/ 
Bio-EnsEMBL-113_51
River stage zero No dependents
/ Bio::EnsEMBL::PaddedSlice

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

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

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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      : -