File Coverage

Bio/Factory/SequenceStreamI.pm
Criterion Covered Total %
statement 6 9 66.6
branch n/a
condition n/a
subroutine 2 5 40.0
pod 3 3 100.0
total 11 17 64.7


line stmt bran cond sub pod time code
1             #
2             # BioPerl module for Bio::Factory::SequenceStreamI
3             #
4             # Please direct questions and support issues to
5             #
6             # Cared for by Jason Stajich
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
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 85     85   24815 use strict;
  85         124  
  85         2297  
79              
80 85     85   279 use base qw(Bio::Root::RootI);
  85         100  
  85         8582  
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
101              
102             =cut
103              
104             sub next_seq {
105 0     0 1   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 0     0 1   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 0     0 1   shift->throw_not_implemented();
135             }
136              
137             1;