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

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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