File Coverage

Bio/SeqFeature/CollectionI.pm
Criterion Covered Total %
statement 9 11 81.8
branch n/a
condition n/a
subroutine 3 5 60.0
pod 2 2 100.0
total 14 18 77.7


line stmt bran cond sub pod time code
1             #
2             # BioPerl module for Bio::SeqFeature::CollectionI
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::SeqFeature::CollectionI - An interface for a collection of SeqFeatureI objects.
17              
18             =head1 SYNOPSIS
19              
20              
21             # get a Bio::SeqFeature::CollectionI somehow
22             # perhaps a Bio::SeqFeature::Collection
23              
24              
25             use Bio::SeqFeature::Collection;
26             my $collection = Bio::SeqFeature::Collection->new();
27             $collection->add_features(\@featurelist);
28              
29              
30             $collection->features(-attributes =>
31             [ { 'location' => Bio::Location::Simple->new
32             (-start=> 1, -end => 300) ,
33             'overlaps' }]);
34              
35             =head1 DESCRIPTION
36              
37             This interface describes the basic methods needed for a collection of Sequence Features.
38              
39             =head1 FEEDBACK
40              
41             =head2 Mailing Lists
42              
43             User feedback is an integral part of the evolution of this and other
44             Bioperl modules. Send your comments and suggestions preferably to
45             the Bioperl mailing list. Your participation is much appreciated.
46              
47             bioperl-l@bioperl.org - General discussion
48             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
49              
50             =head2 Support
51              
52             Please direct usage questions or support issues to the mailing list:
53              
54             I
55              
56             rather than to the module maintainer directly. Many experienced and
57             reponsive experts will be able look at the problem and quickly
58             address it. Please include a thorough description of the problem
59             with code and data examples if at all possible.
60              
61             =head2 Reporting Bugs
62              
63             Report bugs to the Bioperl bug tracking system to help us keep track
64             of the bugs and their resolution. Bug reports can be submitted via the
65             web:
66              
67             https://github.com/bioperl/bioperl-live/issues
68              
69             =head1 AUTHOR - Jason Stajich
70              
71             Email jason@bioperl.org
72              
73             =head1 APPENDIX
74              
75             The rest of the documentation details each of the object methods.
76             Internal methods are usually preceded with a _
77              
78             =cut
79              
80              
81             # Let the code begin...
82              
83              
84             package Bio::SeqFeature::CollectionI;
85 3     3   12 use strict;
  3         6  
  3         60  
86 3     3   6 use Carp;
  3         3  
  3         123  
87              
88 3     3   9 use base qw(Bio::Root::RootI);
  3         3  
  3         252  
89              
90              
91             =head2 add_features
92              
93             Title : add_features
94             Usage : $collection->add_features(\@features);
95             Function:
96             Returns : number of features added
97             Args : arrayref of Bio::SeqFeatureI objects to index
98              
99             =cut
100              
101             sub add_features{
102 0     0 1   shift->throw_not_implemented();
103             }
104              
105              
106             =head2 features
107              
108             Title : features
109             Usage : my @f = $collection->features(@args);
110             Returns : a list of Bio::SeqFeatureI objects
111             Args : see below
112             Status : public
113              
114             This routine will retrieve features associated with this collection
115             object. It can be used to return all features, or a subset based on
116             their type, location, or attributes.
117              
118             -types List of feature types to return. Argument is an array
119             of Bio::Das::FeatureTypeI objects or a set of strings
120             that can be converted into FeatureTypeI objects.
121              
122             -callback A callback to invoke on each feature. The subroutine
123             will be passed to each Bio::SeqFeatureI object in turn.
124              
125             -attributes A hash reference containing attributes to match.
126              
127             The -attributes argument is a hashref containing one or more attributes
128             to match against:
129              
130             -attributes => { Gene => 'abc-1',
131             Note => 'confirmed' }
132              
133             Attribute matching is simple exact string matching, and multiple
134             attributes are ANDed together. See L for a
135             more sophisticated take on this.
136              
137             If one provides a callback, it will be invoked on each feature in
138             turn. If the callback returns a false value, iteration will be
139             interrupted. When a callback is provided, the method returns undef.
140              
141             =cut
142              
143             sub features{
144 0     0 1   shift->throw_not_implemented();
145             }
146              
147             1;