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::Coordinate

SYNOPSIS

DESCRIPTION

Representation of a mapped region in a sequence; returned from Mapper.pm when the target region maps on to valid sequence.

METHODS

new

Arg [1]     char|int id of object in mapped region
Arg [2]     int start of region   
Arg [3]     int end of region
Arg [4]     int strand if region
Arg [5]     Bio::EnsEMBL::CoordSystem  coordsytem of the region
Function    creates a new Coordinate object
Returntype  Bio::EnsEMBL::Mapper::Coordinate
Exceptions  none
Status      Stable

start

Arg  1      int $start
            start coordinate of object in mapped region
Function    getter/setter method
Returntype  int
Exceptions  none
Caller      Bio::EnsEMBL::Mapper::Coordinate
Status      Stable

end

Arg  1      int $end
            end coordinate of object in mapped region
Function    getter/setter method
Returntype  int
Exceptions  none
Caller      Bio::EnsEMBL::Mapper::Coordinate
Status      Stable

strand

Arg  1      int $strand
            strand of object in mapped region
Function    getter/setter method
Returntype  int
Exceptions  none
Caller      Bio::EnsEMBL::Mapper::Coordinate
Status      Stable

id

  Arg  1      char|int $id
              id of object in mapped region
	      e.g. seq_region_id
  Function    getter/setter method
  Returntype  char|int
  Exceptions  none
  Caller      Bio::EnsEMBL::Mapper::Coordinate
  Status      Stable

name

  Arg  1      char name
              name of object in mapped region
	      e.g. seq_region_name
  Function    getter/setter method
  Returntype  char
  Exceptions  none
  Caller      Bio::EnsEMBL::Mapper::Coordinate
  Status      Stable

coord_system

Arg  1      Bio::EnsEMBL::CoordSystem
Function    getter/setter method
Returntype  Bio::EnsEMBL::CoordSystem
Exceptions  none
Caller      Bio::EnsEMBL::Mapper::Coordinate
Status      Stable

length

Function    getter method
Returntype  int
Exceptions  none
Caller      ?
Status      Stable