File Coverage

Bio/Factory/SequenceFactoryI.pm
Criterion Covered Total %
statement 6 6 100.0
branch n/a
condition n/a
subroutine 2 2 100.0
pod n/a
total 8 8 100.0


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1             #
2             # BioPerl module for Bio::Factory::SequenceFactoryI
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::Factory::SequenceFactoryI - This interface allows for generic building of sequences in factories which create sequences (like SeqIO)
17              
18             =head1 SYNOPSIS
19              
20             # do not use this object directly it is an interface
21             # get a Bio::Factory::SequenceFactoryI object like
22              
23             use Bio::Seq::SeqFactory;
24             my $seqbuilder = Bio::Seq::SeqFactory->new('-type' => 'Bio::PrimarySeq');
25              
26             my $seq = $seqbuilder->create(-seq => 'ACTGAT',
27             -display_id => 'exampleseq');
28              
29             print "seq is a ", ref($seq), "\n";
30              
31             =head1 DESCRIPTION
32              
33             A generic way to build Sequence objects via a pluggable factory. This
34             reduces the amount of code that looks like
35              
36             if( $type eq 'Bio::PrimarySeq' ) { ... }
37             elsif( $type eq 'Bio::Seq::RichSeq' ) { ... }
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-at-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::Factory::SequenceFactoryI;
85              
86 176     176   1167 use strict;
  176         315  
  176         4790  
87              
88 176     176   766 use base qw(Bio::Factory::ObjectFactoryI);
  176         273  
  176         36045  
89              
90             =head2 create
91              
92             Title : create
93             Usage : my $seq = $seqbuilder->create(-seq => 'CAGT',
94             -id => 'name');
95             Function: Instantiates new Bio::PrimarySeqI (or one of its child classes)
96             This object allows us to genericize the instantiation of sequence
97             objects.
98             Returns : Bio::PrimarySeqI
99             Args : initialization parameters specific to the type of sequence
100             object we want. Typically
101             -seq => $str,
102             -display_id => $name
103              
104             =cut
105              
106             1;