File Coverage

Bio/SeqEvolution/EvolutionI.pm
Criterion Covered Total %
statement 6 9 66.6
branch n/a
condition n/a
subroutine 2 5 40.0
pod 3 3 100.0
total 11 17 64.7


line stmt bran cond sub pod time code
1             #
2             # BioPerl module for Bio::SeqEvolution::EvolutionI
3             #
4             # Please direct questions and support issues to
5             #
6             # Cared for by Heikki Lehvaslaiho
7             #
8             # Copyright Heikki Lehvaslaiho
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::SeqEvolution::EvolutionI - the interface for evolving sequences
17              
18             =head1 SYNOPSIS
19              
20             # not an instantiable class
21              
22             =head1 DESCRIPTION
23              
24             This is the interface that all classes that mutate sequence objects in
25             constant fashion must implement. A good example is
26             Bio::SeqEvolution::DNAPoint.
27              
28             =head1 FEEDBACK
29              
30             =head2 Mailing Lists
31              
32             User feedback is an integral part of the evolution of this and other
33             Bioperl modules. Send your comments and suggestions preferably to
34             the Bioperl mailing list. Your participation is much appreciated.
35              
36             bioperl-l@bioperl.org - General discussion
37             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
38              
39             =head2 Support
40              
41             Please direct usage questions or support issues to the mailing list:
42              
43             I
44              
45             rather than to the module maintainer directly. Many experienced and
46             reponsive experts will be able look at the problem and quickly
47             address it. Please include a thorough description of the problem
48             with code and data examples if at all possible.
49              
50             =head2 Reporting Bugs
51              
52             Report bugs to the Bioperl bug tracking system to help us keep track
53             of the bugs and their resolution. Bug reports can be submitted via the
54             web:
55              
56             https://github.com/bioperl/bioperl-live/issues
57              
58             =head1 AUTHOR
59              
60             Heikki Lehvaslaiho Eheikki at bioperl dot orgE
61              
62             =head1 CONTRIBUTORS
63              
64             Additional contributor's names and emails here
65              
66             =head1 APPENDIX
67              
68             The rest of the documentation details each of the object methods.
69             Internal methods are usually preceded with a _
70              
71             =cut
72              
73              
74             # Let the code begin...
75              
76              
77             package Bio::SeqEvolution::EvolutionI;
78 1     1   5 use strict;
  1         1  
  1         27  
79              
80 1     1   4 use base qw(Bio::Root::RootI);
  1         1  
  1         109  
81              
82             =head2 annotation
83              
84             Title : annotation
85             Usage : $obj->annotation($newval)
86             Function: Get the annotation collection for this annotatable object.
87             Example :
88             Returns : a Bio::AnnotationCollectionI implementing object, or undef
89             Args : on set, new value (a Bio::AnnotationCollectionI
90             implementing object, optional) (an implementation may not
91             support changing the annotation collection)
92              
93             See L
94              
95             =cut
96              
97              
98             =head2 seq
99              
100             Title : seq
101             Usage : $obj->seq($newval)
102             Function: Set the sequence object for the original sequence
103             Returns : The sequence object
104             Args : newvalue (optional)
105              
106             Setting this will reset mutation and generated mutation counters.
107              
108             =cut
109              
110 0     0 1   sub seq { shift->throw_not_implemented(); }
111              
112             =head2 next_seq
113              
114             Title : next_seq
115             Usage : $obj->next_seq
116             Function: Evolve the reference sequence to desired level
117             Returns : A new sequence object mutated from the reference sequence
118             Args : -
119              
120             =cut
121              
122 0     0 1   sub next_seq{ shift->throw_not_implemented(); }
123              
124              
125             =head2 mutate
126              
127             Title : mutate
128             Usage : $obj->mutate
129             Function: mutate the sequence at the given location according to the model
130             Returns : true
131             Args : integer, start location of the mutation, required argument
132              
133             Called from next_seq().
134              
135             =cut
136              
137 0     0 1   sub mutate { shift->throw_not_implemented(); }
138              
139              
140             1;