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

List of all members.


Class Summary

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.

Available Methods

public coord_system ()
public end ()
public id ()
public length ()
public new ()
public rank ()
public start ()
public strand ()

Method Documentation

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:
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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:
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public Bio::EnsEMBL::Mapper::Coordinate::id ( )
  Arg  1      char|int $id
              id of object in mapped region
	      e.g. seq_region_id / seq_region_name
  Function    getter/setter method
  Returntype  char|int
  Exceptions  none
  Caller      Bio::EnsEMBL::Mapper::Coordinate
  Status      Stable
 
Code:
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public Bio::EnsEMBL::Mapper::Coordinate::length ( )
  Function    getter method
  Returntype  int
  Exceptions  none
  Caller      ?
  Status      Stable
 
Code:
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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:
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Reimplemented in Bio::EnsEMBL::Mapper::IndelCoordinate.

public Bio::EnsEMBL::Mapper::Coordinate::rank ( )

Undocumented method

Code:
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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:
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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: