Raw content of Bio::EnsEMBL::Funcgen::ResultFeature
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# Ensembl module for Bio::EnsEMBL::Funcgen::ResultFeature
#
# You may distribute this module under the same terms as Perl itself
=head1 NAME
Bio::EnsEMBL::Funcgen::ResultFeature - A module to represent a lightweight ResultFeature object
=head1 SYNOPSIS
use Bio::EnsEMBL::Funcgen::ResultFeature;
my $rfeature = Bio::EnsEMBL::Funcgen::ResultFeature->new_fast([$start, $end, $score ]);
my @rfeatures = @{$rset->get_displayable_ResultFeature_by_Slice($slice)};
foreach my $rfeature (@rfeatures){
my $score = $rfeature->score();
my $rf_start = $rfeature->start();
my $rf_end = $rfeature->end();
}
=head1 DESCRIPTION
This is a very sparse class designed to be as lightweight as possible to enable fast rendering in the web browser.
As such only the information absolutely required is contained. Any a piori information is omitted e.g. seq_region_id,
this will already be known as ResultFeatures are retrieved via a Slice method in ResultSet via the ResultSetAdaptor,
likewise with analysis and experimental_chip information. ResultFeatures are transient objects, in that they are not
stored in the DB, but are a very small subset of information from the result and oligo_feature tables. ResultFeatures
should only be generated by the ResultSetAdaptorast here is no parameter checking in place.
=head1 AUTHOR
This module was written by Nathan Johnson.
=head1 CONTACT
Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=head1 METHODS
=cut
use strict;
use warnings;
#Could set global named vars here for element names. Would take more memory
package Bio::EnsEMBL::Funcgen::ResultFeature;
use base ('Bio::EnsEMBL::Feature');
=head2 new_fast
Args : Array with attributes start, end, strand, score, probe, result_set_id, winow_size IN THAT ORDER.
WARNING: None of these are validated, hence can omit some where not needed
Example : none
Description: Fast and list version of new. Only works if the code is very disciplined.
Returntype : Bio::EnsEMBL::Funcgen::ResultFeature
Exceptions : None
Caller : ResultSetAdaptor
Status : At Risk
=cut
sub new_fast {
my ($class, @args) = @_;
#return bless ($arrayref, $class);
#Passing arrayref here may cause problems with changing vars after obj creation
#warn "in new fast with @args";
bless \@args, $class;
}
=head2 start
Example : my $start = $rf->start();
Description: Getter of the start attribute for ResultFeature
objects.
Returntype : int
Exceptions : None
Caller : General
Status : At Risk
=cut
sub start { $_[0]->[0];}
=head2 end
Example : my $start = $rf->end();
Description: Getter of the end attribute for ResultFeature
objects.
Returntype : int
Exceptions : None
Caller : General
Status : At Risk
=cut
sub end { $_[0]->[1];}
#Do we need to chacnge this to strand and have slice strand context, as with start and end
sub strand { $_[0]->[2];}
=head2 score
Example : my $score = $rf->score();
Description: Getter of the score attribute for ResultFeature
objects
Returntype : string/float/double?
Exceptions : None
Caller : General
Status : At Risk
=cut
sub score { $_[0]->[3];}
=head2 probe
Example : my $probe = $rf->probe();
Description: Getter of the probe attribute for ResultFeature
objects
Returntype : Bio::EnsEMBL::Funcgen::Probe
Exceptions : None
Caller : General
Status : At Risk - This can only be used for Features with window 0.
=cut
#probe_id is currently not available in the result_feature table, so this would be a result/probe_feature query.
sub probe { $_[0]->[4];}
#The following are only used for storage and retrieval, hence why they are not included in new_fast which is streamlined
#for performance
#These have no validation so all thi smust be done in the caller/storer i.e. the adaptor
sub result_set_id { $_[0]->[5];}
sub window_size { $_[0]->[6];}
#May not ever need this
#We pass the slice to store
#Don't want to remap, so don't need furing fetch
sub slice { $_[0]->[7];}
#Had to reimplement these as they used direct hash calls rather than acessor
#redefined to use accessors to array
sub length {
my $self = shift;
return $self->end - $self->start + 1;
}
=head2 move
Arg [1] : int start
Arg [2] : int end
Arg [3] : (optional) int strand
Example : None
Description: Sets the start, end and strand in one call rather than in
3 seperate calls to the start(), end() and strand() methods.
This is for convenience and for speed when this needs to be
done within a tight loop.
Returntype : none
Exceptions : Thrown is invalid arguments are provided
Caller : general
Status : Stable
=cut
sub move {
my $self = shift;
throw('start and end arguments are required') if(@_ < 2);
my $start = shift;
my $end = shift;
my $strand = shift;
if(defined($start) && defined($end) && $end < $start) {
throw('start must be less than or equal to end');
}
if(defined($strand) && $strand != 0 && $strand != -1 && $strand != 1) {
throw('strand must be 0, -1 or 1');
}
$self->[0] = $start;
$self->[1] = $end;
$self->[2] = $strand if(defined($strand));
}
1;
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