Bio::EnsEMBL::Mapper::IndelCoordinate Class Reference

Inheritance diagram for Bio::EnsEMBL::Mapper::IndelCoordinate:

Public Member Functions
public Bio::EnsEMBL::Mapper::IndelCoordinate	new ()
public Int	gap_start ()
public Int	gap_end ()
public Int	gap_length ()
Public Member Functions inherited from Bio::EnsEMBL::Mapper::Coordinate
public	new ()
public	start ()
public	end ()
public	strand ()
public	id ()
public	name ()
public	coord_system ()
public	length ()
public	rank ()
Public Member Functions inherited from Bio::EnsEMBL::Mapper::Gap
public Bio::EnsEMBL::Mapper::Gap	new ()
public Int	start ()
public String	end ()
public Int	length ()
public	rank ()

Detailed Description

Synopsis

Description

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

Definition at line 16 of file IndelCoordinate.pm.

Member Function Documentation

gap_end()

public Int Bio::EnsEMBL::Mapper::IndelCoordinate::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

Code:

gap_length()

public Int Bio::EnsEMBL::Mapper::IndelCoordinate::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

Code:

gap_start()

public Int Bio::EnsEMBL::Mapper::IndelCoordinate::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

Code:

new()

public Bio::EnsEMBL::Mapper::IndelCoordinate Bio::EnsEMBL::Mapper::IndelCoordinate::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

Code:

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

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