Bio::LiveSeq DNA
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Summary
Bio::LiveSeq::DNA - DNA object for LiveSeq
Package variables
No package variables defined.
Inherit
Bio::LiveSeq::SeqI
Synopsis
  # documentation needed
Description
This holds the DNA sequence (or the RNA in the case of cDNA entries)
and is accessed by exons, genes, transcripts... objects
Methods
newDescriptionCode
start
No description
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length
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valid
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Code
Methods description
newcode    nextTop
  Title   : new
Usage : $dna = Bio::LiveSeq::DNA->new(-seq => "atcgaccaatggacctca",
-offset => 3 );
Function: generates a new Bio::LiveSeq::DNA Returns : reference to a new object of class DNA Errorcode -1 Args : a string AND an optional offset to create nucleotide labels (default is 1, i.e. starting the count of labels from "1") -> do not bother using it -> it could be used by alternative loaders !EMBL format NOTE : strand of DNA is set to 1 by default
Methods code
newdescriptionprevnextTop
sub new {
  my ($thing, %args) = @_;
  my $class = ref($thing) || $thing;
  my (%empty,$obj);

  if ($args{-seq}) {
    $obj = $thing->string2chain($args{-seq},$args{-offset}); # inherited from ChainI
$obj = bless $obj, $class; } else { $obj=\%empty; $obj = bless $obj, $class; $obj->throw("$class not initialized properly"); } $obj->{'alphabet'}='dna'; # set alphabet default
$obj->{'strand'}=1; # set strand default = 1
$obj->{'seq'}=$obj; # set seq field to itself
return $obj; } # START method
# it has to be redefined here because default from SeqI accesses field "start"
}
startdescriptionprevnextTop
sub start {
  my $self = shift;
  return $self->{'begin'}; # the chain's start is called begin
} # it is overridden to provide faster output
}
lengthdescriptionprevnextTop
sub length {
  my $self=shift;
  return $self->chain_length();
}

# it is overridden to provide MUCH faster output
}
validdescriptionprevnextTop
sub valid {
  my $self=shift(@_);
  return $self->label_exists(@_);
}

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 _