|
0
|
1 # $Id: SequenceFactoryI.pm,v 1.6 2002/10/22 07:45:14 lapp Exp $
|
|
|
2 #
|
|
|
3 # BioPerl module for Bio::Factory::SequenceFactoryI
|
|
|
4 #
|
|
|
5 # Cared for by Jason Stajich <jason@bioperl.org>
|
|
|
6 #
|
|
|
7 # Copyright Jason Stajich
|
|
|
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::Factory::SequenceFactoryI - This interface allows for generic building of sequences in factories which create sequences (like SeqIO)
|
|
|
16
|
|
|
17 =head1 SYNOPSIS
|
|
|
18
|
|
|
19 # do not use this object directly it is an interface
|
|
|
20 # get a Bio::Factory::SequenceFactoryI object like
|
|
|
21
|
|
|
22 use Bio::Seq::SeqFactory;
|
|
|
23 my $seqbuilder = new Bio::Seq::SeqFactory('type' => 'Bio::PrimarySeq');
|
|
|
24
|
|
|
25 my $seq = $seqbuilder->create(-seq => 'ACTGAT',
|
|
|
26 -display_id => 'exampleseq');
|
|
|
27
|
|
|
28 print "seq is a ", ref($seq), "\n";
|
|
|
29
|
|
|
30 =head1 DESCRIPTION
|
|
|
31
|
|
|
32 Describe the interface here
|
|
|
33
|
|
|
34 =head1 FEEDBACK
|
|
|
35
|
|
|
36 =head2 Mailing Lists
|
|
|
37
|
|
|
38 User feedback is an integral part of the evolution of this and other
|
|
|
39 Bioperl modules. Send your comments and suggestions preferably to
|
|
|
40 the Bioperl mailing list. Your participation is much appreciated.
|
|
|
41
|
|
|
42 bioperl-l@bioperl.org - General discussion
|
|
|
43 http://bioperl.org/MailList.shtml - About the mailing lists
|
|
|
44
|
|
|
45 =head2 Reporting Bugs
|
|
|
46
|
|
|
47 Report bugs to the Bioperl bug tracking system to help us keep track
|
|
|
48 of the bugs and their resolution. Bug reports can be submitted via
|
|
|
49 email or the web:
|
|
|
50
|
|
|
51 bioperl-bugs@bioperl.org
|
|
|
52 http://bugzilla.bioperl.org/
|
|
|
53
|
|
|
54 =head1 AUTHOR - Jason Stajich
|
|
|
55
|
|
|
56 Email jason@bioperl.org
|
|
|
57
|
|
|
58 Describe contact details here
|
|
|
59
|
|
|
60 =head1 CONTRIBUTORS
|
|
|
61
|
|
|
62 Additional contributors names and emails here
|
|
|
63
|
|
|
64 =head1 APPENDIX
|
|
|
65
|
|
|
66 The rest of the documentation details each of the object methods.
|
|
|
67 Internal methods are usually preceded with a _
|
|
|
68
|
|
|
69 =cut
|
|
|
70
|
|
|
71
|
|
|
72 # Let the code begin...
|
|
|
73
|
|
|
74
|
|
|
75 package Bio::Factory::SequenceFactoryI;
|
|
|
76
|
|
|
77 use vars qw(@ISA);
|
|
|
78 use strict;
|
|
|
79 use Bio::Factory::ObjectFactoryI;
|
|
|
80
|
|
|
81 @ISA = qw(Bio::Factory::ObjectFactoryI);
|
|
|
82
|
|
|
83 =head2 create
|
|
|
84
|
|
|
85 Title : create
|
|
|
86 Usage : my $seq = $seqbuilder->create(-seq => 'CAGT',
|
|
|
87 -id => 'name');
|
|
|
88 Function: Instantiates new Bio::PrimarySeqI (or one of its child classes)
|
|
|
89 This object allows us to genericize the instantiation of sequence
|
|
|
90 objects.
|
|
|
91 Returns : Bio::PrimarySeqI
|
|
|
92 Args : initialization parameters specific to the type of sequence
|
|
|
93 object we want. Typically
|
|
|
94 -seq => $str,
|
|
|
95 -display_id => $name
|
|
|
96
|
|
|
97 =cut
|
|
|
98
|
|
|
99 1;
|
