LICENSE

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

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NAME

Bio::EnsEMBL::Mapper::IndelCoordinate

SYNOPSIS

DESCRIPTION

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

METHODS

new

Arg [1]    : Bio::EnsEMBL::Mapper::Gap $gap
Arg [2]    : Bio::EnsEMBL::Mapper::Coordinate $coordinate
Example    : $indelCoord = Bio::EnsEMBL::Mapper::IndelCoordinate($gap, $coordinate);
Description: Creates a new IndelCoordinate object.
Returntype : Bio::EnsEMBL::Mapper::IndelCoordinate
Exceptions : none
Caller     : Bio::EnsEMBL::Mapper

gap_start

Arg[1]      : (optional) int $gap_start
Example     : $gap_start = $ic->gap_start()
Description : Getter/Setter for the start of the Gap region
ReturnType  : int
Exceptions  : none
Caller      : general

gap_end

Arg[1]      : (optional) int $gap_end
Example     : $gap_end = $ic->gap_end()
Description : Getter/Setter for the end of the Gap region
ReturnType  : int
Exceptions  : none
Caller      : general

gap_length

Args        : None
Example     : $gap_length = $ic->gap_length()
Description : Getter for the length of the Gap region
ReturnType  : int
Exceptions  : none
Caller      : general