File Coverage

Bio/SearchIO/EventHandlerI.pm
Criterion Covered Total %
statement 9 29 31.0
branch n/a
condition n/a
subroutine 3 13 23.0
pod 10 10 100.0
total 22 52 42.3


line stmt bran cond sub pod time code
1             #
2             # BioPerl module for Bio::SearchIO::EventHandlerI
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::SearchIO::EventHandlerI - An abstract Event Handler for Search Result parsing
17              
18             =head1 SYNOPSIS
19              
20             # do not use this object directly it is an interface
21             # See Bio::SearchIO::SearchResultEventBuilder for an implementation
22              
23             use Bio::SearchIO::SearchResultEventBuilder;
24             my $handler = Bio::SearchIO::SearchResultEventBuilder->new();
25              
26             =head1 DESCRIPTION
27              
28             This interface describes the basic methods needed to handle Events
29             thrown from parsing a Search Result such as FASTA, BLAST, or HMMer.
30              
31             =head1 FEEDBACK
32              
33             =head2 Mailing Lists
34              
35             User feedback is an integral part of the evolution of this and other
36             Bioperl modules. Send your comments and suggestions preferably to
37             the Bioperl mailing list. Your participation is much appreciated.
38              
39             bioperl-l@bioperl.org - General discussion
40             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
41              
42             =head2 Support
43              
44             Please direct usage questions or support issues to the mailing list:
45              
46             I
47              
48             rather than to the module maintainer directly. Many experienced and
49             reponsive experts will be able look at the problem and quickly
50             address it. Please include a thorough description of the problem
51             with code and data examples if at all possible.
52              
53             =head2 Reporting Bugs
54              
55             Report bugs to the Bioperl bug tracking system to help us keep track
56             of the bugs and their resolution. Bug reports can be submitted via the
57             web:
58              
59             https://github.com/bioperl/bioperl-live/issues
60              
61             =head1 AUTHOR - Jason Stajich
62              
63             Email jason-at-bioperl.org
64              
65             =head1 APPENDIX
66              
67             The rest of the documentation details each of the object methods.
68             Internal methods are usually preceded with a _
69              
70             =cut
71              
72              
73             # Let the code begin...
74              
75              
76             package Bio::SearchIO::EventHandlerI;
77 30     30   131 use strict;
  30         43  
  30         666  
78 30     30   90 use Carp;
  30         31  
  30         1311  
79              
80              
81 30     30   95 use base qw(Bio::Event::EventHandlerI);
  30         28  
  30         7921  
82              
83             =head2 start_result
84              
85             Title : start_result
86             Usage : $handler->start_result($data)
87             Function: Begins a result event cycle
88             Returns : none
89             Args : Type of Result
90              
91             =cut
92              
93             sub start_result {
94 0     0 1   my ($self) = @_;
95 0           $self->throw_not_implemented();
96             }
97              
98             =head2 end_result
99              
100             Title : end_result
101             Usage : $handler->end_result($data)
102             Function: Ends a result event cycle
103             Returns : Bio::Search::Result::ResultI object
104             Args : none
105              
106              
107             =cut
108              
109             sub end_result{
110 0     0 1   my ($self,@args) = @_;
111 0           $self->throw_not_implemented();
112             }
113              
114             =head2 start_hsp
115              
116             Title : start_hsp
117             Usage : $handler->start_hsp($data)
118             Function: Start a HSP event cycle
119             Returns : none
120             Args : type of element
121             associated hashref
122              
123             =cut
124              
125             sub start_hsp{
126 0     0 1   my ($self,@args) = @_;
127 0           $self->throw_not_implemented();
128             }
129              
130             =head2 end_hsp
131              
132             Title : end_hsp
133             Usage : $handler->end_hsp()
134             Function: Ends a HSP event cycle
135             Returns : Bio::Search::HSP::HSPI object
136             Args : type of event and associated hashref
137              
138             =cut
139              
140             sub end_hsp{
141 0     0 1   my ($self,@args) = @_;
142 0           $self->throw_not_implemented();
143             }
144              
145             =head2 start_hit
146              
147             Title : start_hit
148             Usage : $handler->start_hit()
149             Function: Starts a Hit event cycle
150             Returns : none
151             Args : type of event and associated hashref
152              
153              
154             =cut
155              
156             sub start_hit {
157 0     0 1   my ($self,@args) = @_;
158 0           $self->throw_not_implemented
159             }
160              
161             =head2 end_hit
162              
163             Title : end_hit
164             Usage : $handler->end_hit()
165             Function: Ends a Hit event cycle
166             Returns : Bio::Search::Hit::HitI object
167             Args : type of event and associated hashref
168              
169              
170             =cut
171              
172             sub end_hit {
173 0     0 1   my ($self,@args) = @_;
174 0           $self->throw_not_implemented();
175             }
176              
177             =head2 start_iteration
178              
179             Title : start_iteration
180             Usage : $handler->start_iteration()
181             Function: Starts an Iteration event cycle
182             Returns : none
183             Args : type of event and associated hashref
184              
185              
186             =cut
187              
188             sub start_iteration {
189 0     0 1   my ($self,@args) = @_;
190 0           $self->throw_not_implemented
191             }
192              
193             =head2 end_iteration
194              
195             Title : end_iteration
196             Usage : $handler->end_iteration()
197             Function: Ends an Iterationevent cycle
198             Returns : Bio::Search::Iteration::IterationI object
199             Args : type of event and associated hashref
200              
201              
202             =cut
203              
204             sub end_iteration {
205 0     0 1   my ($self,@args) = @_;
206 0           $self->throw_not_implemented();
207             }
208              
209             =head2 register_factory
210              
211             Title : register_factory
212             Usage : $handler->register_factory('TYPE',$factory);
213             Function: Register a specific factory for a object type class
214             Returns : none
215             Args : string representing the class and
216             Bio::Factory::ObjectFactoryI
217              
218             See L for more information
219              
220             =cut
221              
222             sub register_factory{
223 0     0 1   my ($self,@args) = @_;
224 0           $self->throw_not_implemented();
225             }
226              
227              
228             =head2 factory
229              
230             Title : factory
231             Usage : my $f = $handler->factory('TYPE');
232             Function: Retrieves the associated factory for requested 'TYPE'
233             Returns : a Bio::Factory::ObjectFactoryI
234             Throws : Bio::Root::BadParameter if none registered for the supplied type
235             Args : name of factory class to retrieve
236              
237             See L for more information
238              
239             =cut
240              
241             sub factory{
242 0     0 1   my ($self,@args) = @_;
243 0           $self->throw_not_implemented();
244             }
245              
246              
247             =head2 Bio::Event::EventHandlerI methods
248              
249             =cut
250              
251             =head2 will_handle
252              
253             Title : will_handle
254             Usage : if( $handler->will_handle($event_type) ) { ... }
255             Function: Tests if this event builder knows how to process a specific event
256             Returns : boolean
257             Args : event type name
258              
259              
260             =cut
261              
262             =head2 SAX methods
263              
264             See L for the additional SAX methods.
265              
266             =cut
267              
268              
269             1;