File Coverage

Bio/Seq/LargeSeqI.pm
Criterion Covered Total %
statement 6 8 75.0
branch n/a
condition n/a
subroutine 2 3 66.6
pod 1 1 100.0
total 9 12 75.0


line stmt bran cond sub pod time code
1             #
2             # BioPerl module for Bio::Seq::LargeSeqI
3             #
4             # Please direct questions and support issues to
5             #
6             # Cared for by Albert Vilella
7             #
8             # Copyright Albert Vilella
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::LargeSeqI - Interface class for sequences that cache their
17             residues in a temporary file
18              
19             =head1 SYNOPSIS
20              
21             #
22              
23             =head1 DESCRIPTION
24              
25             The interface class defines a group of sequence classes that do not
26             keep their sequence information in memory but store it in a file. This
27             makes it possible to work with very large files even with limited RAM.
28              
29             The most important consequence of file caching for sequences is that
30             you do not want to inspect the sequence unless absolutely
31             necessary. These sequences typically override the length() method not
32             to check the sequence.
33              
34             The seq() method is not resetable, if you want to add to the end of the
35             sequence you have to use add_sequence_as_string(), for any other sequence changes you'll
36             have to create a new object.
37              
38             =head1 FEEDBACK
39              
40             =head2 Mailing Lists
41              
42             User feedback is an integral part of the evolution of this and other
43             Bioperl modules. Send your comments and suggestions preferably to
44             the Bioperl mailing list. Your participation is much appreciated.
45              
46             bioperl-l@bioperl.org - General discussion
47             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
48              
49             =head2 Support
50              
51             Please direct usage questions or support issues to the mailing list:
52              
53             I
54              
55             rather than to the module maintainer directly. Many experienced and
56             reponsive experts will be able look at the problem and quickly
57             address it. Please include a thorough description of the problem
58             with code and data examples if at all possible.
59              
60             =head2 Reporting Bugs
61              
62             Report bugs to the Bioperl bug tracking system to help us keep track
63             of the bugs and their resolution. Bug reports can be submitted via
64             email or the web:
65              
66             https://github.com/bioperl/bioperl-live/issues
67              
68             =head1 AUTHOR - Albert Vilella
69              
70             Email avilella-AT-gmail-DOT-com
71              
72             =head1 CONTRIBUTORS
73              
74             Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
75              
76             =head1 APPENDIX
77              
78             The rest of the documentation details each of the object methods.
79             Internal methods are usually preceded with a _
80              
81             =cut
82              
83              
84             # Let the code begin...
85              
86              
87             package Bio::Seq::LargeSeqI;
88 4     4   20 use strict;
  4         6  
  4         103  
89              
90              
91 4     4   12 use base qw(Bio::Root::RootI);
  4         5  
  4         310  
92              
93              
94             =head2 add_sequence_as_string
95              
96             Title : add_sequence_as_string
97             Usage : $seq->add_sequence_as_string("CATGAT");
98             Function: Appends additional residues to an existing object.
99             This allows one to build up a large sequence without
100             storing entire object in memory.
101             Returns : Current length of sequence
102             Args : string to append
103              
104             =cut
105              
106             sub add_sequence_as_string {
107 0     0 1   my ($self) = @_;
108 0           $self->throw_not_implemented();
109             }
110              
111              
112             1;