PredictionExon.pm

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=head1 LICENSE
 
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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::PredictionExon - A class representing an Exon from an ab
initio prediction method
 
=head1 SYNOPSIS
 
  $exon = new Bio::EnsEMBL::PredictionExon(
    -START   => 100,
    -END     => 200,
    -STRAND  => 1,
    -SLICE   => $slice,
    -DBID    => $dbID,
    -P_VALUE => 23.5,
    -SCORE   => 99
  );
 
  # seq() returns a Bio::Seq
  my $seq = $exon->seq->seq();
 
  # peptide() only makes sense within transcript context
  my $pep = $exon->peptide($transcript)->seq();
 
  # Normal feature operations can be performed:
  $exon = $exon->transform('clone');
  $exon->move( $new_start, $new_end, $new_strand );
  print $exon->slice->seq_region_name();
 
=head1 DESCRIPTION
 
This is a class which represents an prediction exon which is part of a
predcition transcript. See Bio::EnsEMBL:PredictionTranscript
 
=head1 METHODS
 
=cut
 
package Bio::EnsEMBL::PredictionExon;
 
use vars qw(@ISA);
use strict;
 
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Exon;
use Bio::EnsEMBL::Utils::Exception qw( warning throw );
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
 
 
@ISA = qw(Bio::EnsEMBL::Exon);
 
 
=head2 new
 
  Args       : see SUPERCLASS Bio::EnsEMBL::Exon
  Example    : none
  Description: create an Exon object
  Returntype : Bio::EnsEMBL::PredictionExon 
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub new {
  my $class = shift;
 
  $class = ref $class || $class;
 
  my $self = $class->SUPER::new( @_ );
 
  my ( $p_value, $score ) = 
    rearrange( [ "P_VALUE", "SCORE" ], @_ );
 
  $self->{'p_value'} = $p_value;
  $self->{'score'} = $score;
 
  return $self;
}
 
 
=head2 score
 
  Arg [1]    : string $newval (optional) 
               The new value to set the score attribute to
  Example    : $score = $obj->score()
  Description: Getter/Setter for the score attribute
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub score{
  my $self = shift;
  $self->{'score'} = shift if(@_);
  return $self->{'score'};
}
 
 
 
=head2 p_value
 
  Arg [1]    : string $newval (optional) 
               The new value to set the p_value attribute to
  Example    : $p_value = $obj->p_value()
  Description: Getter/Setter for the p_value attribute
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub p_value{
  my $self = shift;
  $self->{'p_value'} = shift if(@_);
  return $self->{'p_value'};
}
 
 
=head2 end_phase
 
  Arg [1]    : (optional) int $end_phase
  Example    : $end_phase = $feat->end_phase;
  Description: Gets/Sets the end phase of the exon.
               end_phase = number of bases from the last incomplete codon of 
               this exon.
               Usually, end_phase = (phase + exon_length)%3
               but end_phase could be -1 if the exon is half-coding and its 3 
               prime end is UTR.
  Returntype : int
  Exceptions : warning if end_phase is called without an argument and the
               value is not set.
  Caller     : general
  Status     : Stable
 
=cut
 
 
 
sub end_phase {
  my $self = shift;
  if( @_ ) {
    throw( "End_phase setting not supported" );
  }
  return ($self->phase() + $self->length()) % 3;
}
 
 
=head2 transform
 
  Arg  1     : String $coordinate_system_name
  Arg [2]    : String $coordinate_system_version
  Description: moves this exon to the given coordinate system. If this exon has
               attached supporting evidence, they move as well.
  Returntype : Bio::EnsEMBL::Exon
  Exceptions : wrong parameters
  Caller     : general
  Status     : Stable
 
=cut
 
 
sub transform {
  my $self = shift;
 
  # catch for old style transform calls
  if( !@_ || ( ref $_[0] && ($_[0]->isa( "Bio::EnsEMBL::Slice" ) or $_[0]->isa( "Bio::EnsEMBL::LRGSlice" )))) {
    throw( "transform needs coordinate systems details now," .
           "please use transfer" );
  }
 
  my $new_exon = Bio::EnsEMBL::Feature::transform( $self, @_ );
  return undef unless $new_exon;
 
  #dont want to share the same sequence cache
  delete $new_exon->{'_seq_cache'};
 
  return $new_exon;
}
 
 
 
=head2 transfer
 
  Arg [1]    : Bio::EnsEMBL::Slice $destination_slice
  Example    : none
  Description: Moves this Exon to given target slice coordinates. If Features
               are attached they are moved as well. Returns a new exon.
  Returntype : Bio::EnsEMBL::Gene
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub transfer {
  my $self  = shift;
 
  my $new_exon = Bio::EnsEMBL::Feature::transfer( $self, @_ );
  return undef unless $new_exon;
 
  #dont want to share the same sequence cache
  delete $new_exon->{'_seq_cache'};
 
  return $new_exon;
}
 
=head2 summary_as_hash
 
  Example       : $exon_summary = $exon->summary_as_hash();
  Description   : Extends Feature::summary_as_hash
                  Retrieves a summary of this prediction exon.
  Returns       : hashref of descriptive strings
  Status        : Intended for internal use
=cut
 
sub summary_as_hash {
  my $self = shift;
  my $summary_ref = $self->SUPER::summary_as_hash;
  delete $summary_ref->{'constitutive'};
  delete $summary_ref->{'ensembl_phase'};
  delete $summary_ref->{'ensembl_end_phase'};
  $summary_ref->{'Parent'} = $self->transcript->dbID() if $self->transcript();
  $summary_ref->{'source'} = $self->prediction_transcript->analysis->gff_source() || 'ensembl';
  return $summary_ref;
}
 
=head2 transcript
  Example     : $prediction_transcript = $exon->transcript;
  Description : Locates the parent prediction transcript using an exon dbID
                Same as prediction_transcript, duplicated for compatibility
                with Exon feature
  Returns     : Bio::EnsEMBL::PredictionTranscript
 
=cut
 
sub transcript {
  my $self = shift;
  return $self->prediction_transcript;
}
 
=head2 prediction_transcript
 
  Example     : $prediction_transcript = $exon->prediction_transcript;
  Description : Locates the parent prediction transcript using an exon dbID
  Returns     : Bio::EnsEMBL::PredictionTranscript
 
=cut
 
sub prediction_transcript{
  my $self = shift;
  my $prediction_transcript_adaptor = $self->adaptor->db->get_PredictionTranscriptAdaptor();
  my $parent_prediction_transcript = $prediction_transcript_adaptor->fetch_by_prediction_exon_id($self->dbID);
  return $parent_prediction_transcript;
}
 
 
=head2 add_supporting_features
 
  Description: For compatibility with Bio::EnsEMBL::Exon
               Does nothing.
  Returntype : none
  Status     : Stable
 
=cut
 
sub add_supporting_features { }
 
 
=head2 get_all_supporting_features
 
  Description: For compatibility with Bio::EnsEMBL::Exon
               Does nothing and returns empty list
  Returntype : empty list.
  Status     : Stable
 
=cut
 
sub get_all_supporting_features { return []; }
 
 
=head2 find_supporting_evidence
 
  Description: For compatibility with Bio::EnsEMBL::Exon
               Does nothing.
  Returntype : empty list.
  Status     : Stable
 
=cut
 
sub find_supporting_evidence { return []; }
 
 
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