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

Filename/Users/ap13/perl5/lib/perl5/Bio/Factory/SequenceFactoryI.pm
StatementsExecuted 5 statements in 60µs
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11115µs28µsBio::Factory::SequenceFactoryI::::BEGIN@86Bio::Factory::SequenceFactoryI::BEGIN@86
1119µs424µsBio::Factory::SequenceFactoryI::::BEGIN@88Bio::Factory::SequenceFactoryI::BEGIN@88
Call graph for these subroutines as a Graphviz dot language file.
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Code
1#
2# BioPerl module for Bio::Factory::SequenceFactoryI
3#
4# Please direct questions and support issues to <bioperl-l@bioperl.org>
5#
6# Cared for by Jason Stajich <jason@bioperl.org>
7#
8# Copyright Jason Stajich
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
16Bio::Factory::SequenceFactoryI - This interface allows for generic building of sequences in factories which create sequences (like SeqIO)
17
18=head1 SYNOPSIS
19
20# do not use this object directly it is an interface
21# get a Bio::Factory::SequenceFactoryI object like
22
23 use Bio::Seq::SeqFactory;
24 my $seqbuilder = Bio::Seq::SeqFactory->new('-type' => 'Bio::PrimarySeq');
25
26 my $seq = $seqbuilder->create(-seq => 'ACTGAT',
27 -display_id => 'exampleseq');
28
29 print "seq is a ", ref($seq), "\n";
30
31=head1 DESCRIPTION
32
33A generic way to build Sequence objects via a pluggable factory. This
34reduces the amount of code that looks like
35
36 if( $type eq 'Bio::PrimarySeq' ) { ... }
37 elsif( $type eq 'Bio::Seq::RichSeq' ) { ... }
38
39=head1 FEEDBACK
40
41=head2 Mailing Lists
42
43User feedback is an integral part of the evolution of this and other
44Bioperl modules. Send your comments and suggestions preferably to
45the Bioperl mailing list. Your participation is much appreciated.
46
47 bioperl-l@bioperl.org - General discussion
48 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
49
50=head2 Support
51
52Please direct usage questions or support issues to the mailing list:
53
54I<bioperl-l@bioperl.org>
55
56rather than to the module maintainer directly. Many experienced and
57reponsive experts will be able look at the problem and quickly
58address it. Please include a thorough description of the problem
59with code and data examples if at all possible.
60
61=head2 Reporting Bugs
62
63Report bugs to the Bioperl bug tracking system to help us keep track
64of the bugs and their resolution. Bug reports can be submitted via the
65web:
66
67 https://github.com/bioperl/bioperl-live/issues
68
69=head1 AUTHOR - Jason Stajich
70
71Email jason-at-bioperl.org
72
73=head1 APPENDIX
74
75The rest of the documentation details each of the object methods.
76Internal methods are usually preceded with a _
77
78=cut
79
80
81# Let the code begin...
82
83
84package Bio::Factory::SequenceFactoryI;
85
86231µs242µs
# spent 28µs (15+13) within Bio::Factory::SequenceFactoryI::BEGIN@86 which was called: # once (15µs+13µs) by base::import at line 86
use strict;
# spent 28µs making 1 call to Bio::Factory::SequenceFactoryI::BEGIN@86 # spent 13µs making 1 call to strict::import
87
88227µs2424µs
# spent 424µs (9+415) within Bio::Factory::SequenceFactoryI::BEGIN@88 which was called: # once (9µs+415µs) by base::import at line 88
use base qw(Bio::Factory::ObjectFactoryI);
# spent 424µs making 1 call to Bio::Factory::SequenceFactoryI::BEGIN@88 # spent 415µs making 1 call to base::import, recursion: max depth 1, sum of overlapping time 415µs
89
90=head2 create
91
92 Title : create
93 Usage : my $seq = $seqbuilder->create(-seq => 'CAGT',
94 -id => 'name');
95 Function: Instantiates new Bio::PrimarySeqI (or one of its child classes)
96 This object allows us to genericize the instantiation of sequence
97 objects.
98 Returns : Bio::PrimarySeqI
99 Args : initialization parameters specific to the type of sequence
100 object we want. Typically
101 -seq => $str,
102 -display_id => $name
103
104=cut
105
10612µs1;