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 bran cond 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   139 use strict;
  31         37  
  31         858  
138              
139              
140 31     31   97 use base qw(Bio::Root::RootI);
  31         29  
  31         2247  
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__