Raw content of Bio::EnsEMBL::Funcgen::FeatureSet
<![CDATA[#
# Ensembl module for Bio::EnsEMBL::Funcgen::FeatureSet
#
# You may distribute this module under the same terms as Perl itself
=head1 NAME
Bio::EnsEMBL::FeatureSet - A module to represent FeatureSet.
=head1 SYNOPSIS
use Bio::EnsEMBL::Funcgen::FeatureSet;
my $result_set = Bio::EnsEMBL::Funcgen::FeatureSet->new(
);
=head1 DESCRIPTION
A FeatureSet object provides access to a set of feature predictions and their details, which may have been generated from a
single or multiple Experiments with potentially differing analyses. The FeatureSet itself will only have a single analysis
which may be one or a combination of programs but will be represented by one analysis record.
=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::FeatureSet;
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
use Bio::EnsEMBL::Utils::Exception qw( throw warning deprecate);
use Bio::EnsEMBL::Funcgen::Set;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Funcgen::Set);
=head2 new
Arg [-EXPERIMENT_ID] : Experiment dbID
#or
#Arg [-EXPERIMENT] : Bio::EnsEMBL::Funcgen::Experiment
Arg [-SLICE] : Bio::EnsEMBL::Slice
Example : my $feature = Bio::EnsEMBL::Funcgen::FeatureSet->new(
-dbid => $dbid,
-analysis => $analysis,
-feature_type => $ftype,
-cell_type => $ctype,
-name => $name,
-type => 'annotated',
-description => 'Release 3.1',
-display_label => 'Short name',
);
Description: Constructor for FeatureSet objects.
Returntype : Bio::EnsEMBL::Funcgen::FeatureSet
Exceptions : Throws if no experiment_id defined
Caller : General
Status : At risk
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
my ($type, $desc)
= rearrange(['TYPE', 'DESCRIPTION'],@_);
throw ('Must provide a FeatureType') if(! defined $self->feature_type);
#explicit type check here to avoid invalid types being imported as NULL
#subsequently throwing errors on retrieval
if(! ($type && grep /$type/, ('annotated', 'external', 'regulatory'))){
throw("You must define a valid FeatureSet type e.g. 'annotated', 'external' or 'regulatory'");
}
$self->type($type);
$self->description($desc) if defined $desc;
return $self;
}
=head2 new_fast
Args : Hashref with all internal attributes set
Example : none
Description: Quick and dirty version of new. Only works if the code is very
disciplined.
Returntype : Bio::EnsEMBL::Funcgen::FeatureSet
Exceptions : None
Caller : General
Status : At Risk
=cut
sub new_fast {
my ($class, $hashref) = @_;
return bless ($hashref, $class);
}
#methods
#set wide display label(predicted_feature) + more wordy label for wiggle tracks?
#defined by experiment type i.e. time course would require timepoint in display label
#deal with this dynamically or have display_label in table
#Need call on type, or fetch all would
#_get_ec_ids or contigsets?
#this should now be an intrinsic part of this class/adaptor
#cell line
#feature_type
#displayable...should have one for the whole set and one for each raw and predicted?
#have analysis as arg? Or do we get all analysis sets?
#we need to be able to set analyses for FeatureSets dynamically from DB
#pick up all FeatureSets
#displayable field in FeatureSets also?
#If we have mixed types in the same experiment then we could get promoter features and histone wiggle tracks displayed togeter
#Not v.good for display purposes? We may want to separate the promoter and histone tracks, or we may want ll the experiment data together but of mixed types.
#We need to be able to pull back the experiment type for each set, therefore this needs setting on an ec level, not an experiment level.
#This is also v.reliant on putting contig set info in place, otherwise we may get mixed chip types in same set.
#get_raw_analysis_name
#get_predicted_feature_analysis_name
#set ResultFeatures and AnnotatedFeatures in hash keyed by analysis_name?
=head2 description
Example : print "Feature set description is:\t".$fset->description."\n";
Description: Getter/Setter for the description of this FeatureSet. e.g. Release 3.1
Returntype : String
Exceptions : None
Caller : General
Status : At Risk
=cut
sub description {
my $self = shift;
$self->{'description'} = shift if @_;
return $self->{'description'};
}
=head2 type
Example : my $type = $fset->type('annotated');
Description: Getter/Setter for the type of this FeatureSet.
Valid values are 'annotated', 'regulatory' or 'external'.
Returntype : String
Exceptions : None
Caller : General
Status : At Risk
=cut
sub type {
my $self = shift;
#add validation of enum here..or leave to DB
$self->{'type'} = shift if @_;
return $self->{'type'};
}
=head2 display_label
Example : print $rset->display_label();
Description: Getter/Setter for the display_label attribute for this FeatureSet.
This is more appropriate for the predicted_features of the set.
Use the individual display_labels for each raw result set.
Returntype : str
Exceptions : None
Caller : General
Status : At Risk
=cut
sub display_label {
my $self = shift;
$self->{'display_label'} = shift if @_;
if(! $self->{'display_label'}){
if($self->feature_type->class() eq 'Regulatory Feature'){
$self->{'display_label'} = 'Regulatory Features';
}
else{
$self->{'display_label'} = $self->feature_type->name()." - ".$self->cell_type->name()." Enriched Sites";
}
}
return $self->{'display_label'};
}
=head2 get_FeatureAdaptor
Example :
Description: Retrieves and caches FeatureAdaptor of feature_set type
Returntype : Bio::EnsEMBL::Funcgen::DBSQL::ucfirst($self->type())FeatureAdaptor
Exceptions : None
Caller : General
Status : At Risk
=cut
sub get_FeatureAdaptor{
my $self = shift;
if(! exists $self->{'adaptor_refs'}){
#can we code ref this?
$self->{'adaptor_refs'} = {(
annotated => $self->adaptor->db->get_AnnotatedFeatureAdaptor,
regulatory => $self->adaptor->db->get_RegulatoryFeatureAdaptor,
external => $self->adaptor->db->get_ExternalFeatureAdaptor,
)};
}
return $self->{'adaptor_refs'}->{$self->type()};
}
=head2 get_Features_by_Slice
Example : my @features = @{$FeatureSet->get_Features_by_Slice($slice)};
Description: Retrieves all Features for this FeatureSet for a given Slice
Returntype : ARRAYREF containing Features of the feature_set type i.e. Annotated, Regulatory or Supporting;
Exceptions : None
Caller : General
Status : At Risk
=cut
sub get_Features_by_Slice{
my ($self, $slice) = @_;
return $self->get_FeatureAdaptor->fetch_all_by_Slice_FeatureSets($slice, [$self]);
}
=head2 get_Features_by_FeatureType
Arg[0] : Bio::EnsEMBL::Funcgen::FeatureType
Example : my @features = @{$FeatureSet->get_Features_by_FeatureType($ftype)};
Description: Retrieves all Features for this FeatureSet for a given FeatureType
Returntype : ARRAYRE
Exceptions : None
Caller : General
Status : At Risk
=cut
sub get_Features_by_FeatureType{
my ($self, $type) = @_;
return $self->get_FeatureAdaptor->fetch_all_by_FeatureType_FeatureSets($type, [$self]);
}
1;
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