File Coverage

Bio/Factory/SeqAnalysisParserFactoryI.pm
Criterion Covered Total %
statement 9 11 81.8
branch n/a
condition n/a
subroutine 3 4 75.0
pod 1 1 100.0
total 13 16 81.2


line stmt bran cond sub pod time code
1             #
2             # BioPerl module for Bio::Factory::SeqAnalysisParserFactoryI
3             #
4             # Please direct questions and support issues to
5             #
6             # Cared for by Jason Stajich ,
7             # and Hilmar Lapp
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              
17             Bio::Factory::SeqAnalysisParserFactoryI - interface describing objects capable
18             of creating SeqAnalysisParserI compliant parsers
19              
20             =head1 SYNOPSIS
21              
22             # initialize an object implementing this interface, e.g.
23             $factory = Bio::Factory::SeqAnalysisParserFactory->new();
24             # obtain a parser object
25             $parser = $factory->get_parser(-input=>$inputobj,
26             -params=>[@params],
27             -method => $method);
28             # $parser is an object implementing Bio::SeqAnalysisParserI
29             # annotate sequence with features produced by parser
30             while(my $feat = $parser->next_feature()) {
31             $seq->add_SeqFeature($feat);
32             }
33              
34             =head1 DESCRIPTION
35              
36             This is an interface for factory classes capable of instantiating
37             SeqAnalysisParserI implementing parsers.
38              
39             The concept behind the interface is a generic analysis result parsing
40             in high-throughput automated sequence annotation pipelines. See
41             L for more documentation of this concept.
42              
43             =head1 FEEDBACK
44              
45             =head2 Mailing Lists
46              
47             User feedback is an integral part of the evolution of this
48             and other Bioperl modules. Send your comments and suggestions preferably
49             to one of the Bioperl mailing lists.
50             Your participation is much appreciated.
51              
52             bioperl-l@bioperl.org - General discussion
53             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
54              
55             =head2 Support
56              
57             Please direct usage questions or support issues to the mailing list:
58              
59             I
60              
61             rather than to the module maintainer directly. Many experienced and
62             reponsive experts will be able look at the problem and quickly
63             address it. Please include a thorough description of the problem
64             with code and data examples if at all possible.
65              
66             =head2 Reporting Bugs
67              
68             Report bugs to the Bioperl bug tracking system to help us keep track
69             the bugs and their resolution. Bug reports can be submitted via the
70             web:
71              
72             https://github.com/bioperl/bioperl-live/issues
73              
74             =head1 AUTHOR - Hilmar Lapp, Jason Stajich
75              
76             Email Hilmar Lapp Ehlapp@gmx.netE, Jason Stajich Ejason@bioperl.orgE
77              
78             =head1 APPENDIX
79              
80             The rest of the documentation details each of the object
81             methods. Internal methods are usually preceded with a _
82              
83             =cut
84              
85             package Bio::Factory::SeqAnalysisParserFactoryI;
86 1     1   5 use strict;
  1         1  
  1         24  
87              
88 1     1   3 use Carp;
  1         1  
  1         44  
89              
90 1     1   4 use base qw(Bio::Root::RootI);
  1         1  
  1         81  
91              
92             =head2 get_parser
93              
94             Title : get_parser
95             Usage : $factory->get_parser(-input=>$inputobj,
96             [ -params=>[@params] ],
97             -method => $method)
98             Function: Creates and returns a parser object for the given input and method.
99             The type of input which is suitable depends on the implementation,
100             but a good-style implementation should allow both file names and
101             streams (filehandles).
102              
103             A particular implementation may not be able to create a parser for
104             the requested method. In this case it shall return undef.
105              
106             Parameters (-params argument) are passed on to the parser object
107             and therefore are specific to the parser to be created. An
108             implementation of this interface should make this argument optional.
109             Example :
110             Returns : A Bio::SeqAnalysisParserI implementing object.
111             Args : B - object/file where analysis results are coming from,
112             B - parameter to use when parsing/running analysis
113             B - method of analysis
114              
115             =cut
116              
117             sub get_parser {
118 0     0 1   my ( $self, @args) = @_;
119 0           $self->throw_not_implemented();
120             }
121              
122             1;