Raw content of Bio::EnsEMBL::Funcgen::SetFeature
<![CDATA[# Ensembl module for Bio::EnsEMBL::Funcgen::SetFeature
#
# Copyright (c) 2007 Ensembl
#
=head1 NAME
Bio::EnsEMBL::Funcgen::SetFeature - Ensembl specific set feature.
=head1 SYNOPSIS
my $feat = new Bio::EnsEMBL::Feature(-start => 100,
-end => 220,
-strand => -1,
-slice => $slice,
-feature_set => $fset,
-display_label => $label,
);
my $start = $feat->start;
my $end = $feat->end;
my $strand = $feat->strand;
#move the feature to the chromosomal coordinate system
$feature = $feature->transform('chromosome');
#move the feature to a different slice (possibly on another coord system)
$feature = $feature->transfer($new_slice);
#project the feature onto another coordinate system possibly across
#boundaries:
@projection = @{$feature->project('contig')};
#change the start, end, and strand of the feature in place
$feature->move($new_start, $new_end, $new_strand);
=head1 DESCRIPTION
This is a simple wrapper method for the core Feature class to contain common generic
Funcgen SetFeature methods.
=head1 CONTACT
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::Funcgen::SetFeature;
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Funcgen::Storable;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Feature Bio::EnsEMBL::Funcgen::Storable);
#Bio::EnsEMBL::Funcgen::Storable
#gives access to DBEntry type methods
#This only works as the DBEntry methods in the core API are at the Gene/Transcript/Translation level
#This would not be a problem if this was integrated back into the core code
=head2 new
Arg [-FEATURE_SET] : Bio::EnsEMBL::Funcgen::FeatureSet
Arg [-ANALYSIS] : Bio::EnsEMBL::Analysis
Arg [-SLICE] : Bio::EnsEMBL::Slice - The slice on which this feature is.
Arg [-START] : int - The start coordinate of this feature relative to the start of the slice
it is sitting on. Coordinates start at 1 and are inclusive.
Arg [-END] : int -The end coordinate of this feature relative to the start of the slice
it is sitting on. Coordinates start at 1 and are inclusive.
Arg [-DISPLAY_LABEL]: string - Display label for this feature
Arg [-STRAND] : int - The orientation of this feature. Valid values are 1, -1 and 0.
Arg [-dbID] : (optional) int - Internal database ID.
Arg [-ADAPTOR] : (optional) Bio::EnsEMBL::DBSQL::BaseAdaptor - Database adaptor.
Example : my $feature = Bio::EnsEMBL::Funcgen::AnnotatedFeature->new(
-SLICE => $chr_1_slice,
-START => 1_000_000,
-END => 1_000_024,
http://www.hinxton.wellcome.ac.uk/onsite/menus/index.html -STRAND => -1,
-DISPLAY_LABEL => $text,
-FEATURE_SET => $fset,
);
Description: Constructor for SetFeature objects. Should never be called directly, only by children.
Returntype : Bio::EnsEMBL::Funcgen::SetFeature
Exceptions : None
Caller : General
Status : At Risk
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
my ($display_label, $fset, $ftype, $assoc_ftypes)
= rearrange(['DISPLAY_LABEL', 'FEATURE_SET', 'FEATURE_TYPE', 'ASSOCIATED_FEATURE_TYPES'], @_);
if($ftype){
if(! (ref($ftype) && $ftype->isa('Bio::EnsEMBL::Funcgen::FeatureType'))){
throw('feature_type param must be a valid Bio::EnsEMBL::Funcgen::FeatureType');
}
$self->{'feature_type'} = $ftype;
}
if(! (ref($fset) && $fset->isa("Bio::EnsEMBL::Funcgen::FeatureSet"))){
throw("Must pass valid Bio::EnsEMBL::Funcgen::FeatureSet object");
}
$self->{'feature_set'}= $fset;
#Do not move this as it depends on the above being set
$self->display_label($display_label) if $display_label;
$self->associated_feature_types($assoc_ftypes) if(defined $assoc_ftypes);
return $self;
}
=head2 new_fast
Args : Hashref with all internal attributes set
Example : none
Description: Quick and dirty version of new. Only works if the calling code
is very disciplined.
Returntype : Bio::EnsEMBL::Funcgen::SetFeature
Exceptions : None
Caller : General
Status : At Risk
=cut
sub new_fast {
return bless ($_[1], $_[0]);
}
=head2 feature_set
Arg [1] : (optional) Bio::EnsEMBL::FeatureSet
Example : $efeature->feature_set($fset);
Description: Getter for the FeatureSet attribute for this feature.
