File Coverage

Bio/Search/Result/WABAResult.pm
Criterion Covered Total %
statement 15 15 100.0
branch 3 4 75.0
condition n/a
subroutine 4 4 100.0
pod 2 2 100.0
total 24 25 96.0


line stmt bran cond sub pod time code
1             #
2             # BioPerl module for Bio::Search::Result::WABAResult
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::Search::Result::WABAResult - Result object for WABA alignment output
17              
18             =head1 SYNOPSIS
19              
20             # use this object exactly as you would a GenericResult
21             # the only extra method is query_database which is the
22             # name of the file where the query sequence came from
23              
24             =head1 DESCRIPTION
25              
26             This object is for WABA result output, there is little difference
27             between this object and a GenericResult save the addition of one
28             method query_database. Expect many of the fields for GenericResult to
29             be empty however as WABA was not intended to provide a lot of extra
30             information other than the alignment.
31              
32             =head1 FEEDBACK
33              
34             =head2 Mailing Lists
35              
36             User feedback is an integral part of the evolution of this and other
37             Bioperl modules. Send your comments and suggestions preferably to
38             the Bioperl mailing list. Your participation is much appreciated.
39              
40             bioperl-l@bioperl.org - General discussion
41             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
42              
43             =head2 Support
44              
45             Please direct usage questions or support issues to the mailing list:
46              
47             I
48              
49             rather than to the module maintainer directly. Many experienced and
50             reponsive experts will be able look at the problem and quickly
51             address it. Please include a thorough description of the problem
52             with code and data examples if at all possible.
53              
54             =head2 Reporting Bugs
55              
56             Report bugs to the Bioperl bug tracking system to help us keep track
57             of the bugs and their resolution. Bug reports can be submitted via the
58             web:
59              
60             https://github.com/bioperl/bioperl-live/issues
61              
62             =head1 AUTHOR - Jason Stajich
63              
64             Email jason@bioperl.org
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::Search::Result::WABAResult;
78 1     1   6 use strict;
  1         2  
  1         29  
79              
80              
81 1     1   4 use base qw(Bio::Search::Result::GenericResult);
  1         2  
  1         154  
82              
83             =head2 new
84              
85             Title : new
86             Usage : my $obj = Bio::Search::Result::WABAResult->new();
87             Function: Builds a new Bio::Search::Result::WABAResult object
88             Returns : Bio::Search::Result::WABAResult
89             Args : -query_database => "name of the database where the query came from"
90              
91              
92             =cut
93              
94             sub new {
95 2     2 1 7 my($class,@args) = @_;
96              
97 2         14 my $self = $class->SUPER::new(@args);
98 2         6 my ($db) = $self->_rearrange([qw(QUERY_DATABASE)], @args);
99 2 50       9 defined $db && $self->query_database($db);
100 2         8 return $self;
101             }
102              
103             =head2 query_database
104              
105             Title : query_database
106             Usage : $obj->query_database($newval)
107             Function: Data field for the database filename where the
108             query sequence came from
109             Returns : value of query_database
110             Args : newvalue (optional)
111              
112              
113             =cut
114              
115             sub query_database{
116 4     4 1 9 my ($self,$value) = @_;
117 4 100       9 if( defined $value) {
118 2         3 $self->{'query_database'} = $value;
119             }
120 4         12 return $self->{'query_database'};
121             }
122              
123              
124             =head2 All other methods are inherited from Bio::Search::Result::GenericResult
125              
126             See the L for complete
127             documentation of the rest of the methods that are available for this
128             module.
129              
130             =cut
131              
132             1;