t/AlignIO/AlignIO.t: fix number of tests in plan (fixup c523e6bed866)
[bioperl-live.git] / Bio / SeqIO / chaosxml.pm
blob3e952733bfbabaa11ee68c01b58de095f18f51d7
2 # BioPerl module for Bio::SeqIO::chaosxml
4 # Chris Mungall <cjm@fruitfly.org>
6 # You may distribute this module under the same terms as perl itself
8 # POD documentation - main docs before the code
10 =head1 NAME
12 Bio::SeqIO::chaosxml - chaosxml sequence input/output stream
14 =head1 SYNOPSIS
16 #In general you will not want to use this module directly;
17 #use the chaosxml format via SeqIO
19 $outstream = Bio::SeqIO->new(-file => $filename, -format => 'chaosxml');
21 while ( my $seq = $instream->next_seq() ) {
22 $outstream->write_seq($seq);
25 =head1 DESCRIPTION
27 This object can transform Bio::Seq objects to and from chaos files.
29 B<CURRENTLY WRITE ONLY>
31 ChaosXML is an XML mapping of the chado relational database; for more
32 information, see http://www.fruitfly.org/chaos-xml
34 Chaos can have other syntaxes than XML (eg S-Expressions, Indented text)
36 See L<Bio::SeqIO::chaos> for a full description
39 =head1 VERY VERY IMPORTANT
41 !!!!!!!!!!!CHADO AND CHAOS USE INTERBASE COORDINATES!!!!!!!!!!!!!!!!
43 =head1 FEEDBACK
45 =head2 Mailing Lists
47 User feedback is an integral part of the evolution of this and other
48 Bioperl modules. Send your comments and suggestions preferably to one
49 of the Bioperl mailing lists. Your participation is much appreciated.
51 bioperl-l@bioperl.org - General discussion
52 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
54 =head2 Support
56 Please direct usage questions or support issues to the mailing list:
58 I<bioperl-l@bioperl.org>
60 rather than to the module maintainer directly. Many experienced and
61 reponsive experts will be able look at the problem and quickly
62 address it. Please include a thorough description of the problem
63 with code and data examples if at all possible.
65 =head2 Reporting Bugs
67 Report bugs to the Bioperl bug tracking system to help us keep track
68 the bugs and their resolution. Bug reports can be submitted via the web:
70 https://github.com/bioperl/bioperl-live/issues
72 =head1 AUTHOR - Chris Mungall
74 Email cjm@fruitfly.org
76 =head1 APPENDIX
78 The rest of the documentation details each of the object
79 methods. Internal methods are usually preceded with a _
81 =cut
83 # Let the code begin...
85 package Bio::SeqIO::chaosxml;
86 use strict;
88 use Data::Stag::XMLWriter;
90 use base qw(Bio::SeqIO::chaos);
92 sub default_handler_class {
93 return Data::Stag->getformathandler('xml');