Bio::EnsEMBL::Funcgen AnnotatedFeature
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Summary
Bio::EnsEMBL::AnnotatedFeature - A module to represent a feature mapping as
predicted by the eFG pipeline.
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Funcgen::FeatureType
Bio::EnsEMBL::Funcgen::SetFeature
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Bio::EnsEMBL::Utils::Exception qw ( throw )
Inherit
Bio::EnsEMBL::Funcgen::SetFeature
Synopsis
use Bio::EnsEMBL::Funcgen::AnnotatedFeature;
my $feature = Bio::EnsEMBL::Funcgen::AnnotatedFeature->new(
-SLICE => $chr_1_slice,
-START => 1_000_000,
-END => 1_000_024,
-STRAND => -1,
-DISPLAY_LABEL => $text,
-SCORE => $score,
-FEATURE_SET => $fset,
);
Description
A AnnotatedFeature object represents the genomic placement of a prediction
generated by the eFG analysis pipeline, which may have originated from one or many
separate experiments.
Methods
display_labelDescriptionCode
newDescriptionCode
scoreDescriptionCode
Methods description
display_labelcode    nextTop
  Arg [1]    : string - display label
  Example    : my $label = $feature->display_label();
  Description: Getter and setter for the display label of this feature.
  Returntype : str
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
newcodeprevnextTop
 
  Arg [-SCORE]: (optional) int - Score assigned by analysis pipeline
  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,
									                                      -STRAND        => -1,
									                                      -DISPLAY_LABEL => $text,
									                                      -SCORE         => $score,
                                                                          -FEATURE_SET   => $fset,
                                                                         );

  Description: Constructor for AnnotatedFeature objects.
  Returntype : Bio::EnsEMBL::Funcgen::AnnotatedFeature
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
scorecodeprevnextTop
  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     : Low Risk
Methods code
display_labeldescriptionprevnextTop
sub display_label {
    my $self = shift;
	
    $self->{'display_label'} = shift if @_;


    #auto generate here if not set in table
    #need to go with one or other, or can we have both, split into diplay_name and display_label?
    
    if(! $self->{'display_label'}  && $self->adaptor()){
      $self->{'display_label'} = $self->feature_type->name()." -";
      $self->{'display_label'} .= " ".$self->cell_type->name();# if $self->cell_type->display_name();
      $self->{'display_label'} .= " Enriched Site";
    }
	
    return $self->{'display_label'};
}



1;
}
newdescriptionprevnextTop
sub new {
  my $caller = shift;
	
  my $class = ref($caller) || $caller;
  
  my $self = $class->SUPER::new(@_);
  
  my ($score,)
    = rearrange(['SCORE'], @_);
  
  
  $self->score($score) if $score;
 	
	
  return $self;
}
scoredescriptionprevnextTop
sub score {
    my $self = shift;
	
    $self->{'score'} = shift if @_;
		
    return $self->{'score'};
}
General documentation
AUTHORTop
This module was created by Nathan Johnson.
This module is part of the Ensembl project: /
CONTACTTop
Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk