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::PaddedSlice

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.

METHODS

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      : -

start()

  Example     : $slice->start();
  Description : Always returns 1 since all padded slices start at 1
  Returntype  : Int
  Exceptions  : None 
  Caller      : public
  Status      : -

end()

  Example     : $slice->end();
  Description : Always returns the backing slice sequence region length
  Returntype  : Int
  Exceptions  : None 
  Caller      : public
  Status      : -

length()

  Example     : $slice->length();
  Description : Delegates to C<end()>
  Returntype  : Int
  Exceptions  : None 
  Caller      : public
  Status      : -

seq()

  Example     : 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      : -

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     : 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      : -

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     : 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      : -

__resolver()

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