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1 # $Id: chadoxml.pm,v 1.2 2002/12/05 13:46:36 heikki Exp $
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2 #
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3 # BioPerl module for Bio::SeqIO::chadoxml
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4 #
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5 # Chris Mungall <cjm@fruitfly.org>
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6 #
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7 # You may distribute this module under the same terms as perl itself
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8
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9 # POD documentation - main docs before the code
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10
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11 =head1 NAME
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12
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13 Bio::SeqIO::chadoxml - chadoxml sequence input/output stream
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14
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15 =head1 SYNOPSIS
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16
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17 It is probably best not to use this object directly, but
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18 rather go through the SeqIO handler system. Go:
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19
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20 $stream = Bio::SeqIO->new(-file => $filename, -format => 'chadoxml');
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21
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22 while ( my $seq = $stream->next_seq() ) {
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23 # do something with $seq
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24 }
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25
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26 =head1 DESCRIPTION
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27
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28 This object can transform Bio::Seq objects to and from chadoxml flat
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29 file databases. CURRENTLY ONLY TO
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30
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31
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32 =head1 FEEDBACK
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33
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34 =head2 Mailing Lists
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35
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36 User feedback is an integral part of the evolution of this
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37 and other Bioperl modules. Send your comments and suggestions preferably
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38 to one of the Bioperl mailing lists.
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39 Your participation is much appreciated.
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40
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41 bioperl-l@bioperl.org - General discussion
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42 http://www.bioperl.org/MailList.shtml - About the mailing lists
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43
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44 =head2 Reporting Bugs
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45
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46 Report bugs to the Bioperl bug tracking system to help us keep track
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47 the bugs and their resolution.
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48 Bug reports can be submitted via email or the web:
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49
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50 bioperl-bugs@bio.perl.org
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51 http://bio.perl.org/bioperl-bugs/
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52
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53 =head1 AUTHOR - Chris Mungall
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54
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55 Email cjm@fruitfly.org
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56
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57 =head1 APPENDIX
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58
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59 The rest of the documentation details each of the object
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60 methods. Internal methods are usually preceded with a _
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61
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62 =cut
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63
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64 # Let the code begin...
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65
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66 package Bio::SeqIO::chadoxml;
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67 use Bio::SeqIO::chado;
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68 use vars qw(@ISA);
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69 use strict;
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70
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71 use Data::Stag::XMLWriter;
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72
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73 @ISA = qw(Bio::SeqIO::chado);
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74
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75 sub default_handler_class {
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76 return "Data::Stag::XMLWriter";
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77 }
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78
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79 1;
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