|
0
|
1 # $Id: SeqAnalysisParserI.pm,v 1.12 2002/12/01 00:05:19 jason Exp $
|
|
|
2 #
|
|
|
3 # BioPerl module for Bio::SeqAnalysisParserI
|
|
|
4 #
|
|
|
5 # Cared for by Jason Stajich <jason@bioperl.org>,
|
|
|
6 # and Hilmar Lapp <hlapp@gmx.net>
|
|
|
7 #
|
|
|
8 # Copyright Jason Stajich, Hilmar Lapp
|
|
|
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::SeqAnalysisParserI - Sequence analysis output parser interface
|
|
|
17
|
|
|
18 =head1 SYNOPSIS
|
|
|
19
|
|
|
20 # get a SeqAnalysisParserI somehow, e.g. by
|
|
|
21 my $parser = Bio::Factory::SeqAnalysisParserFactory->get_parser(
|
|
|
22 '-input' => 'inputfile', '-method' => 'genscan');
|
|
|
23 while( my $feature = $parser->next_feature() ) {
|
|
|
24 print "Feature from ", $feature->start, " to ", $feature->end, "\n";
|
|
|
25 }
|
|
|
26
|
|
|
27 =head1 DESCRIPTION
|
|
|
28
|
|
|
29 SeqAnalysisParserI is a generic interface for describing sequence analysis
|
|
|
30 result parsers. Sequence analysis in this sense is a search for similarities
|
|
|
31 or the identification of features on the sequence, like a databank search or a
|
|
|
32 a gene prediction result.
|
|
|
33
|
|
|
34 The concept behind this interface is to have a generic interface in sequence
|
|
|
35 annotation pipelines (as used e.g. in high-throughput automated
|
|
|
36 sequence annotation). This interface enables plug-and-play for new analysis
|
|
|
37 methods and their corresponding parsers without the necessity for modifying
|
|
|
38 the core of the annotation pipeline. In this concept the annotation pipeline
|
|
|
39 has to rely on only a list of methods for which to process the results, and a
|
|
|
40 factory from which it can obtain the corresponding parser implementing this
|
|
|
41 interface.
|
|
|
42
|
|
|
43 See Bio::Factory::SeqAnalysisParserFactoryI and
|
|
|
44 Bio::Factory::SeqAnalysisParserFactory for interface and an implementation
|
|
|
45 of the corresponding factory.
|
|
|
46
|
|
|
47 =head1 FEEDBACK
|
|
|
48
|
|
|
49 =head2 Mailing Lists
|
|
|
50
|
|
|
51 User feedback is an integral part of the evolution of this
|
|
|
52 and other Bioperl modules. Send your comments and suggestions preferably
|
|
|
53 to one of the Bioperl mailing lists.
|
|
|
54 Your participation is much appreciated.
|
|
|
55
|
|
|
56 bioperl-l@bioperl.org - General discussion
|
|
|
57 http://bio.perl.org/MailList.html - About the mailing lists
|
|
|
58
|
|
|
59 =head2 Reporting Bugs
|
|
|
60
|
|
|
61 Report bugs to the Bioperl bug tracking system to help us keep track
|
|
|
62 the bugs and their resolution.
|
|
|
63 Bug reports can be submitted via email or the web:
|
|
|
64
|
|
|
65 bioperl-bugs@bio.perl.org
|
|
|
66 http://bugzilla.bioperl.org/
|
|
|
67
|
|
|
68 =head1 AUTHOR - Hilmar Lapp, Jason Stajich
|
|
|
69
|
|
|
70 Email Hilmar Lapp E<lt>hlapp@gmx.netE<gt>, Jason Stajich E<lt>jason@bioperl.orgE<gt>
|
|
|
71
|
|
|
72 =head1 APPENDIX
|
|
|
73
|
|
|
74 The rest of the documentation details each of the object methods.
|
|
|
75 Internal methods are usually preceded with a _
|
|
|
76
|
|
|
77 =cut
|
|
|
78
|
|
|
79 package Bio::SeqAnalysisParserI;
|
|
|
80 use strict;
|
|
|
81 use vars qw(@ISA);
|
|
|
82 use Bio::Root::RootI;
|
|
|
83 use Carp;
|
|
|
84 @ISA = qw(Bio::Root::RootI);
|
|
|
85
|
|
|
86 =head2 next_feature
|
|
|
87
|
|
|
88 Title : next_feature
|
|
|
89 Usage : $seqfeature = $obj->next_feature();
|
|
|
90 Function: Returns the next feature available in the analysis result, or
|
|
|
91 undef if there are no more features.
|
|
|
92 Example :
|
|
|
93 Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
|
|
|
94 more features.
|
|
|
95 Args : none
|
|
|
96
|
|
|
97 =cut
|
|
|
98
|
|
|
99 sub next_feature {
|
|
|
100 my ($self) = shift;
|
|
|
101 $self->throw_not_implemented();
|
|
|
102 }
|
|
|
103
|
|
|
104 1;
|
