Bio/LiveSeq/DNA.pm

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