File Coverage

Bio/Seq/RichSeqI.pm
Criterion Covered Total %
statement 6 20 30.0
branch n/a
condition n/a
subroutine 2 9 22.2
pod 7 7 100.0
total 15 36 41.6


line stmt bran cond sub pod time code
1             #
2             # BioPerl module for Bio::Seq::RichSeqI
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::Seq::RichSeqI - interface for sequences from rich data sources, mostly databases
17              
18             =head1 SYNOPSIS
19              
20             @secondary = $richseq->get_secondary_accessions;
21             $division = $richseq->division;
22             $mol = $richseq->molecule;
23             @dates = $richseq->get_dates;
24             $seq_version = $richseq->seq_version;
25             $pid = $richseq->pid;
26             @keywords = $richseq->get_keywords;
27              
28             =head1 DESCRIPTION
29              
30             This interface extends the L interface to give additional
31             functionality to sequences with richer data sources, in particular from database
32             sequences (EMBL, GenBank and Swissprot). For a general implementation, please
33             see the documentation for L.
34              
35             =head1 FEEDBACK
36              
37             =head2 Mailing Lists
38              
39             User feedback is an integral part of the evolution of this
40             and other Bioperl modules. Send your comments and suggestions preferably
41             to one of the Bioperl mailing lists.
42             Your participation is much appreciated.
43              
44             bioperl-l@bioperl.org - General discussion
45             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
46              
47             =head2 Support
48              
49             Please direct usage questions or support issues to the mailing list:
50              
51             I
52              
53             rather than to the module maintainer directly. Many experienced and
54             reponsive experts will be able look at the problem and quickly
55             address it. Please include a thorough description of the problem
56             with code and data examples if at all possible.
57              
58             =head2 Reporting Bugs
59              
60             Report bugs to the Bioperl bug tracking system to help us keep track
61             the bugs and their resolution. Bug reports can be submitted via the
62             web:
63              
64             https://github.com/bioperl/bioperl-live/issues
65              
66             =head1 AUTHOR - Ewan Birney
67              
68             Email birney@ebi.ac.uk
69              
70             =head1 APPENDIX
71              
72             The rest of the documentation details each of the object methods. Internal
73             methods are usually preceded with a _
74              
75             =cut
76              
77              
78             # Let the code begin...
79              
80              
81             package Bio::Seq::RichSeqI;
82 37     37   200 use strict;
  37         44  
  37         975  
83              
84 37     37   244 use base qw(Bio::SeqI);
  37         47  
  37         8061  
85              
86              
87             =head2 get_secondary_accessions
88              
89             Title : get_secondary_accessions
90             Usage :
91             Function: Get the secondary accessions for a sequence.
92              
93             An implementation that allows modification of this array
94             property should provide the methods add_secondary_accession
95             and remove_secondary_accessions, with obvious purpose.
96              
97             Example :
98             Returns : an array of strings
99             Args : none
100              
101              
102             =cut
103              
104             sub get_secondary_accessions{
105 0     0 1   my ($self,@args) = @_;
106              
107 0           $self->throw("hit get_secondary_accessions in interface definition - error");
108              
109             }
110              
111              
112             =head2 division
113              
114             Title : division
115             Usage :
116             Function: Get (and set, depending on the implementation) the divison for
117             a sequence.
118              
119             Examples from GenBank are PLN (plants), PRI (primates), etc.
120             Example :
121             Returns : a string
122             Args :
123              
124              
125             =cut
126              
127             sub division{
128 0     0 1   my ($self,@args) = @_;
129              
130 0           $self->throw("hit division in interface definition - error");
131              
132             }
133              
134              
135             =head2 molecule
136              
137             Title : molecule
138             Usage :
139             Function: Get (and set, depending on the implementation) the molecule
140             type for the sequence.
141              
142             This is not necessarily the same as Bio::PrimarySeqI::alphabet(),
143             because it is databank-specific.
144             Example :
145             Returns : a string
146             Args :
147              
148              
149             =cut
150              
151             sub molecule{
152 0     0 1   my ($self,@args) = @_;
153              
154 0           $self->throw("hit molecule in interface definition - error");
155             }
156              
157             =head2 pid
158              
159             Title : pid
160             Usage :
161             Function: Get (and set, depending on the implementation) the PID property
162             for the sequence.
163             Example :
164             Returns : a string
165             Args :
166              
167              
168             =cut
169              
170             sub pid {
171 0     0 1   my ($self,@args) = @_;
172              
173 0           $self->throw("hit pid in interface definition - error");
174             }
175              
176             =head2 get_dates
177              
178             Title : get_dates
179             Usage :
180             Function: Get (and set, depending on the implementation) the dates the
181             databank entry specified for the sequence
182              
183             An implementation that allows modification of this array
184             property should provide the methods add_date and
185             remove_dates, with obvious purpose.
186              
187             Example :
188             Returns : an array of strings
189             Args :
190              
191              
192             =cut
193              
194             sub get_dates{
195 0     0 1   my ($self,@args) = @_;
196              
197 0           $self->throw("hit get_dates in interface definition - error");
198              
199             }
200              
201              
202             =head2 seq_version
203              
204             Title : seq_version
205             Usage :
206             Function: Get (and set, depending on the implementation) the version string
207             of the sequence.
208             Example :
209             Returns : a string
210             Args :
211             Note : this differs from Bio::PrimarySeq version() in that this explicitly
212             refers to the sequence record version one would find in a typical
213             sequence file. It is up to the implementation whether this is set
214             separately or falls back to the more generic Bio::Seq::version()
215              
216             =cut
217              
218             sub seq_version{
219 0     0 1   my ($self,@args) = @_;
220              
221 0           $self->throw("hit seq_version in interface definition - error");
222              
223             }
224              
225             =head2 get_keywords
226              
227             Title : get_keywords
228             Usage : $obj->get_keywords()
229             Function: Get the keywords for this sequence object.
230              
231             An implementation that allows modification of this array
232             property should provide the methods add_keyword and
233             remove_keywords, with obvious purpose.
234              
235             Returns : an array of strings
236             Args :
237              
238              
239             =cut
240              
241             sub get_keywords {
242 0     0 1   my ($self) = @_;
243 0           $self->throw("hit keywords in interface definition - error");
244             }
245              
246             1;