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

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NAME

Bio::EnsEMBL::Mapper::Gap

SYNOPSIS

DESCRIPTION

Representation of a gap in a sequence; returned from Mapper.pm when the target region is in a gap.

METHODS

new

Arg [1]    : int $start
Arg [2]    : int $end
Example    : $gap = Bio::EnsEMBL::Mapper::Gap($start, $end);
Description: Creates a new Gap object.
Returntype : Bio::EnsEMBL::Mapper::Gap
Exceptions : none
Caller     : Bio::EnsEMBL::Mapper
Status     : Stable

start

Arg [1]    : (optional) int $start
             start coordinate of gap region
Example    : $start = $gap->start();
Description: Getter/Setter for the start attribute
Returntype : int
Exceptions : none
Caller     : general
Status     : Stable

end

Arg [1]    : (optional) int $newval
             The new value to set the end coordinate to
Example    : $end = $gap->end()
Description: Getter/Setter for the end coordinate of the gap region
Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

length

Arg [1]    : none
Example    : $len = $gap->length();
Description: Getter for the length of this gap region
Returntype : int
Exceptions : none
Caller     : general
Status     : Stable