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For bin/pan_genome_post_analysis
  Run on Fri Mar 27 11:43:32 2015
Reported on Fri Mar 27 11:45:28 2015

Filename/Users/ap13/perl5/lib/perl5/Bio/SeqAnalysisParserI.pm
StatementsExecuted 7 statements in 113µs
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11123µs57µsBio::SeqAnalysisParserI::::BEGIN@91Bio::SeqAnalysisParserI::BEGIN@91
11111µs62µsBio::SeqAnalysisParserI::::BEGIN@92Bio::SeqAnalysisParserI::BEGIN@92
11110µs71µsBio::SeqAnalysisParserI::::BEGIN@93Bio::SeqAnalysisParserI::BEGIN@93
0000s0sBio::SeqAnalysisParserI::::next_featureBio::SeqAnalysisParserI::next_feature
Call graph for these subroutines as a Graphviz dot language file.
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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
17Bio::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
30SeqAnalysisParserI is a generic interface for describing sequence analysis
31result parsers. Sequence analysis in this sense is a search for similarities
32or the identification of features on the sequence, like a databank search or a
33a gene prediction result.
34
35The concept behind this interface is to have a generic interface in sequence
36annotation pipelines (as used e.g. in high-throughput automated
37sequence annotation). This interface enables plug-and-play for new analysis
38methods and their corresponding parsers without the necessity for modifying
39the core of the annotation pipeline. In this concept the annotation pipeline
40has to rely on only a list of methods for which to process the results, and a
41factory from which it can obtain the corresponding parser implementing this
42interface.
43
44See Bio::Factory::SeqAnalysisParserFactoryI and
45Bio::Factory::SeqAnalysisParserFactory for interface and an implementation
46of the corresponding factory.
47
48=head1 FEEDBACK
49
50=head2 Mailing Lists
51
52User feedback is an integral part of the evolution of this
53and other Bioperl modules. Send your comments and suggestions preferably
54 to one of the Bioperl mailing lists.
55Your 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
62Please direct usage questions or support issues to the mailing list:
63
64I<bioperl-l@bioperl.org>
65
66rather than to the module maintainer directly. Many experienced and
67reponsive experts will be able look at the problem and quickly
68address it. Please include a thorough description of the problem
69with code and data examples if at all possible.
70
71=head2 Reporting Bugs
72
73Report bugs to the Bioperl bug tracking system to help us keep track
74the bugs and their resolution. Bug reports can be submitted via the
75web:
76
77 https://github.com/bioperl/bioperl-live/issues
78
79=head1 AUTHOR - Hilmar Lapp, Jason Stajich
80
81Email Hilmar Lapp E<lt>hlapp@gmx.netE<gt>, Jason Stajich E<lt>jason@bioperl.orgE<gt>
82
83=head1 APPENDIX
84
85The rest of the documentation details each of the object methods.
86Internal methods are usually preceded with a _
87
88=cut
89
90package Bio::SeqAnalysisParserI;
91230µs292µs
# spent 57µs (23+34) within Bio::SeqAnalysisParserI::BEGIN@91 which was called: # once (23µs+34µs) by base::import at line 91
use strict;
# spent 57µs making 1 call to Bio::SeqAnalysisParserI::BEGIN@91 # spent 34µs making 1 call to strict::import
92228µs2114µs
# spent 62µs (11+51) within Bio::SeqAnalysisParserI::BEGIN@92 which was called: # once (11µs+51µs) by base::import at line 92
use Carp;
# spent 62µs making 1 call to Bio::SeqAnalysisParserI::BEGIN@92 # spent 51µs making 1 call to Exporter::import
93253µs271µs
# spent 71µs (10+62) within Bio::SeqAnalysisParserI::BEGIN@93 which was called: # once (10µs+62µs) by base::import at line 93
use base qw(Bio::Root::RootI);
# 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 = $obj->next_feature();
99 Function: Returns the next feature available in the analysis result, or
100 undef if there are no more features.
101 Example :
102 Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
103 more features.
104 Args : none
105
106=cut
107
108sub next_feature {
109 my ($self) = shift;
110 $self->throw_not_implemented();
111}
112
11312µs1;