view variant_effect_predictor/Bio/EnsEMBL/Funcgen/SetFeature.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

#
# Ensembl module for Bio::EnsEMBL::Funcgen::SetFeature
#


=head1 LICENSE

  Copyright (c) 1999-2012 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::Funcgen::SetFeature - Base class for features of a Set.

=head1 SYNOPSIS

  # Would normally be created from an in inheriting class e.g. AnnotatedFeature.pm

  use base qw(Bio::Ensembl::Funcgen::SetFeature);

  sub new {
    my $caller = shift;
    my $class  = ref($caller) || $caller;
    my $self   = $class->SUPER::new(@_);
    # More construction here
  }

  # Alternative direct contruction

  my $feat = Bio::EnsEMBL::Funcgen::SetFeature->
    (
     -start         => 100,
     -end           => 220,
     -strand        => -1,
     -slice         => $slice,
     -set           => $fset,
     -feature_type  => $ftype,
     -display_label => $label,
    );

  # Accessing some attributes

 
  my $start     = $feat->start;
  my $end       = $feat->end;
  my $strand    = $feat->strand;
  my $fset      = $feat->set;
  my $cell_type = $feat->cell_type;

  # Printing some information

  print $feature->display_label.' has the FeatureType '.$feat->feature_type->name."\n";

=head1 DESCRIPTION

This is a base class for features which are contained within a Funcgen FeatureSet or ResultSet.
It provides generic methods for attributes which are common across all inheriting classes.

=cut


package Bio::EnsEMBL::Funcgen::SetFeature;

use strict;
use warnings;

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

use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Feature Bio::EnsEMBL::Funcgen::Storable);
#can't use base with dual inheritance

=head2 new


  Arg [-SET]          : Bio::EnsEMBL::Funcgen::ResultSet or FeatureSet.
  Arg [-DISPLAY_LABEL]: (optional) String - Display label for this feature
  Arg [-FEATURE_TYPE] : (optional) Bio::EnsEMBL::Funcgen::FeatureType.
                        Defaults to Feature/ResultSet FeatureType.
  
  #Bio::EnsEMBL::Feature arguments
  Arg [-SLICE]        : Bio::EnsEMBL::Slice - The slice on which this feature is.
  Arg [-STRAND]       : (optional) Int - The orientation of this feature relative to the 
                        strand it is on. Valid values are 1, -1 and 0.
  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 [-ANALYSIS]     : (optional) Bio::EnsEMBL::Analysis. Defaults to Feature/ResultSet Analysis.
  Arg [-dbID]         : (optional) Int - Internal database ID.
  Arg [-ADAPTOR]      : (optional) Bio::EnsEMBL::Funcgen::DBSQL::BaseFeatureAdaptor



  Example             : my $feature = Bio::EnsEMBL::Funcgen::SetFeature->new
                                        (
                                         -SLICE         => $chr_1_slice,
                                         -START         => 1000000,
                                         -END           => 1000024,
                                         -STRAND        => -1,
							                           -DISPLAY_LABEL => $text,
							                           -SET           => $fset,
                                        );

  Description: Constructor for SetFeature objects. Should never be called directly, only by its children.
  Returntype : Bio::EnsEMBL::Funcgen::SetFeature
  Exceptions : Throws if no valid ResultSet or FeatureSet passed
               Throws if FeatureType is passed but not valid
  Caller     : General
  Status     : At Risk - FEATURE_SET arg to be removed, superceded by SET in v67

=cut

sub new {
  my $caller = shift;
  my $class = ref($caller) || $caller;

  my ($display_label, $fset, $ftype, $set)
    = rearrange(['DISPLAY_LABEL', 'FEATURE_SET', 'FEATURE_TYPE', 'SET'], @_);

  $set ||= $fset;

  if( ( ref($set) ne 'Bio::EnsEMBL::Funcgen::FeatureSet') &&
	  ( ref($set) ne 'Bio::EnsEMBL::Funcgen::ResultSet') ){
    throw("Must pass valid Bio::EnsEMBL::Funcgen::FeatureSet or ResultSet object");
  }

  #Grab FeatureSet first so we can pass analysis to base Feature class
  #Funcgen analysis is currently always at the Set level
  #if this ever changes the SetFeature->analysis method will also need changing
  my $self = $class->SUPER::new(@_, -analysis => $set->analysis);
 
  if($ftype){
	
    if (ref($ftype) ne 'Bio::EnsEMBL::Funcgen::FeatureType') {
      throw('feature_type param must be a valid Bio::EnsEMBL::Funcgen::FeatureType');
    }
  
    $self->{feature_type} = $ftype;
  }
 
  #Setting attrs directly removes the need for setter code in methods
  $self->{set}           = $set;
  $self->{display_label} = $display_label if defined $display_label;
 	
  return $self;
}



=head2 feature_set

  Example    : my $set = $efeature->feature_set();
  Description: WARNING: Can now also return ResultSet aswell as FeatureSet attribute for this feature.
  Returntype : Bio::EnsEMBL::Funcgen::FeatureSet or ResultSet
  Exceptions : None
  Caller     : General
  Status     : At Risk - marked as to be removed in v67

=cut

sub feature_set {
  #??? deprecate
  #check webcode?

  return $_[0]->{set};
}


=head2 set

  Example    : my $set = $set_feature->set();
  Description: Getter for the set attribute for this feature.
  Returntype : Bio::EnsEMBL::Funcgen::FeatureSet or ResultSet
  Exceptions : None
  Caller     : General
  Status     : At Risk

=cut

sub set {
  return $_[0]->{set};
}

=head2 cell_type

  Example    : my $cell_name = $set_feature->cell_type->name;
  Description: Getter for the CellType attribute for the Set of this Feature.
  May not always be for some Set types e.g. ExternalFeatures.
  Returntype : Bio::EnsEMBL::Funcgen::CellType
  Exceptions : None
  Caller     : General
  Status     : stable

=cut

sub cell_type{
	return $_[0]->set->cell_type;
}


=head2 feature_type

  Example    : my $ft_name = $set_feature->feature_type->name;
  Description: Getter for the FeatureType attribute for this feature.
               If not explicitly set, defaults to the Set FeatureType
  Returntype : Bio::EnsEMBL::Funcgen::FeatureType
  Exceptions : None
  Caller     : General
  Status     : stable

=cut

sub feature_type{
  my $self = shift;

  if(! defined $self->{feature_type}){
    $self->{feature_type} = $self->set->feature_type;
  }
  
  return $self->{feature_type};
}


=head2 analysis

  Example    : my $analysis = $setfeature->analysis;
  Description: Getter for the Analysis attribute for this feature.
               Re-implementation of Bio::EnsEMBL::Feature->analysis.
  Returntype : Bio::EnsEMBL::Analysis
  Exceptions : None
  Caller     : General
  Status     : stable

=cut

#what about MFs? add as feature_set as MOODS/PWM analysis not represented
#This is a mandatory requirement for Bio::EnsEMBL::Feature
#Do we ever actually have analysis at the feature level?

sub analysis{
  return $_[0]->set->analysis;
}


=head2 display_label

  Example    : my $label = $feature->display_label;
  Description: Getter for the display label of this feature.
  This will most likely be over-ridden by inheriting class
  Returntype : String
  Exceptions : None
  Caller     : General
  Status     : Stable

=cut

sub display_label{
  return $_[0]->{display_label};
}


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