Bio::SearchIO
EventHandlerI
Toolbar
Summary
Bio::SearchIO::EventHandlerI - An abstract Event Handler for Search Result parsing
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
# do not use this object directly it is an interface
# See Bio::SearchIO::SearchResultEventBuilder for an implementation
use Bio::SearchIO::SearchResultEventBuilder;
my $handler = new Bio::SearchIO::SearchResultEventBuilder();
Description
This interface describes the basic methods needed to handle Events
thrown from parsing a Search Result such as FASTA, BLAST, or HMMer.
Methods
Methods description
Title : end_hit
Usage : $handler->end_hit()
Function: Ends a Hit event cycle
Returns : Bio::Search::Hit::HitI object
Args : type of event and associated hashref |
Title : end_hsp
Usage : $handler->end_hsp()
Function: Ends a HSP event cycle
Returns : Bio::Search::HSP::HSPI object
Args : type of event and associated hashref |
Title : end_result
Usage : $handler->end_result($data)
Function: Ends a result event cycle
Returns : Bio::Search::Result::ResultI object
Args : none |
Title : factory
Usage : my $f = $handler->factory('TYPE');
Function: Retrieves the associated factory for requested 'TYPE'
Returns : a Bio::Factory::ObjectFactoryI or undef if none registered
Args : name of factory class to retrieve
See Bio::Factory::ObjectFactoryI for more information |
Title : register_factory
Usage : $handler->register_factory('TYPE',$factory);
Function: Register a specific factory for a object type class
Returns : none
Args : string representing the class and
Bio::Factory::ObjectFactoryI
See Bio::Factory::ObjectFactoryI for more information |
Title : start_hit
Usage : $handler->start_hit()
Function: Starts a Hit event cycle
Returns : none
Args : type of event and associated hashref |
Title : start_hsp
Usage : $handler->start_hsp($data)
Function: Start a HSP event cycle
Returns : none
Args : type of element
associated hashref |
Title : start_result
Usage : $handler->start_result($data)
Function: Begins a result event cycle
Returns : none
Args : Type of Result |
Methods code
sub end_hit
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub end_hsp
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub end_result
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub factory
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub register_factory
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub start_hit
{ my ($self,@args) = @_;
$self->throw_not_implemented } | sub start_hsp
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub start_result
{ my ($self) = @_;
$self->throw_not_implemented();} | General documentation
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
| AUTHOR - Jason Stajich | Top |
Additional contributors names and emails here
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
| Bio::Event::EventHandlerI methods | Top |
Title : will_handle
Usage : if( $handler->will_handle($event_type) ) { ... }
Function: Tests if this event builder knows how to process a specific event
Returns : boolean
Args : event type name