/ 
Bio-EnsEMBL-112.0_53
River stage zero No dependents
/ Bio::EnsEMBL::IdMapping::TinyExon

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
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NAME

Bio::EnsEMBL::IdMapping::TinyExon - lightweight exon object

SYNOPSIS

# fetch an exon from the db and create a lightweight exon object
# from it
my $exon = $exon_adaptor->fetch_by_stable_id('ENSE000345437');
my $lightweight_exon = Bio::EnsEMBL::IdMapping::TinyExon->new_fast( [
    $exon->dbID,
    $exon->stable_id,
    $exon->version,
    $exon->created_date,
    $exon->modified_date,
    $exon->start,
    $exon->end,
    $exon->strand,
    $exon->slice->seq_region_name,
    $exon->slice->coord_system_name,
    $exon->slice->coord_system->version,
    $exon->slice->subseq( $exon->start, $exon->end, $exon->strand ),
    $exon->phase,
    $need_project,
] );

DESCRIPTION

This is a lightweight exon object for the stable Id mapping. See the documentation in TinyFeature for general considerations about its design.

METHODS

start
end
strand
seq_region_name
coord_system_name
coord_system_version
seq
phase
need_project
common_start
common_end
common_strand
common_sr_name
length

start

Arg[1]      : (optional) Int - the exon's start coordinate
Description : Getter/setter for the exon's start coordinate.
Return type : Int
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

end

Arg[1]      : (optional) Int - the exon's end coordinate
Description : Getter/setter for the exon's end coordinate.
Return type : Int
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

strand

Arg[1]      : (optional) Int - the exon's strand
Description : Getter/setter for the exon's strand.
Return type : Int
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

seq_region_name

Arg[1]      : (optional) String - seq_region name
Description : Getter/setter for the seq_region name of the slice the exon is
              on.
Return type : String
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

coord_system_name

Arg[1]      : (optional) String - coord_system name
Description : Getter/setter for the coord_system name of the slice the exon is
              on.
Return type : String
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

coord_system_version

Arg[1]      : (optional) String - coord_system version
Description : Getter/setter for the coord_system version of the slice the
              exon is on.
Return type : String
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

seq

Arg[1]      : (optional) String - the exon's sequence
Description : Getter/setter for the exon's sequence.
Return type : String
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

phase

Arg[1]      : (optional) Int - the exon's phase
Description : Getter/setter for the exon's phase.
Return type : Int
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

need_project

Arg[1]      : (optional) Boolean - attribute to set
Description : Getter/setter for the attribute determining whether an exon
              needs to be projected onto a common coord_system. You don't need
              to do so if the native coord_system is common to the source and
              target assemblies, or if no common coord_system is found (the
              Cache object has methods to determine this).
Return type : Boolean
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

common_start

Arg[1]      : (optional) Int - the exon's start in common coord_system
              coordinates
Description : Getter/setter for the exon's start in common coord_system
              coordinates. Will return $self->start if no projection to a
              common coord_system is required.
Return type : Int
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

common_end

Arg[1]      : (optional) Int - the exon's end in common coord_system
              coordinates
Description : Getter/setter for the exon's end in common coord_system
              coordinates. Will return $self->end if no projection to a
              common coord_system is required.
Return type : Int
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

common_strand

Arg[1]      : (optional) Int - the exon's strand in common coord_system
              coordinates
Description : Getter/setter for the exon's strand in common coord_system
              coordinates. Will return $self->strand if no projection to a
              common coord_system is required.
Return type : Int
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

common_sr_name

Arg[1]      : (optional) String - seq_region name of the exon's slice on the
              common coord_system
Description : Getter/setter for the seq_region name of the exon's slice on the
              common coord_system coordinates. Will return
              $self->seq_region_name if no projection to a common coord_system
              is required.
Return type : String
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

length

Description : Returns the exon length (distance between start and end).
Return type : Int
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development