Bio::LiveSeq Exon
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Summary
Bio::LiveSeq::Exon - Range abstract class for LiveSeq
Package variables
No package variables defined.
Included modules
Bio::LiveSeq::Range 1 .2
Inherit
Bio::LiveSeq::Range
Synopsis
  # documentation needed
Description
Class for EXON objects. They consist of a beginlabel, an endlabel (both
referring to a LiveSeq DNA object) and a strand.
The strand could be 1 (forward strand, default), -1 (reverse strand).
Methods
gene
No description
Code
get_TranscriptDescriptionCode
Methods description
get_Transcriptcode    nextTop
  Title   : get_Transcript
  Usage   : $transcript = $obj->get_Transcript()
  Function: retrieves the reference to the object of class Transcript (if any)
            attached to a LiveSeq object
  Returns : object reference
  Args    : none
  Note    : only Exons that compose a Transcript (i.e. those created out of
            a CDS Entry-Feature) will have an attached Transcript
Methods code
genedescriptionprevnextTop
sub gene {
  my ($self,$value) = @_;
  if (defined $value) {
    $self->{'gene'} = $value;
  }
  unless (exists $self->{'gene'}) {
    unless (exists $self->get_Transcript->{'gene'}) {
      return (0);
    } else {
      return ($self->get_Transcript->{'gene'});
    }
  } else {
    return $self->{'gene'};
  }
}

1;
}
get_TranscriptdescriptionprevnextTop
sub get_Transcript {
  my $self=shift;
  return ($self->{'transcript'}); # this is set on all Exons a Transcript is made of when Transcript->new is called
}

# this checks if the attached Transcript has a Gene object attached
}
General documentation
AUTHOR - Joseph A.L. InsanaTop
Email: Insana@ebi.ac.uk, jinsana@gmx.net
Address: 
     EMBL Outstation, European Bioinformatics Institute
     Wellcome Trust Genome Campus, Hinxton
     Cambs. CB10 1SD, United Kingdom
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
newTop
  Title   : new
  Usage   : $exon1 = Bio::LiveSeq::Exon-> new(-seq => $objref,
					      -start => $startlabel,
					      -end => $endlabel, -strand => 1);

  Function: generates a new Bio::LiveSeq::Exon
  Returns : reference to a new object of class Exon
  Errorcode -1
  Args    : two labels and an integer