File Coverage

Bio/SeqAnalysisParserI.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::SeqAnalysisParserI
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::SeqAnalysisParserI - Sequence analysis output parser interface
18              
19             =head1 SYNOPSIS
20              
21             # get a SeqAnalysisParserI somehow, e.g. by
22             my $parser = Bio::Factory::SeqAnalysisParserFactory->get_parser(
23             '-input' => 'inputfile', '-method' => 'genscan');
24             while( my $feature = $parser->next_feature() ) {
25             print "Feature from ", $feature->start, " to ", $feature->end, "\n";
26             }
27              
28             =head1 DESCRIPTION
29              
30             SeqAnalysisParserI is a generic interface for describing sequence analysis
31             result parsers. Sequence analysis in this sense is a search for similarities
32             or the identification of features on the sequence, like a databank search or a
33             a gene prediction result.
34              
35             The concept behind this interface is to have a generic interface in sequence
36             annotation pipelines (as used e.g. in high-throughput automated
37             sequence annotation). This interface enables plug-and-play for new analysis
38             methods and their corresponding parsers without the necessity for modifying
39             the core of the annotation pipeline. In this concept the annotation pipeline
40             has to rely on only a list of methods for which to process the results, and a
41             factory from which it can obtain the corresponding parser implementing this
42             interface.
43              
44             See Bio::Factory::SeqAnalysisParserFactoryI and
45             Bio::Factory::SeqAnalysisParserFactory for interface and an implementation
46             of the corresponding factory.
47              
48             =head1 FEEDBACK
49              
50             =head2 Mailing Lists
51              
52             User feedback is an integral part of the evolution of this
53             and other Bioperl modules. Send your comments and suggestions preferably
54             to one of the Bioperl mailing lists.
55             Your participation is much appreciated.
56              
57             bioperl-l@bioperl.org - General discussion
58             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
59              
60             =head2 Support
61              
62             Please direct usage questions or support issues to the mailing list:
63              
64             I
65              
66             rather than to the module maintainer directly. Many experienced and
67             reponsive experts will be able look at the problem and quickly
68             address it. Please include a thorough description of the problem
69             with code and data examples if at all possible.
70              
71             =head2 Reporting Bugs
72              
73             Report bugs to the Bioperl bug tracking system to help us keep track
74             the bugs and their resolution. Bug reports can be submitted via the
75             web:
76              
77             https://github.com/bioperl/bioperl-live/issues
78              
79             =head1 AUTHOR - Hilmar Lapp, Jason Stajich
80              
81             Email Hilmar Lapp Ehlapp@gmx.netE, Jason Stajich Ejason@bioperl.orgE
82              
83             =head1 APPENDIX
84              
85             The rest of the documentation details each of the object methods.
86             Internal methods are usually preceded with a _
87              
88             =cut
89              
90             package Bio::SeqAnalysisParserI;
91 146     146   674 use strict;
  146         171  
  146         3367  
92 146     146   449 use Carp;
  146         148  
  146         7134  
93 146     146   510 use base qw(Bio::Root::RootI);
  146         307  
  146         11955  
94              
95             =head2 next_feature
96              
97             Title : next_feature
98             Usage : $seqfeature = $obj->next_feature();
99             Function: Returns the next feature available in the analysis result, or
100             undef if there are no more features.
101             Example :
102             Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
103             more features.
104             Args : none
105              
106             =cut
107              
108             sub next_feature {
109 0     0 1   my ($self) = shift;
110 0           $self->throw_not_implemented();
111             }
112              
113             1;