comparison variant_effect_predictor/Bio/EnsEMBL/Funcgen/SegmentationFeature.pm @ 0:21066c0abaf5 draft

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#
# Ensembl module for Bio::EnsEMBL::Funcgen::SegmentationFeature
#
# You may distribute this module under the same terms as Perl itself

=head1 LICENSE

  Copyright (c) 1999-2011 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <[e-mail]>.

  Questions may also be sent to the Ensembl help desk at
  <[e-mail]>.


=head1 NAME

Bio::EnsEMBL::SegmentationFeature - Genomic segmentation feature

=head1 SYNOPSIS

use Bio::EnsEMBL::Funcgen::SegmentationFeature;

my $feature = Bio::EnsEMBL::Funcgen::SegmentationFeature->new(
	-SLICE         => $chr_1_slice,
	-START         => 1_000_000,
  	-END           => 1_000_024,
	-STRAND        => 0,
    -FEATURE_SET   => $fset,
    -FEATURE_TYPE  => $ftype,
); 



=head1 DESCRIPTION

An SegmentationFeature object represents the genomic placement of a prediction
generated by the eFG analysis pipeline. This normally represents the 
output of a peak calling analysis. It can have a score and/or a summit, the 
meaning of which depend on the specific Analysis used to infer the feature.
For example, in the case of a feature derived from a peak call over a ChIP-seq
experiment, the score is the peak caller score, and summit is the point in the
feature where more reads align with the genome.

=head1 SEE ALSO

Bio::EnsEMBL::Funcgen::DBSQL::SegmentationFeatureAdaptor

=cut

use strict;
use warnings;

package Bio::EnsEMBL::Funcgen::SegmentationFeature;

use Bio::EnsEMBL::Utils::Argument qw( rearrange );
use Bio::EnsEMBL::Utils::Exception qw( throw );
use Bio::EnsEMBL::Funcgen::SetFeature;

use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Funcgen::SetFeature);

=head2 new

  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 [-STRAND]       : int - The orientation of this feature. Valid values are 1, -1 and 0.
  Arg [-FEATURE_SET]  : Bio::EnsEMBL::Funcgen::FeatureSet
  Arg [-FEATURE_TYPE] : Bio::Ensembl::Funcgen::FeatureType
  Arg [-DISPLAY_LABEL]: optional string - Display label for this feature
  Arg [-SCORE]        : optional int - Score assigned by analysis pipeline
  Arg [-dbID]         : optional int - Internal database ID.
  Arg [-ADAPTOR]      : optional Bio::EnsEMBL::DBSQL::BaseAdaptor - Database adaptor.

  Example             : my $feature = Bio::EnsEMBL::Funcgen::SegmentationFeature->new
                                   (
									-SLICE         => $chr_1_slice,
									-START         => 1_000_000,
									-END           => 1_000_024,
                                    -STRAND        => -1,
                                    -FEATURE_SET   => $fset,
                                    -FEATURE_TYPE  => $ftype,
									-DISPLAY_LABEL => $text,
									-SCORE         => $score,
                                   );


  Description: Constructor for SegmentationFeature objects.
  Returntype : Bio::EnsEMBL::Funcgen::SegmentationFeature
  Exceptions : None
  Caller     : General
  Status     : Medium Risk

=cut

sub new {
  my $caller = shift;
	
  my $class = ref($caller) || $caller;
  my $self = $class->SUPER::new(@_);
  #Hard code strand => 0 here? And remove from input params?
  my ($score, $ftype) = rearrange(['SCORE', 'FEATURE_TYPE'], @_);

  #test ftype as SetFeature method defaults to feature_set->feature_type
  throw('You must pass a valid FeatureType') if ! defined $ftype;

  $self->{score} = $score if $score;
  $self->{feature_type} = $ftype;
	
  return $self;
}


=head2 score

  Arg [1]    : (optional) int - score
  Example    : my $score = $feature->score();
  Description: Getter and setter for the score attribute for this feature. 
  Returntype : int
  Exceptions : None
  Caller     : General
  Status     : At Risk

=cut

sub score {
  my $self = shift;		
  return $self->{'score'};
}


=head2 display_label

  Example    : my $label = $feature->display_label();
  Description: Getter for the display label of this feature.
  Returntype : String
  Exceptions : None
  Caller     : General
  Status     : At Risk

=cut

sub display_label {
  my $self = shift;
  
  if(! $self->{'display_label'}  && $self->adaptor){
	$self->{'display_label'} = $self->feature_type->name()." -";
	$self->{'display_label'} .= " ".$self->cell_type->name();
  }
  
  return $self->{'display_label'};
}


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