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Bio-EnsEMBL-112.0.0
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/ Bio::EnsEMBL::RepeatFeature

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

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NAME

Bio::EnsEMBL::RepeatFeature - A feature representing a repeat on a piece of sequence.

SYNOPSIS

my $rf = new Bio::EnsEMBL::Feature(
  -start            => 100,
  -end              => 220,
  -strand           => -1,
  -slice            => $slice,
  -analysis         => $analysis,
  -repeat_consensus => $rc,
  -hstart           => 10,
  -hend             => 100,
  -hstrand          => 1,
  -score            => 83.2
);

my $hstart = $feat->hstart;
my $hend   = $feat->hend;

# 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 a feature representing a repeat region on a sequence

METHODS

new

Arg [REPEAT_CONSENSUS] : Bio::EnsEMBL::RepeatConsensus (optional)
                         The repeat consensus for this repeat feature
Arg [HSTART] : int (optional)
               The hit start on the consensus sequence
Arg [HEND]   : int (optional)
               The hit end on the consensus sequence
Arg [SCORE]  : float (optional)
               The score
Arg [...]    : Named arguments to superclass constructor
               (see Bio::EnsEMBL::Feaure)
Example    : $rf = Bio::EnsEMBL::RepeatFeature->new(-REPEAT_CONSENSUS => $rc,
                                                    -HSTART => 10,
                                                    -HEND   => 100,
                                                    -SCORE  => 58.0,
                                                    -START  => 1_000_100,
                                                    -END    => 1_000_190,
                                                    -STRAND => 1,
                                                    -ANALYSIS => $an,
                                                    -SLICE  => $chr_slice);
Description: Creates a new Bio::EnsEMBL::RepeatFeature object
Returntype : Bio::EnsEMBL::RepeatFeature
Exceptions : none
Caller     : RepeatFeatureAdaptors
Status     : Stable

repeat_consensus

Arg [1]    : (optional) Bio::EnsEMBL::RepeatConsensus
Example    : $repeat_consensus = $repeat->repeat_consensus;
Description: Getter/Setter for the repeat consensus of this repeat
Returntype : Bio::EnsEMBL::RepeatConsensus
Exceptions : none
Caller     : general
Status     : Stable

hstart

Arg [1]    : (optional) int $hstart
Example    : $hit_start = $repeat->hstart;
Description: Getter/Setter for the start bp of this repeat match on the 
             consensus sequence.
Returntype : int
Exceptions : none 
Caller     : general
Status     : Stable

score

Arg [1]    : (optional) float $score
Example    : $score = $repeat->score();
Description: Getter/Setter for the score of this repeat feature
Returntype : int
Exceptions : none
Caller     : general
Status     : Stable

hend

Arg [1]    : (optional) int $hend
Example    : $hit_end = $repeat->hend;
Description: Getter/Setter for the end bp of this repeat match on the 
             consensus sequence.
Returntype : int
Exceptions : none
Caller     : general
Status     : Stable

hstrand

Arg [1]    : none
Example    : none
Description: always returns 1. method exists for consistancy with other 
             features.
Returntype : int
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 repeat_features this is the 
             name of the repeat consensus if it is available otherwise it is
             an empty string.
Returntype : string
Exceptions : none
Caller     : web drawing code
Status     : Stable

summary_as_hash

Example       : $repeat_feature_summary = $protein_feature->summary_as_hash();
Description   : Retrieves a textual summary of this Repeat feature.
                Not inherited from Feature.
Returns       : hashref of arrays of descriptive strings
Status        : Intended for internal use

NAME - Bio::EnsEMBL::RepeatFeature