ($dest_slice_start, $dest_slice_end, $dest_slice_strand); my ($dest_slice_length, $dest_slice_sr_name); if ($dest_slice) { $dest_slice_start = $dest_slice->start(); $dest_slice_end = $dest_slice->end(); $dest_slice_strand = $dest_slice->strand(); $dest_slice_length = $dest_slice->length(); $dest_slice_sr_name = $dest_slice->seq_region_name(); } #This has already been done by
#build seq_region_cache based on slice
#$self->build_seq_region_cache_by_Slice($slice);
my $last_pfid; FEATURE: while ( $sth->fetch() ) { #Need to build a slice adaptor cache here?
#Would only ever want to do this if we enable mapping between assemblies??
#Or if we supported the mapping between cs systems for a given schema_build, which would have to be handled by the core api
#This is only required due to multiple records being returned
#when using fetch_all_by_Arrays type methods
next if($last_pfid && ($last_pfid == $probe_feature_id)); $last_pfid = $probe_feature_id; #get core seq_region_id
$seq_region_id = $self->get_core_seq_region_id($efg_seq_region_id); if(! $seq_region_id){ warn "Cannot get slice for eFG seq_region_id $efg_seq_region_id\n". "The region you are using is not present in the cuirrent dna DB"; next; } # Get the analysis object
my $analysis = $analysis_hash{$analysis_id} ||= $aa->fetch_by_dbID($analysis_id); # Get the slice object
my $slice = $slice_hash{'ID:'.$seq_region_id}; if (!$slice) { $slice = $sa->fetch_by_seq_region_id($seq_region_id); $slice_hash{'ID:'.$seq_region_id} = $slice; $sr_name_hash{$seq_region_id} = $slice->seq_region_name(); $sr_cs_hash{$seq_region_id} = $slice->coord_system(); } #need to check once more here as it may not be in the DB,
#i.e. a supercontig(non-versioned) may have been deleted between releases
my $sr_name = $sr_name_hash{$seq_region_id}; my $sr_cs = $sr_cs_hash{$seq_region_id}; # Remap the feature coordinates to another coord system if a mapper was provided
if ($mapper) { throw("Not yet implmented mapper, check equals are Funcgen calls too!"); ($sr_name, $seq_region_start, $seq_region_end, $seq_region_strand) = $mapper->fastmap($sr_name, $seq_region_start, $seq_region_end, $seq_region_strand, $sr_cs); # Skip features that map to gaps or coord system boundaries
next FEATURE if !defined $sr_name; # Get a slice in the coord system we just mapped to
if ( $asm_cs == $sr_cs || ( $cmp_cs != $sr_cs && $asm_cs->equals($sr_cs) ) ) { $slice = $slice_hash{"NAME:$sr_name:$cmp_cs_name:$cmp_cs_vers"} ||= $sa->fetch_by_region($cmp_cs_name, $sr_name, undef, undef, undef, $cmp_cs_vers); } else { $slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"} ||= $sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef, $asm_cs_vers); } } # If a destination slice was provided convert the coords
# If the destination slice starts at 1 and is forward strand, nothing needs doing
if ($dest_slice) { unless ($dest_slice_start == 1 && $dest_slice_strand == 1) { if ($dest_slice_strand == 1) { $seq_region_start = $seq_region_start - $dest_slice_start + 1; $seq_region_end = $seq_region_end - $dest_slice_start + 1; } else { my $tmp_seq_region_start = $seq_region_start; $seq_region_start = $dest_slice_end - $seq_region_end + 1; $seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1; $seq_region_strand *= -1; } } # Throw away features off the end of the requested slice
next FEATURE if $seq_region_end < 1 || $seq_region_start > $dest_slice_length || ( $dest_slice_sr_name ne $sr_name ); $slice = $dest_slice; } push @features, $self->_new_fast( { 'start' => $seq_region_start, 'end' => $seq_region_end, 'strand' => $seq_region_strand, 'slice' => $slice, 'analysis' => $analysis,#we should lazy load this
'adaptor' => $self, 'dbID' => $probe_feature_id, 'mismatchcount' => $mismatches, 'cigar_line' => $cigar_line, 'probe_id' => $probe_id, #'probeset' => $probeset,#???do we need this?
'_probe_name' => $probe_name } ); } return\@ features;
}
_tablesdescriptionprevnextTop
sub _tables {
	my $self = shift;
	
	return (
			[ 'probe_feature', 'pf' ], 
			[ 'probe',   'p' ], 
			#[ 'array_chip',   'ac' ],#these are required for array based queries not implemented yet
#[ 'array', 'a' ]
);
}
delete_featuresdescriptionprevnextTop
sub delete_features {
	my ($self, $fids_ref) = @_;
	
	if(! @$fids_ref){
	  throw('Need to pass a ref to an array of feature ids');
	}
	
	my $cmd = 'DELETE from probe_feature WHERE probe_feature_id IN ('.join(',', @$fids_ref).')';
	$self->db->dbc->do($cmd);

