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1 | # | ||||
2 | # BioPerl module for Bio::SeqAnalysisParserI | ||||
3 | # | ||||
4 | # Please direct questions and support issues to <bioperl-l@bioperl.org> | ||||
5 | # | ||||
6 | # Cared for by Jason Stajich <jason@bioperl.org>, | ||||
7 | # and Hilmar Lapp <hlapp@gmx.net> | ||||
8 | # | ||||
9 | # Copyright Jason Stajich, Hilmar Lapp | ||||
10 | # | ||||
11 | # You may distribute this module under the same terms as perl itself | ||||
12 | |||||
13 | # POD documentation - main docs before the code | ||||
14 | |||||
15 | =head1 NAME | ||||
16 | |||||
17 | Bio::SeqAnalysisParserI - Sequence analysis output parser interface | ||||
18 | |||||
19 | =head1 SYNOPSIS | ||||
20 | |||||
21 | # get a SeqAnalysisParserI somehow, e.g. by | ||||
22 | my $parser = Bio::Factory::SeqAnalysisParserFactory->get_parser( | ||||
23 | '-input' => 'inputfile', '-method' => 'genscan'); | ||||
24 | while( my $feature = $parser->next_feature() ) { | ||||
25 | print "Feature from ", $feature->start, " to ", $feature->end, "\n"; | ||||
26 | } | ||||
27 | |||||
28 | =head1 DESCRIPTION | ||||
29 | |||||
30 | SeqAnalysisParserI is a generic interface for describing sequence analysis | ||||
31 | result parsers. Sequence analysis in this sense is a search for similarities | ||||
32 | or the identification of features on the sequence, like a databank search or a | ||||
33 | a gene prediction result. | ||||
34 | |||||
35 | The concept behind this interface is to have a generic interface in sequence | ||||
36 | annotation pipelines (as used e.g. in high-throughput automated | ||||
37 | sequence annotation). This interface enables plug-and-play for new analysis | ||||
38 | methods and their corresponding parsers without the necessity for modifying | ||||
39 | the core of the annotation pipeline. In this concept the annotation pipeline | ||||
40 | has to rely on only a list of methods for which to process the results, and a | ||||
41 | factory from which it can obtain the corresponding parser implementing this | ||||
42 | interface. | ||||
43 | |||||
44 | See Bio::Factory::SeqAnalysisParserFactoryI and | ||||
45 | Bio::Factory::SeqAnalysisParserFactory for interface and an implementation | ||||
46 | of the corresponding factory. | ||||
47 | |||||
48 | =head1 FEEDBACK | ||||
49 | |||||
50 | =head2 Mailing Lists | ||||
51 | |||||
52 | User feedback is an integral part of the evolution of this | ||||
53 | and other Bioperl modules. Send your comments and suggestions preferably | ||||
54 | to one of the Bioperl mailing lists. | ||||
55 | Your participation is much appreciated. | ||||
56 | |||||
57 | bioperl-l@bioperl.org - General discussion | ||||
58 | http://bioperl.org/wiki/Mailing_lists - About the mailing lists | ||||
59 | |||||
60 | =head2 Support | ||||
61 | |||||
62 | Please direct usage questions or support issues to the mailing list: | ||||
63 | |||||
64 | I<bioperl-l@bioperl.org> | ||||
65 | |||||
66 | rather than to the module maintainer directly. Many experienced and | ||||
67 | reponsive experts will be able look at the problem and quickly | ||||
68 | address it. Please include a thorough description of the problem | ||||
69 | with code and data examples if at all possible. | ||||
70 | |||||
71 | =head2 Reporting Bugs | ||||
72 | |||||
73 | Report bugs to the Bioperl bug tracking system to help us keep track | ||||
74 | the bugs and their resolution. Bug reports can be submitted via the | ||||
75 | web: | ||||
76 | |||||
77 | https://github.com/bioperl/bioperl-live/issues | ||||
78 | |||||
79 | =head1 AUTHOR - Hilmar Lapp, Jason Stajich | ||||
80 | |||||
81 | Email Hilmar Lapp E<lt>hlapp@gmx.netE<gt>, Jason Stajich E<lt>jason@bioperl.orgE<gt> | ||||
82 | |||||
83 | =head1 APPENDIX | ||||
84 | |||||
85 | The rest of the documentation details each of the object methods. | ||||
86 | Internal methods are usually preceded with a _ | ||||
87 | |||||
88 | =cut | ||||
89 | |||||
90 | package Bio::SeqAnalysisParserI; | ||||
91 | 2 | 30µs | 2 | 92µs | # spent 57µs (23+34) within Bio::SeqAnalysisParserI::BEGIN@91 which was called:
# once (23µs+34µs) by base::import at line 91 # spent 57µs making 1 call to Bio::SeqAnalysisParserI::BEGIN@91
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92 | 2 | 28µs | 2 | 114µs | # spent 62µs (11+51) within Bio::SeqAnalysisParserI::BEGIN@92 which was called:
# once (11µs+51µs) by base::import at line 92 # spent 62µs making 1 call to Bio::SeqAnalysisParserI::BEGIN@92
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93 | 2 | 53µs | 2 | 71µs | # spent 71µs (10+62) within Bio::SeqAnalysisParserI::BEGIN@93 which was called:
# once (10µs+62µs) by base::import at line 93 # spent 71µs making 1 call to Bio::SeqAnalysisParserI::BEGIN@93
# spent 62µs making 1 call to base::import, recursion: max depth 1, sum of overlapping time 62µs |
94 | |||||
95 | =head2 next_feature | ||||
96 | |||||
97 | Title : next_feature | ||||
98 | Usage : $seqfeature = $obj->next_feature(); | ||||
99 | Function: Returns the next feature available in the analysis result, or | ||||
100 | undef if there are no more features. | ||||
101 | Example : | ||||
102 | Returns : A Bio::SeqFeatureI implementing object, or undef if there are no | ||||
103 | more features. | ||||
104 | Args : none | ||||
105 | |||||
106 | =cut | ||||
107 | |||||
108 | sub next_feature { | ||||
109 | my ($self) = shift; | ||||
110 | $self->throw_not_implemented(); | ||||
111 | } | ||||
112 | |||||
113 | 1 | 2µs | 1; |