Filename | /Users/ap13/perl5/lib/perl5/Bio/Factory/SequenceStreamI.pm |
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0 | 0 | 0 | 0s | 0s | sequence_factory | Bio::Factory::SequenceStreamI::
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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 | |||||
16 | Bio::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 | |||||
28 | This interface is for describing objects which produces | ||||
29 | Bio::PrimarySeqI objects or processes Bio::PrimarySeqI objects to a | ||||
30 | data stream. | ||||
31 | |||||
32 | =head1 FEEDBACK | ||||
33 | |||||
34 | =head2 Mailing Lists | ||||
35 | |||||
36 | User feedback is an integral part of the evolution of this and other | ||||
37 | Bioperl modules. Send your comments and suggestions preferably to | ||||
38 | the 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 | |||||
45 | Please direct usage questions or support issues to the mailing list: | ||||
46 | |||||
47 | I<bioperl-l@bioperl.org> | ||||
48 | |||||
49 | rather than to the module maintainer directly. Many experienced and | ||||
50 | reponsive experts will be able look at the problem and quickly | ||||
51 | address it. Please include a thorough description of the problem | ||||
52 | with code and data examples if at all possible. | ||||
53 | |||||
54 | =head2 Reporting Bugs | ||||
55 | |||||
56 | Report bugs to the Bioperl bug tracking system to help us keep track | ||||
57 | of the bugs and their resolution. Bug reports can be submitted via the | ||||
58 | web: | ||||
59 | |||||
60 | https://github.com/bioperl/bioperl-live/issues | ||||
61 | |||||
62 | =head1 AUTHOR - Jason Stajich | ||||
63 | |||||
64 | Email jason@bioperl.org | ||||
65 | |||||
66 | =head1 APPENDIX | ||||
67 | |||||
68 | The rest of the documentation details each of the object methods. | ||||
69 | Internal methods are usually preceded with a _ | ||||
70 | |||||
71 | =cut | ||||
72 | |||||
73 | |||||
74 | # Let the code begin... | ||||
75 | |||||
76 | |||||
77 | package Bio::Factory::SequenceStreamI; | ||||
78 | 2 | 49µs | 2 | 52µs | # spent 38µs (24+14) within Bio::Factory::SequenceStreamI::BEGIN@78 which was called:
# once (24µs+14µs) by parent::import at line 78 # spent 38µs making 1 call to Bio::Factory::SequenceStreamI::BEGIN@78
# spent 14µs making 1 call to strict::import |
79 | |||||
80 | 2 | 147µs | 2 | 213µs | # spent 113µs (12+101) within Bio::Factory::SequenceStreamI::BEGIN@80 which was called:
# once (12µs+101µs) by parent::import at line 80 # 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 | |||||
100 | See L<Bio::Root::RootI> | ||||
101 | |||||
102 | =cut | ||||
103 | |||||
104 | sub 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 | |||||
118 | sub 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 | |||||
133 | sub sequence_factory{ | ||||
134 | shift->throw_not_implemented(); | ||||
135 | } | ||||
136 | |||||
137 | 1 | 2µs | 1; |