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Summary

Bio::EnsEMBL::Funcgen::SetFeature - Ensembl specific set feature.

Package variables

Included modules

Inherit

Bio::EnsEMBL::Feature Bio::EnsEMBL::Funcgen::Storable

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);

Description

This is a simple wrapper method for the core Feature class to contain common generic
Funcgen SetFeature methods.

Methods

Methods description

  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

  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

  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

  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

  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

  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

  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

Methods code

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;

}

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

}

sub cell_type {

	my $self = shift;

	return $self->feature_set->cell_type();

}

sub feature_set {

  my $self = shift;

  return $self->{'feature_set'};

}

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();

}

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;

}

sub new_fast {

  return bless ($_[1], $_[0]);

}

General documentation

Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk