Bio::LiveSeq Exon
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Summary
Bio::LiveSeq::Exon - Range abstract class for LiveSeq
Package variables
No package variables defined.
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
get_TranscriptDescriptionCode
gene
No description
Code
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
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
}
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;
}
General documentation
AUTHOR - Joseph A.L. InsanaTop
Email: Insana@ebi.ac.uk, jinsana@gmx.net
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