Bio/LiveSeq/DNA.pm

   1 # $Id$
   2 #
   3 # bioperl module for Bio::LiveSeq::DNA
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Joseph Insana <insana@ebi.ac.uk> <jinsana@gmx.net>
   8 #
   9 # Copyright Joseph Insana
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12 #
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::LiveSeq::DNA - DNA object for LiveSeq
  18
  19 =head1 SYNOPSIS
  20
  21   # documentation needed
  22
  23 =head1 DESCRIPTION
  24
  25 This holds the DNA sequence (or the RNA in the case of cDNA entries)
  26 and is accessed by exons, genes, transcripts... objects
  27
  28 =head1 AUTHOR - Joseph A.L. Insana
  29
  30 Email:  Insana@ebi.ac.uk, jinsana@gmx.net
  31
  32 =head1 APPENDIX
  33
  34 The rest of the documentation details each of the object
  35 methods. Internal methods are usually preceded with a _
  36
  37 =cut
  38
  39 # Let the code begin...
  40
  41 package Bio::LiveSeq::DNA;
  42
  43 use strict;
  44 use base qw(Bio::LiveSeq::SeqI);
  45
  46 =head2 new
  47
  48   Title   : new
  49   Usage   : $dna = Bio::LiveSeq::DNA->new(-seq => "atcgaccaatggacctca",
  50                                           -offset => 3 );
  51
  52   Function: generates a new Bio::LiveSeq::DNA
  53   Returns : reference to a new object of class DNA
  54   Errorcode -1
  55   Args    : a string
  56         AND an optional offset to create nucleotide labels (default is 1, i.e.
  57             starting the count of labels from "1") -> do not bother using it ->
  58             it could be used by alternative loaders !EMBL format
  59   NOTE    : strand of DNA is set to 1 by default
  60
  61 =cut
  62
  63 sub new {
  64   my ($thing, %args) = @_;
  65   my $class = ref($thing) || $thing;
  66   my (%empty,$obj);
  67
  68   if ($args{-seq}) {
  69     $obj = $thing->string2chain($args{-seq},$args{-offset}); # inherited from ChainI
  70     $obj = bless $obj, $class;
  71   } else {
  72     $obj=\%empty;
  73     $obj = bless $obj, $class;
  74     $obj->throw("$class not initialized properly");
  75   }
  76
  77   $obj->{'alphabet'}='dna'; # set alphabet default
  78   $obj->{'strand'}=1; # set strand default = 1
  79   $obj->{'seq'}=$obj; # set seq field to itself
  80
  81   return $obj;
  82 }
  83
  84 # START method
  85 # it has to be redefined here because default from SeqI accesses field "start"
  86 sub start {
  87   my $self = shift;
  88   return $self->{'begin'}; # the chain's start is called begin
  89 }
  90
  91 # it is overridden to provide faster output
  92 sub length {
  93   my $self=shift;
  94   return $self->chain_length();
  95 }
  96
  97 # it is overridden to provide MUCH faster output
  98 sub valid {
  99   my $self=shift(@_);
 100   return $self->label_exists(@_);
 101 }
 102
 103 1;