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For bin/pan_genome_post_analysis
  Run on Fri Mar 27 11:43:32 2015
Reported on Fri Mar 27 11:45:50 2015

Filename/Users/ap13/perl5/lib/perl5/Bio/Factory/SequenceStreamI.pm
StatementsExecuted 5 statements in 198µs
Subroutines
Calls P F Exclusive
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Time
Subroutine
11124µs38µsBio::Factory::SequenceStreamI::::BEGIN@78Bio::Factory::SequenceStreamI::BEGIN@78
11112µs113µsBio::Factory::SequenceStreamI::::BEGIN@80Bio::Factory::SequenceStreamI::BEGIN@80
0000s0sBio::Factory::SequenceStreamI::::next_seqBio::Factory::SequenceStreamI::next_seq
0000s0sBio::Factory::SequenceStreamI::::sequence_factoryBio::Factory::SequenceStreamI::sequence_factory
0000s0sBio::Factory::SequenceStreamI::::write_seqBio::Factory::SequenceStreamI::write_seq
Call graph for these subroutines as a Graphviz dot language file.
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Code
1#
2# BioPerl module for Bio::Factory::SequenceStreamI
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::SequenceStreamI - Interface describing the basics of a Sequence Stream.
17
18=head1 SYNOPSIS
19
20 # get a SequenceStreamI object somehow like with SeqIO
21 use Bio::SeqIO;
22 my $in = Bio::SeqIO->new(-file => '< fastafile');
23 while( my $seq = $in->next_seq ) {
24 }
25
26=head1 DESCRIPTION
27
28This interface is for describing objects which produces
29Bio::PrimarySeqI objects or processes Bio::PrimarySeqI objects to a
30data stream.
31
32=head1 FEEDBACK
33
34=head2 Mailing Lists
35
36User feedback is an integral part of the evolution of this and other
37Bioperl modules. Send your comments and suggestions preferably to
38the Bioperl mailing list. Your participation is much appreciated.
39
40 bioperl-l@bioperl.org - General discussion
41 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
42
43=head2 Support
44
45Please direct usage questions or support issues to the mailing list:
46
47I<bioperl-l@bioperl.org>
48
49rather than to the module maintainer directly. Many experienced and
50reponsive experts will be able look at the problem and quickly
51address it. Please include a thorough description of the problem
52with code and data examples if at all possible.
53
54=head2 Reporting Bugs
55
56Report bugs to the Bioperl bug tracking system to help us keep track
57of the bugs and their resolution. Bug reports can be submitted via the
58web:
59
60 https://github.com/bioperl/bioperl-live/issues
61
62=head1 AUTHOR - Jason Stajich
63
64Email jason@bioperl.org
65
66=head1 APPENDIX
67
68The rest of the documentation details each of the object methods.
69Internal methods are usually preceded with a _
70
71=cut
72
73
74# Let the code begin...
75
76
77package Bio::Factory::SequenceStreamI;
78249µs252µs
# spent 38µs (24+14) within Bio::Factory::SequenceStreamI::BEGIN@78 which was called: # once (24µs+14µs) by parent::import at line 78
use strict;
# spent 38µs making 1 call to Bio::Factory::SequenceStreamI::BEGIN@78 # spent 14µs making 1 call to strict::import
79
802147µs2213µs
# spent 113µs (12+101) within Bio::Factory::SequenceStreamI::BEGIN@80 which was called: # once (12µs+101µs) by parent::import at line 80
use base qw(Bio::Root::RootI);
# spent 113µs making 1 call to Bio::Factory::SequenceStreamI::BEGIN@80 # spent 101µs making 1 call to base::import
81
82=head2 next_seq
83
84 Title : next_seq
85 Usage : $seq = stream->next_seq
86 Function: Reads the next sequence object from the stream and returns it.
87
88 Certain driver modules may encounter entries in the stream that
89 are either misformatted or that use syntax not yet understood
90 by the driver. If such an incident is recoverable, e.g., by
91 dismissing a feature of a feature table or some other non-mandatory
92 part of an entry, the driver will issue a warning. In the case
93 of a non-recoverable situation an exception will be thrown.
94 Do not assume that you can resume parsing the same stream after
95 catching the exception. Note that you can always turn recoverable
96 errors into exceptions by calling $stream->verbose(2).
97 Returns : a Bio::Seq sequence object
98 Args : none
99
100See L<Bio::Root::RootI>
101
102=cut
103
104sub next_seq {
105 shift->throw_not_implemented();
106}
107
108=head2 write_seq
109
110 Title : write_seq
111 Usage : $stream->write_seq($seq)
112 Function: writes the $seq object into the stream
113 Returns : 1 for success and 0 for error
114 Args : Bio::Seq object
115
116=cut
117
118sub write_seq {
119 shift->throw_not_implemented();
120}
121
122=head2 sequence_factory
123
124 Title : sequence_factory
125 Usage : $seqio->sequence_factory($seqfactory)
126 Function: Get the Bio::Factory::SequenceFactoryI
127 Returns : Bio::Factory::SequenceFactoryI
128 Args : none
129
130
131=cut
132
133sub sequence_factory{
134 shift->throw_not_implemented();
135}
136
13712µs1;