File Coverage

Bio/SeqI.pm
Criterion Covered Total %
statement 6 17 35.2
branch 0 2 0.0
condition n/a
subroutine 2 6 33.3
pod 4 4 100.0
total 12 29 41.3


line stmt bran cond sub pod time code
1             #
2             # BioPerl module for Bio::SeqI
3             #
4             # Please direct questions and support issues to
5             #
6             # Cared for by Ewan Birney
7             #
8             # Copyright Ewan Birney
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::SeqI - [Developers] Abstract Interface of Sequence (with features)
17              
18             =head1 SYNOPSIS
19              
20             # Bio::SeqI is the interface class for sequences.
21              
22             # If you are a newcomer to bioperl, you should
23             # start with Bio::Seq documentation. This
24             # documentation is mainly for developers using
25             # Bioperl.
26              
27             # Bio::SeqI implements Bio::PrimarySeqI
28             $seq = $seqobj->seq(); # actual sequence as a string
29             $seqstr = $seqobj->subseq(10,50);
30              
31             # Bio::SeqI has annotationcollections
32              
33             $ann = $seqobj->annotation(); # annotation object
34              
35             # Bio::SeqI has sequence features
36             # features must implement Bio::SeqFeatureI
37              
38             @features = $seqobj->get_SeqFeatures(); # just top level
39             @features = $seqobj->get_all_SeqFeatures(); # descend into sub features
40              
41             =head1 DESCRIPTION
42              
43             Bio::SeqI is the abstract interface of annotated Sequences. These
44             methods are those which you can be guaranteed to get for any Bio::SeqI.
45             For most users of the package the documentation (and methods) in this
46             class are not at useful - this is a developers only class which
47             defines what methods have to be implemented by other Perl objects to
48             comply to the Bio::SeqI interface. Go "perldoc Bio::Seq" or "man
49             Bio::Seq" for more information.
50              
51             There aren't many method here, because too many complicated functions here
52             would prevent implementations which are just wrappers around a database or
53             similar delayed mechanisms.
54              
55             Most of the clever stuff happens inside the SeqFeatureI system.
56              
57             A good reference implementation is Bio::Seq which is a pure perl
58             implementation of this class with a lot of extra pieces for extra
59             manipulation. However, if you want to be able to use any sequence
60             object in your analysis, if you can do it just using these methods,
61             then you know you will be future proof and compatible with other
62             implementations of Seq.
63              
64             =head1 FEEDBACK
65              
66             =head2 Mailing Lists
67              
68             User feedback is an integral part of the evolution of this and other
69             Bioperl modules. Send your comments and suggestions preferably to one
70             of the Bioperl mailing lists. Your participation is much appreciated.
71              
72             bioperl-l@bioperl.org - General discussion
73             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
74              
75             =head2 Support
76              
77             Please direct usage questions or support issues to the mailing list:
78              
79             I
80              
81             rather than to the module maintainer directly. Many experienced and
82             reponsive experts will be able look at the problem and quickly
83             address it. Please include a thorough description of the problem
84             with code and data examples if at all possible.
85              
86             =head2 Reporting Bugs
87              
88             Report bugs to the Bioperl bug tracking system to help us keep track
89             the bugs and their resolution. Bug reports can be submitted via the
90             web:
91              
92             https://github.com/bioperl/bioperl-live/issues
93              
94             =head1 AUTHOR - Ewan Birney
95              
96             Email birney@ebi.ac.uk
97              
98              
99             =head1 APPENDIX
100              
101             The rest of the documentation details each of the object
102             methods. Internal methods are usually preceded with a _
103              
104             =cut
105              
106             #'
107             # Let the code begin...
108              
109              
110             package Bio::SeqI;
111 181     181   819 use strict;
  181         219  
  181         4874  
112              
113              
114             # Object preamble - inherits from Bio::PrimarySeqI
115              
116 181     181   617 use base qw(Bio::PrimarySeqI Bio::AnnotatableI Bio::FeatureHolderI);
  181         241  
  181         52091  
117              
118             =head2 get_SeqFeatures
119              
120             Title : get_SeqFeatures
121             Usage : my @feats = $seq->get_SeqFeatures();
122             Function: retrieve just the toplevel sequence features attached to this seq
123             Returns : array of Bio::SeqFeatureI objects
124             Args : none
125              
126             This method comes through extension of Bio::FeatureHolderI. See
127             L and L for more information.
128              
129             =head2 get_all_SeqFeatures
130              
131             Title : get_all_SeqFeatures
132             Usage : my @feats = $seq->get_all_SeqFeatures();
133             Function: returns all SeqFeatures, including sub SeqFeatures
134             Returns : an array of Bio::SeqFeatureI objects
135             Args : none
136              
137             This method comes through extension of Bio::FeatureHolderI. See
138             L and L for more information.
139              
140             =head2 feature_count
141              
142             Title : feature_count
143             Usage : my $count = $seq->feature_count();
144             Function: Return the number of SeqFeatures attached to a sequence
145             Returns : integer representing the number of SeqFeatures
146             Args : none
147              
148             This method comes through extension of Bio::FeatureHolderI. See
149             L for more information.
150              
151             =head2 seq
152              
153             Title : seq
154             Usage : my $string = $seq->seq();
155             Function: Retrieves the sequence string for the sequence object
156             Returns : string
157             Args : none
158              
159              
160             =cut
161              
162             sub seq {
163 0     0 1   my ($self) = @_;
164 0           $self->throw_not_implemented();
165             }
166              
167             =head2 write_GFF
168              
169             Title : write_GFF
170             Usage : $seq->write_GFF(\*FILEHANDLE);
171             Function: Convenience method to write out all the sequence features
172             in GFF format to the provided filehandle (STDOUT by default)
173             Returns : none
174             Args : [optional] filehandle to write to (default is STDOUT)
175              
176              
177             =cut
178              
179             sub write_GFF {
180 0     0 1   my ($self,$fh) = @_;
181              
182 0 0         $fh || do { $fh = \*STDOUT; };
  0            
183              
184 0           foreach my $sf ( $self->get_all_SeqFeatures() ) {
185 0           print $fh $sf->gff_string, "\n";
186             }
187              
188             }
189              
190             =head2 annotation
191              
192             Title : annotation
193             Usage : my $ann = $seq->annotation($seq_obj);
194             Function: retrieve the attached annotation object
195             Returns : Bio::AnnotationCollectionI or none;
196              
197             See L and L
198             for more information. This method comes through extension from
199             L.
200              
201             =head2 species
202              
203             Title : species
204             Usage :
205             Function: Gets or sets the species
206             Example : my $species = $seq->species();
207             Returns : Bio::Species object
208             Args : Bio::Species object or none;
209              
210             See L for more information
211              
212             =cut
213              
214             sub species {
215 0     0 1   my ($self) = @_;
216 0           $self->throw_not_implemented();
217             }
218              
219             =head2 primary_seq
220              
221             Title : primary_seq
222             Usage : my $primaryseq = $seq->primary_seq($newval)
223             Function: Retrieve the underlying Bio::PrimarySeqI object if available.
224             This is in the event one has a sequence with lots of features
225             but want to be able to narrow the object to just one with
226             the basics of a sequence (no features or annotations).
227             Returns : Bio::PrimarySeqI
228             Args : Bio::PrimarySeqI or none;
229              
230             See L for more information
231              
232             =cut
233              
234             sub primary_seq {
235 0     0 1   my ($self) = @_;
236 0           $self->throw_not_implemented;
237             }
238              
239             1;