	#This will fail anyway?
#if($?){
# throw("SQL Command failed:\t$sql\n$@");
#}
return; } 1;
}
fetch_all_by_ProbedescriptionprevnextTop
sub fetch_all_by_Probe {
  my $self  = shift;
  my $probe = shift;
  
  if ( !ref($probe) && !$probe->isa('Bio::EnsEMBL::Funcgen::Probe') ) {
    throw('fetch_all_by_Probe requires a Bio::EnsEMBL::Funcgen::Probe object');
  }

  if ( !defined $probe->dbID() ) {
    throw('fetch_all_by_Probe requires a stored Bio::EnsEMBL::Funcgen::Probe object');
  }
	
  return $self->generic_fetch( 'pf.probe_id = ' . $probe->dbID() );
}
fetch_all_by_Probe_iddescriptionprevnextTop
sub fetch_all_by_Probe_id {
  my $self  = shift;
  my $pid = shift;
  
  if ( ! defined $pid ) {
    throw('Need to specify a probe _id');
  }
	
  return $self->generic_fetch( 'pf.probe_id = ' . $pid );
}
fetch_all_by_Slice_ArraydescriptionprevnextTop
sub fetch_all_by_Slice_Array {
  my ($self, $slice, $array) = @_;

  throw("Need pass a valid stored Bio::EnsEMBL::Funcgen::Array object") 
	if (! (ref($array) && $array->isa("Bio::EnsEMBL::Funcgen::Array") && $array->dbID));

  my @ac_ids = map $_->dbID, @{$array->get_ArrayChips};
  
  my $constraint = " p.array_chip_id IN (".join(", ", @ac_ids).") AND p.probe_id = pf.probe_id ";
  
    
  return $self->SUPER::fetch_all_by_Slice_constraint($slice, $constraint);
}
fetch_all_by_Slice_ArraysdescriptionprevnextTop
sub fetch_all_by_Slice_Arrays {
  my ($self, $slice, $arrays, $params) = @_;

  my $logic_name;
  $logic_name = $params->{'logic_name'} if exists ${$params}{'logic_names'};


  if(!(ref($arrays) eq 'ARRAY' &&  @$arrays)){
	throw('Must pass an ARRAYREF of Bio::EnsEMBL::Funcgen::Array objects');
  }

  my @ac_ids;

  foreach my $array(@$arrays){

	throw("Must pass an ARRAYREF of valid stored Bio::EnsEMBL::Funcgen::Array objects")
	  if (! (ref($array) && $array->isa("Bio::EnsEMBL::Funcgen::Array") && $array->dbID));

	push @ac_ids, (map $_->dbID, @{$array->get_ArrayChips});
  }

  my $constraint = " p.array_chip_id IN (".join(", ", @ac_ids).") AND p.probe_id = pf.probe_id ";
  return $self->SUPER::fetch_all_by_Slice_constraint($slice, $constraint, $logic_name);
}
fetch_all_by_Slice_ExperimentalChipsdescriptionprevnextTop
sub fetch_all_by_Slice_ExperimentalChips {
  my ($self, $slice, $exp_chips) = @_;

  my (%nr);


  foreach my $ec(@$exp_chips){
    
    throw("Need pass listref of valid Bio::EnsEMBL::Funcgen::ExperimentalChip objects") 
      if ! $ec->isa("Bio::EnsEMBL::Funcgen::ExperimentalChip");
    
    $nr{$ec->array_chip_id()} = 1;
  }
   
  my $constraint = " p.array_chip_id IN (".join(", ", keys %nr).") AND p.probe_id = pf.probe_id ";

    
  return $self->SUPER::fetch_all_by_Slice_constraint($slice, $constraint);
}
fetch_all_by_Slice_arraynamedescriptionprevnextTop
sub fetch_all_by_Slice_arrayname {
	my ($self, $slice, @arraynames) = @_;

	throw("This should return data from all experiments, but will break if arrays are mapped to different coord_systems");
	
	throw('Need array name as parameter') if !@arraynames;
	
