Bio::EnsEMBL::Mapper::Coordinate Class Reference

Inheritance diagram for Bio::EnsEMBL::Mapper::Coordinate:

Public Member Functions
public	new ()
public	start ()
public	end ()
public	strand ()
public	id ()
public	name ()
public	coord_system ()
public	length ()
public	rank ()

Detailed Description

Synopsis

Description

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

Definition at line 14 of file Coordinate.pm.

Member Function Documentation

coord_system()

public Bio::EnsEMBL::Mapper::Coordinate::coord_system

(

)

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

Code:

end()

public Bio::EnsEMBL::Mapper::Coordinate::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

Code:

id()

public Bio::EnsEMBL::Mapper::Coordinate::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

Code:

length()

public Bio::EnsEMBL::Mapper::Coordinate::length

(

)

  Function    getter method
  Returntype  int
  Exceptions  none
  Caller      ?
  Status      Stable

Code:

name()

public Bio::EnsEMBL::Mapper::Coordinate::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

Code:

new()

public Bio::EnsEMBL::Mapper::Coordinate::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

Code:

rank()

public Bio::EnsEMBL::Mapper::Coordinate::rank

(

)

Undocumented method

Code:

start()

public Bio::EnsEMBL::Mapper::Coordinate::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

Code:

strand()

public Bio::EnsEMBL::Mapper::Coordinate::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

Code:

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The documentation for this class was generated from the following file:

• ensembl/modules/Bio/EnsEMBL/Mapper/Coordinate.pm