PaddedSlice.pm

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=head1 LICENSE
 
See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
 
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.
 
=cut
 
 
=head1 CONTACT
 
  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
 
  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.
 
=cut
 
=head1 NAME
 
Bio::EnsEMBL::PaddedSlice
 
=head1 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 C<subseq()> calls.
 
=head1 METHODS
 
=cut
 
package Bio::EnsEMBL::PaddedSlice;
 
use strict;
use warnings;
 
use Bio::EnsEMBL::Utils::Argument qw/rearrange/;
use Bio::EnsEMBL::Utils::Scalar qw/assert_ref assert_strand/;
use base qw/Bio::EnsEMBL::Utils::Proxy/;
 
=head2 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      : -
 
=cut
 
sub new {
  my ($class, @args) = @_;
  my ($slice) = rearrange([qw/slice/], @args);
  return $class->SUPER::new($slice);
}
 
=head2 start()
 
  Example     : $slice->start();
  Description : Always returns 1 since all padded slices start at 1
  Returntype  : Int
  Exceptions  : None 
  Caller      : public
  Status      : -
 
=cut
 
sub start {
  my ($self) = @_;
  return 1;
}
 
=head2 end()
  
  Example     : $slice->end();
  Description : Always returns the backing slice sequence region length
  Returntype  : Int
  Exceptions  : None 
  Caller      : public
  Status      : -
 
=cut
 
sub end {
  my ($self) = @_;
  return $self->seq_region_length();
}
 
=head2 length()
  
  Example     : $slice->length();
  Description : Delegates to C<end()>
  Returntype  : Int
  Exceptions  : None 
  Caller      : public
  Status      : -
 
=cut
 
sub length {
  my ($self) = @_;
  return $self->end();
}
 
=head2 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      : -
 
=cut
 
sub seq {
  my ($self) = @_;
  my $parent_slice = $self->__proxy();
  my $pad_start = 'N' x ( $parent_slice->start() - 1 );
  my $pad_end   = 'N' x ( $parent_slice->seq_region_length() - $parent_slice->end() );
  my $seq = $parent_slice->seq();
  return $pad_start . $seq . $pad_end;
}
 
=head2 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      : -
 
=cut
 
sub subseq {
  my ( $self, $start, $end, $strand ) = @_;
 
  if ( $end+1 < $start ) {
    throw("End coord + 1 is less than start coord");
  }
  
  return '' if( $start == $end + 1);
  
  $strand = 1 unless(defined $strand);
  assert_strand($strand, 'strand');
  
  my $parent_slice = $self->__proxy();
    
  #Coords relative to the SeqRegion i.e. huge
  my $parent_start = $parent_slice->start();
  my $parent_end = $parent_slice->end();
  
  #Return if we were upstream of overlap
  if($start < $parent_start && $end < $parent_start) {
    return 'N' x (( $end - $start )+1);
  }
  #Return if we were downstream of overlap
  if($start > $parent_end && $end > $parent_end) {
    return 'N' x (( $end - $start )+1);
  }
  
  my $prefix  = '';
  my $suffix = '';
  my $subslice_start = ($start - $parent_start)+1;
  my $subslice_end = ($end - $parent_start) + 1;
  if($start < $parent_start) {
    $prefix = 'N' x ($parent_start - $start);
    $subslice_start = 1;
  }
  if($end > $parent_end) {
    $suffix = 'N' x ($end - $parent_end);
    $subslice_end = (($parent_end - $parent_start)+1);
  }
  
  my $subseq = $parent_slice->subseq($subslice_start, $subslice_end, $strand);
  
  return $prefix . $subseq . $suffix;
}
 
=head2 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      : -
 
=cut
 
sub sub_Slice {
  die "Unsupported";
}
 
 
=head2 __resolver()
 
  Description : Delegates all non-overriden actions onto the backing slice 
  Returntype  : CodeRef
  Exceptions  : None 
  Caller      : public
  Status      : -
 
=cut
 
sub __resolver {
  my ($self, $package_name, $method) = @_;
  return sub {
    my ($local_self, @args) = @_;
    return $local_self->__proxy()->$method(@args);
  };
}
 
 
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