Bio::EnsEMBL PredictionExon
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Summary
Bio::EnsEMBL::PredictionExon - A class representing an Exon from an ab
initio prediction method
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Exon
Bio::EnsEMBL::Feature
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Bio::EnsEMBL::Utils::Exception qw ( warning throw deprecate )
Inherit
Bio::EnsEMBL::Exon
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();
Description
This is a class which represents an prediction exon which is part of a
predcition transcript. See Bio::EnsEMBL:PredictionTranscript
Methods
add_supporting_featuresDescriptionCode
end_phaseDescriptionCode
find_supporting_evidenceDescriptionCode
get_all_supporting_featuresDescriptionCode
newDescriptionCode
p_valueDescriptionCode
scoreDescriptionCode
transferDescriptionCode
transformDescriptionCode
Methods description
add_supporting_featurescode    nextTop
  Description: For compatibility with Bio::EnsEMBL::Exon
Does nothing.
Returntype : none
Status : Stable
end_phasecodeprevnextTop
  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
find_supporting_evidencecodeprevnextTop
  Description: For compatibility with Bio::EnsEMBL::Exon
Does nothing.
Returntype : empty list.
Status : Stable
get_all_supporting_featurescodeprevnextTop
  Description: For compatibility with Bio::EnsEMBL::Exon
Does nothing and returns empty list
Returntype : empty list.
Status : Stable
newcodeprevnextTop
  Args       : see SUPERCLASS Bio::EnsEMBL::Exon
Example : none
Description: create an Exon object
Returntype : Bio::EnsEMBL::PredictionExon
Exceptions : none
Caller : general
Status : Stable
p_valuecodeprevnextTop
  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
scorecodeprevnextTop
  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
transfercodeprevnextTop
  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
transformcodeprevnextTop
  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
Methods code
add_supporting_featuresdescriptionprevnextTop
sub add_supporting_features {
}
end_phasedescriptionprevnextTop
sub end_phase {
  my $self = shift;
  if( @_ ) {
    throw( "End_phase setting not supported" );
  }
  return ($self->phase() + $self->length()) % 3;
}
find_supporting_evidencedescriptionprevnextTop
sub find_supporting_evidence {
 return [];
}
get_all_supporting_featuresdescriptionprevnextTop
sub get_all_supporting_features {
 return [];
}
newdescriptionprevnextTop
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;
}
p_valuedescriptionprevnextTop
sub p_value {
  my $self = shift;
  $self->{'p_value'} = shift if(@_);
  return $self->{'p_value'};
}
scoredescriptionprevnextTop
sub score {
  my $self = shift;
  $self->{'score'} = shift if(@_);
  return $self->{'score'};
}
transferdescriptionprevnextTop
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;
}
transformdescriptionprevnextTop
sub transform {
  my $self = shift;

  # catch for old style transform calls
if( !@_ || ( ref $_[0] && $_[0]->isa( "Bio::EnsEMBL::Slice" ))) { 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;
}
General documentation
LICENSETop
  Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license. For license details, please see /info/about/code_licence.html
CONTACTTop
  Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at <helpdesk@ensembl.org>.