Returntype : Bio::EnsEMBL::Funcgen::FeatureSet
Exceptions : None
Caller : General
Status : At Risk
=cut
sub feature_set {
my $self = shift;
return $self->{'feature_set'};
}
=head2 cell_type
Example : my $cell_name = $efeature->cell_type()->name();
Description: Getter for the cell_type attribute for this feature.
May not always be set for ExternalFeatures.
Returntype : Bio::EnsEMBL::Funcgen:CellType
Exceptions : None
Caller : General
Status : At risk
=cut
sub cell_type{
my $self = shift;
return $self->feature_set->cell_type();
}
=head2 feature_type
Example : my $ft_name = $efeature->feature_type()->name();
Description: Getter for the feature_type attribute for this feature.
Returntype : Bio::EnsEMBL::Funcgen:FeatureType
Exceptions : None
Caller : General
Status : At risk
=cut
sub feature_type{
my $self = shift;
#why is this not a setter?
#this should only be set in new
return (defined $self->{'feature_type'}) ? $self->{'feature_type'} : $self->feature_set->feature_type();
}
=head2 associated_feature_types
Example : my @associated_ftypes = @{$feature->associated_feature_types()};
Description: Getter/Setter for other associated FeatureTypes.
Returntype : ARRAYREF of Bio::EnsEMBL::Funcgen:FeatureType objects
Exceptions : None
Caller : General
Status : At risk
=cut
sub associated_feature_types{
my ($self, $ftypes) = @_;
#Lazy load as we don't want to have to do a join on all features when most will not have any
#How are we going to retrieve these?
#We don't really want to join on associated_feature_type for every feature query as very few will have them.
#Could use FeatureTypeAdaptor->fetch_by_associated_Feature
#But would have to do join again everytime unless we have a separate query
#Don't want a separate adaptor
#May aswell do separate query here for now, and just use the FeatureTypeAdaptor->fetch_by_dbID();
#Can we not use generic_fetch with an in constraint?
#The fetch should really be implemented in FeatureTypeAdaptor
#
#Should we split this into an add and a get method?
#Need to split this?
if(defined $ftypes){
if(ref($ftypes) eq 'ARRAY'){
foreach my $ftype(@$ftypes){
#Can we do this if it is not yet stored?
#This cannot be tested here as the SetFeature may not have an adaptor
#Test here not useing method or wait until store?
if( ! $ftype->isa('Bio::EnsEMBL::Funcgen::FeatureType') ){
throw('You must pass and ARRAYREF of stored Bio::EnsEMBL::Funcgen::FeatureType objects');
}
}
if(defined $self->{'associated_feature_types'}){
warn('You are overwriting associated feature types');
#we could simply add the new ones and make them NR.
}
$self->{'associated_feature_types'} = $ftypes;
}
else{
throw('You must pass and ARRAYREF of stored Bio::EnsEMBL::Funcgen::FeatureType objects');
}
}
if(! defined $self->{'associated_feature_types'}){
#This will fail if we have not stored yet
if(defined $self->adaptor){
$self->{'associated_feature_types'} = $self->adaptor->db->get_FeatureTypeAdaptor->fetch_all_by_associated_SetFeature($self);
}
}
#This has the potential to return undef, or an arrayref which may be empty.
return $self->{'associated_feature_types'};
}
#redefined from Feature to use FeatureSet, unless specifically set
=head2 analysis
Example : my $analysis = $efeature->feature_type()->name();
Description: Getter for the type attribute for this feature.
Returntype : Bio:EnsEMBL::Funcgen::FeatureType
Exceptions : Throws if analysis passed is not a valid Bio::EnsEMBL::Analysis
Caller : General
Status : At risk
=cut
sub analysis{
my $self = shift;
#this is to allow multi analysis sets, but the adaptor currently throws if they are not the same on store
if(@_){
if($_[0]->isa("Bio::EnsEMBL::Analysis")){
$self->{'analysis'} = $_[0];
}else{
throw("Must pass a valid Bio::EnsEMBL::Analysis");
}
}
return (defined $self->{'analysis'}) ? $self->{'analysis'} : $self->feature_set->analysis();
}
#These DBEntry methods should really be in Funcgen::Storable to support FeatureType xrefs
#However, eFG SetFeatures are not eFG Storables, rather they inherit directly from Ensembl::Feature
#This causes inheritance problems, and we don't need the eFG Storable methods for Features.
#Cater for FeatureTypes separately for now as we may remove DBEntries for these at some point.
#And currently not used anywhere in the website??? Current xrefs are fly BioTIFFIN motif xrefs to FlyBase coding gene names?
1;
]]>