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

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.

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