Bio::EnsEMBL::PaddedSlice Class Reference

Inheritance diagram for Bio::EnsEMBL::PaddedSlice:

Public Member Functions
public Bio::EnsEMBL::PaddedSlice	new ()
public Int	start ()
public Int	end ()
public Int	length ()
public Scalar	seq ()
public Scalar	subseq ()
public	sub_Slice ()
protected CodeRef	__resolver ()
Public Member Functions inherited from Bio::EnsEMBL::Utils::Proxy
public Bio::EnsEMBL::Utils::Proxy	new ()
protected Any	__proxy ()
public Boolean	isa ()
public Code	can ()
public void	DESTROY ()
public void	AUTOLOAD ()
protected	__resolver ()

Detailed Description

Description

Used when dumping Slices which represet a portion of the sequence region
they map to e.g. the first section of human Y. The code will return N
as sequence if an attempt is made to retrieve sequence not covered by the
Slice given. This makes the code very memory efficient if sequence dumping
is carried out using subseq() calls.

Definition at line 14 of file PaddedSlice.pm.

Member Function Documentation

__resolver()

protected CodeRef Bio::EnsEMBL::PaddedSlice::__resolver

(

)

  Description : Delegates all non-overriden actions onto the backing slice 
  Returntype  : CodeRef
  Exceptions  : None 
  Caller      : public
  Status      : -

Code:

end()

public Int Bio::EnsEMBL::PaddedSlice::end

(

)

  
  Example     :

@co
de $slice->end();

  Description : Always returns the backing slice sequence region length
  Returntype  : Int
  Exceptions  : None 
  Caller      : public
  Status      : -

Code:

length()

public Int Bio::EnsEMBL::PaddedSlice::length

(

)

  
  Example     :

@co
de $slice->length();

  Description : Delegates to end()
  Returntype  : Int
  Exceptions  : None 
  Caller      : public
  Status      : -

Code:

new()

public Bio::EnsEMBL::PaddedSlice Bio::EnsEMBL::PaddedSlice::new

(

)

  Arg [SLICE] : The Slice to proxy  
  Example     :

my $newobj = Bio::EnsEMBL::PaddedSlice->new($myobj);

  Description : Provides a new instance of a padded slice
  Returntype  : Bio::EnsEMBL::PaddedSlice
  Exceptions  : None 
  Caller      : public
  Status      : -

Code:

seq()

public Scalar Bio::EnsEMBL::PaddedSlice::seq

(

)

  
  Example     :

@co
de my $seq = $slice->seq()

  Description : Returns the entire sequence of the backing slice but padded
                with N's at the beginning and the end of the slice where
                applicable
  Returntype  : Scalar string
  Exceptions  : None 
  Caller      : public
  Status      : -

Code:

start()

public Int Bio::EnsEMBL::PaddedSlice::start

(

)

  Example     :

$slice->start();

  Description : Always returns 1 since all padded slices start at 1
  Returntype  : Int
  Exceptions  : None 
  Caller      : public
  Status      : -

Code:

sub_Slice()

public Bio::EnsEMBL::PaddedSlice::sub_Slice

(

)

Undocumented method

Code:

subseq()

public Scalar Bio::EnsEMBL::PaddedSlice::subseq

(

)

  
  Arg [1]     : Int; start position of the subslice
  Arg [2]     : Int; end position of the subslice
  Arg [3]     : Int; strand of the subslice  
  Example     :

@co
de my $subseq = $slice->subseq(1, 1_000_000);

  Description : Returns a portion of the sequence padded with N's if required 
  Returntype  : Scalar string
  Exceptions  : None 
  Caller      : public
  Status      : -

Code:

  
  Arg [1]     : Int; start position of the subslice
  Arg [2]     : Int; end position of the subslice
  Arg [3]     : Int; strand of the subslice  
  Example     :

@co
de my $subseq = $slice->subseq(1, 1_000_000);

  Description : Returns a portion of the sequence padded with N's if required 
  Returntype  : Scalar string
  Exceptions  : None 
  Caller      : public
  Status      : -

/**

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

• ensembl/modules/Bio/EnsEMBL/PaddedSlice.pm