LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

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NAME

Bio::EnsEMBL::SimpleFeature - A simple feature with a location and label

SYNOPSIS

  use Bio::EnsEMBL::SimpleFeature;

  $feature = Bio::EnsEMBL::SimpleFeature->new(
    -start         => 100,
    -end           => 220,
    -strand        => -1,
    -slice         => $slice,
    -analysis      => $analysis,
    -score         => 58,
    -display_label => 'EponineTSS',
    -dbID          => 1230,
    -adaptor       => $adaptor
  );

DESCRIPTION

This is a simple feature which extends the Feature class to add display_label and score attributes.

METHODS

new

  Arg [DISPLAY_LABEL]: The label assigned to this simple feature
  Arg [...]  : Named arguments passed to superclass
  Example    : $feature = Bio::EnsEMBL::SimpleFeature->new
                        (-start    => 1,
                         -end      => 100,
                         -strand   => 1,
                         -slice    => $slice,
                         -analysis => $analysis,
                         -adaptor => $adaptor,
                         -dbID    => 10,
                         -display_label => 'EponineTSS',
                         -score => 100);
  Description: Constructs a new Bio::EnsEMBL::Feature.  Generally subclasses
               of this method are instantiated, rather than this class itself.
  Returntype : Bio::EnsEMBL::Feature
  Exceptions : Thrown on invalid -SLICE, -ANALYSIS, -STRAND arguments
  Caller     : general, subclass constructors
  Status     : Stable

display_label

  Arg [1]    : (optional) string $value
  Example    : $label = $simple_feature->display_label();
  Description: Getter/Setter for the display label associated with this
               feature.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

display_id

  Arg [1]    : none
  Example    : print $rf->display_id();
  Description: This method returns a string that is considered to be
               the 'display' identifier.  For simple features this is the 
               display_label if it is available otherwise it is an empty 
               string.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

score

  Arg [1]    : (optional) string $value
  Example    : $score = $simple_feature->score();
  Description: Getter/Setter for the score associated with this
               feature.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

summary_as_hash

  Example    : my $hash = $simple_feature->summary_as_hash();
  Description: Generates a HashRef compatible with GFFSerializer. Adds
               score, external_name and logic_name to the basic Feature
               hash
  Returntype : Hash
  Exceptions : none
  Caller     : general
  Status     : Stable