	my $constraint;
	if (scalar @arraynames == 1) {
		#Will this work
#will this pick up the array_chip_id link from array_chip to probe?
$constraint = qq( a.name = '$arraynames[0]' AND a.array_id = ac.array_id ); #$constraint = qq( a.name = '$arraynames[0]' );
} else { throw("Not implemented for multple arrays"); $constraint = join q(','), @arraynames; $constraint = qq( a.name IN ('$constraint') ); } return $self->SUPER::fetch_all_by_Slice_constraint($slice, $constraint); } #should this take >1 EC? What if we can't fit a all mappings onto one chip
#Would possibly miss some from the slice
}
fetch_all_by_probesetdescriptionprevnextTop
sub fetch_all_by_probeset {
	my $self     = shift;
	my $probeset = shift;
	
	throw("Not implmeneted\n");

	if (!$probeset) {
		throw('fetch_all_by_probeset requires a probeset argument');
	}
	
	

	return $self->generic_fetch( "p.probeset = '$probeset'" );
}


#Need to add:
#fetch_all_by_Slice_Experiment
#fetch_all_by_Slice_experimentname ? name not unique enough?
}
list_dbIDsdescriptionprevnextTop
sub list_dbIDs {
	my $self = shift;
	
	return $self->_list_dbIDs('probe_feature');
}


#Probe cache methods?
}
reassign_feature_to_probedescriptionprevnextTop
sub reassign_feature_to_probe {
	my ($self, $fids_ref, $pid) = @_;
	
	if(! @$fids_ref || ! $pid){
	  throw('Need to pass a ref to an array of feature ids and a probe id to reassign to');
	}
	
	my $cmd = 'UPDATE probe_feature SET probe_id='.$pid.' WHERE probe_feature_id IN ('.join(',', @$fids_ref).')';
	$self->db->dbc->do($cmd);

	#This will fail anyway?
#if($?){
# throw("SQL Command failed:\t$sql\n$@");
#}
return;
}
storedescriptionprevnextTop
sub store {
	my ($self, @ofs) = @_;

	if (scalar(@ofs) == 0) {
		throw('Must call store with a list of ProbeFeature objects');
	}

	my $sth = $self->prepare("
		INSERT INTO probe_feature (
			seq_region_id,  seq_region_start,
			seq_region_end, seq_region_strand,
          	probe_id,  analysis_id,
			mismatches, cigar_line
		) VALUES (?, ?, ?, ?, ?, ?, ?, ?)
	");

	my $db = $self->db();
	my $analysis_adaptor = $db->get_AnalysisAdaptor();

	FEATURE: foreach my $of (@ofs) {

		if( ! ref $of || ! $of->isa('Bio::EnsEMBL::Funcgen::ProbeFeature') ) {
			throw('Feature must be an ProbeFeature object');
		}

		if ( $of->is_stored($db) ) {
			warning('ProbeFeature [' . $of->dbID() . '] is already stored in the database');
			next FEATURE;
		}

		if ( !defined $of->analysis() ) {
			throw('An analysis must be attached to the ProbeFeature objects to be stored.');
		}

		# Store the analysis if it has not been stored yet
if ( !$of->analysis->is_stored($db) ) { $analysis_adaptor->store( $of->analysis() ); } my $seq_region_id; ($of, $seq_region_id) = $self->_pre_store($of); $sth->bind_param(1, $seq_region_id, SQL_INTEGER); $sth->bind_param(2, $of->start(), SQL_INTEGER); $sth->bind_param(3, $of->end(), SQL_INTEGER); $sth->bind_param(4, $of->strand(), SQL_TINYINT); $sth->bind_param(5, $of->probe_id(), SQL_INTEGER); $sth->bind_param(6, $of->analysis->dbID(), SQL_INTEGER); $sth->bind_param(7, $of->mismatchcount(), SQL_TINYINT); $sth->bind_param(8, $of->cigar_line(), SQL_VARCHAR); $sth->execute(); $of->dbID( $sth->{'mysql_insertid'} ); $of->adaptor($self); } #No need to return this really as the dbID and adaptor has been
#updated in the passed arrays of features via the object
#reference
return\@ ofs
}
General documentation
AUTHORTop
This module was created by Nathan Johnson.
This module is part of the Ensembl project: /
CONTACTTop
Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
reassign_features_to_probeTop
  Arg[0]     : ARRAYREF - feature dbIDs to reassign
Arg[1] : int - probe dbID to reassign to
Example : $ofa->reassign_feature_to_probe(\@fids, $pid);
Description: Update features to link to given probe dbID
Returntype : None
Exceptions : Throws is args not met
Caller : Importer
Status : At Risk