|
0
|
1 # $Id: DNA.pm,v 1.9 2001/10/22 08:22:51 heikki Exp $
|
|
|
2 #
|
|
|
3 # bioperl module for Bio::LiveSeq::DNA
|
|
|
4 #
|
|
|
5 # Cared for by Joseph Insana <insana@ebi.ac.uk> <jinsana@gmx.net>
|
|
|
6 #
|
|
|
7 # Copyright Joseph Insana
|
|
|
8 #
|
|
|
9 # You may distribute this module under the same terms as perl itself
|
|
|
10 #
|
|
|
11 # POD documentation - main docs before the code
|
|
|
12
|
|
|
13 =head1 NAME
|
|
|
14
|
|
|
15 Bio::LiveSeq::DNA - DNA object for LiveSeq
|
|
|
16
|
|
|
17 =head1 SYNOPSIS
|
|
|
18
|
|
|
19 # documentation needed
|
|
|
20
|
|
|
21 =head1 DESCRIPTION
|
|
|
22
|
|
|
23 This holds the DNA sequence (or the RNA in the case of cDNA entries)
|
|
|
24 and is accessed by exons, genes, transcripts... objects
|
|
|
25
|
|
|
26 =head1 AUTHOR - Joseph A.L. Insana
|
|
|
27
|
|
|
28 Email: Insana@ebi.ac.uk, jinsana@gmx.net
|
|
|
29
|
|
|
30 Address:
|
|
|
31
|
|
|
32 EMBL Outstation, European Bioinformatics Institute
|
|
|
33 Wellcome Trust Genome Campus, Hinxton
|
|
|
34 Cambs. CB10 1SD, United Kingdom
|
|
|
35
|
|
|
36 =head1 APPENDIX
|
|
|
37
|
|
|
38 The rest of the documentation details each of the object
|
|
|
39 methods. Internal methods are usually preceded with a _
|
|
|
40
|
|
|
41 =cut
|
|
|
42
|
|
|
43 # Let the code begin...
|
|
|
44
|
|
|
45 package Bio::LiveSeq::DNA;
|
|
|
46 $VERSION=1.4;
|
|
|
47
|
|
|
48 # Version history:
|
|
|
49 # Mon Mar 20 19:21:22 GMT 2000 v.1.0 begun
|
|
|
50 # Tue Mar 21 14:20:30 GMT 2000 v.1.1 new() is now here, not inherited
|
|
|
51 # Wed Mar 22 19:43:20 GMT 2000 v.1.2 length override
|
|
|
52 # Thu Jun 22 20:02:39 BST 2000 v 1.3 valid() from SeqI now moved here, as override
|
|
|
53 # Wed Mar 28 17:01:59 BST 2001 v 1.4 changed croaks into throw
|
|
|
54
|
|
|
55 use strict;
|
|
|
56 use vars qw($VERSION @ISA);
|
|
|
57 use Bio::LiveSeq::SeqI 3.2; # uses SeqI, inherits from it
|
|
|
58 @ISA=qw(Bio::LiveSeq::SeqI);
|
|
|
59
|
|
|
60 =head2 new
|
|
|
61
|
|
|
62 Title : new
|
|
|
63 Usage : $dna = Bio::LiveSeq::DNA->new(-seq => "atcgaccaatggacctca",
|
|
|
64 -offset => 3 );
|
|
|
65
|
|
|
66 Function: generates a new Bio::LiveSeq::DNA
|
|
|
67 Returns : reference to a new object of class DNA
|
|
|
68 Errorcode -1
|
|
|
69 Args : a string
|
|
|
70 AND an optional offset to create nucleotide labels (default is 1, i.e.
|
|
|
71 starting the count of labels from "1") -> do not bother using it ->
|
|
|
72 it could be used by alternative loaders !EMBL format
|
|
|
73 NOTE : strand of DNA is set to 1 by default
|
|
|
74
|
|
|
75 =cut
|
|
|
76
|
|
|
77 sub new {
|
|
|
78 my ($thing, %args) = @_;
|
|
|
79 my $class = ref($thing) || $thing;
|
|
|
80 my (%empty,$obj);
|
|
|
81
|
|
|
82 if ($args{-seq}) {
|
|
|
83 $obj = $thing->string2chain($args{-seq},$args{-offset}); # inherited from ChainI
|
|
|
84 $obj = bless $obj, $class;
|
|
|
85 } else {
|
|
|
86 $obj=\%empty;
|
|
|
87 $obj = bless $obj, $class;
|
|
|
88 $obj->throw("$class not initialized properly");
|
|
|
89 }
|
|
|
90
|
|
|
91 $obj->{'alphabet'}='dna'; # set alphabet default
|
|
|
92 $obj->{'strand'}=1; # set strand default = 1
|
|
|
93 $obj->{'seq'}=$obj; # set seq field to itself
|
|
|
94
|
|
|
95 return $obj;
|
|
|
96 }
|
|
|
97
|
|
|
98 # START method
|
|
|
99 # it has to be redefined here because default from SeqI accesses field "start"
|
|
|
100 sub start {
|
|
|
101 my $self = shift;
|
|
|
102 return $self->{'begin'}; # the chain's start is called begin
|
|
|
103 }
|
|
|
104
|
|
|
105 # it is overridden to provide faster output
|
|
|
106 sub length {
|
|
|
107 my $self=shift;
|
|
|
108 return $self->chain_length();
|
|
|
109 }
|
|
|
110
|
|
|
111 # it is overridden to provide MUCH faster output
|
|
|
112 sub valid {
|
|
|
113 my $self=shift(@_);
|
|
|
114 return $self->label_exists(@_);
|
|
|
115 }
|
|
|
116
|
|
|
117 1;
|
