File Coverage

Bio/AnalysisParserI.pm

Criterion	Covered	Total	%
statement	6	8	75.0
branch			n/a
condition			n/a
subroutine	2	3	66.6
pod	1	1	100.0
total	9	12	75.0

line	stmt	sub	pod	time	code
1					#---------------------------------------------------------------
2					#
3					# BioPerl module Bio::AnalysisParserI
4					#
5					# Please direct questions and support issues to
6					#
7					# Cared for by Steve Chervitz
8					#
9					# Derived from Bio::SeqAnalysisParserI by Jason Stajich, Hilmar Lapp.
10					#
11					# You may distribute this module under the same terms as perl itself
12					#---------------------------------------------------------------
13
14					=head1 NAME
15
16					Bio::AnalysisParserI - Generic analysis output parser interface
17
18					=head1 SYNOPSIS
19
20					# get a AnalysisParserI somehow.
21					# Eventually, there may be an Bio::Factory::AnalysisParserFactory.
22					# For now a SearchIO object, an implementation of AnalysisParserI, can be created
23					# directly, as in the following:
24					my $parser = Bio::SearchIO->new(
25					'-file' => 'inputfile',
26					'-format' => 'blast');
27
28					while( my $result = $parser->next_result() ) {
29					print "Result: ", $result->analysis_method,
30					", Query: ", $result->query_name, "\n";
31
32					while( my $feature = $result->next_feature() ) {
33					print "Feature from ", $feature->start, " to ",
34					$feature->end, "\n";
35					}
36					}
37
38					=head1 DESCRIPTION
39
40					AnalysisParserI is a interface for describing generic analysis
41					result parsers. This module makes no assumption about the nature of
42					analysis being parsed, only that zero or more result sets can be
43					obtained from the input source.
44
45					This module was derived from Bio::SeqAnalysisParserI, the differences being
46
47					=over 4
48
49					=item 1. next_feature() was replaced with next_result().
50
51					Instead of flattening a stream containing potentially multiple
52					analysis results into a single set of features, AnalysisParserI
53					segments the stream in terms of analysis result sets
54					(Bio::AnalysisResultI objects). Each AnalysisResultI can then be
55					queried for its features (if any) as well as other information
56					about the result
57
58					=item 2. AnalysisParserI is a pure interface.
59
60					It does not inherit from Bio::Root::RootI and does not provide a new()
61					method. Implementations are free to choose how to implement it.
62
63					=back
64
65					=head2 Rationale (copied from Bio::SeqAnalysisParserI)
66
67					The concept behind this interface is to have a generic interface in sequence
68					annotation pipelines (as used e.g. in high-throughput automated
69					sequence annotation). This interface enables plug-and-play for new analysis
70					methods and their corresponding parsers without the necessity for modifying
71					the core of the annotation pipeline. In this concept the annotation pipeline
72					has to rely on only a list of methods for which to process the results, and a
73					factory from which it can obtain the corresponding parser implementing this
74					interface.
75
76					=head2 TODO
77
78					Create Bio::Factory::AnalysisParserFactoryI and
79					Bio::Factory::AnalysisParserFactory for interface and an implementation.
80					Note that this factory could return Bio::SearchIO-derived objects.
81
82					=head1 FEEDBACK
83
84					=head2 Mailing Lists
85
86					User feedback is an integral part of the evolution of this
87					and other Bioperl modules. Send your comments and suggestions preferably
88					to one of the Bioperl mailing lists.
89					Your participation is much appreciated.
90
91					bioperl-l@bioperl.org - General discussion
92					http://bioperl.org/wiki/Mailing_lists - About the mailing lists
93
94					=head2 Support
95
96					Please direct usage questions or support issues to the mailing list:
97
98					I
99
100					rather than to the module maintainer directly. Many experienced and
101					reponsive experts will be able look at the problem and quickly
102					address it. Please include a thorough description of the problem
103					with code and data examples if at all possible.
104
105					=head2 Reporting Bugs
106
107					Report bugs to the Bioperl bug tracking system to help us keep track
108					the bugs and their resolution. Bug reports can be submitted via the
109					web:
110
111					https://github.com/bioperl/bioperl-live/issues
112
113					=head1 AUTHOR - Steve Chervitz, Jason Stajich, Hilmar Lapp
114
115					Email sac@bioperl.org
116
117					Authors of Bio::SeqAnalysisParserI on which this module is based:
118					Email jason@bioperl.org
119					Email hlapp@gmx.net
120
121					=head1 COPYRIGHT
122
123					Copyright (c) 2001 Steve Chervitz. All Rights Reserved.
124
125					=head1 DISCLAIMER
126
127					This software is provided "as is" without warranty of any kind.
128
129					=head1 APPENDIX
130
131					The rest of the documentation details each of the object methods.
132					Internal methods are usually preceded with a _
133
134					=cut
135
136					package Bio::AnalysisParserI;
137	31	31		136	use strict;
	31			35
	31			798
138
139
140	31	31		96	use base qw(Bio::Root::RootI);
	31			31
	31			2254
141
142					=head2 next_result
143
144					Title : next_result
145					Usage : $result = $obj->next_result();
146					Function: Returns the next result available from the input, or
147					undef if there are no more results.
148					Example :
149					Returns : A Bio::Search::Result::ResultI implementing object,
150					or undef if there are no more results.
151					Args : none
152
153					=cut
154
155					sub next_result {
156	0	0	1		my ($self);
157	0				$self->throw_not_implemented;
158					}
159
160
161					1;
162					__END__