Bio::SearchIO::EventHandlerI - An abstract Event Handler for Search Result parsing

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::SearchIO::EventHandlerI - An abstract Event Handler for Search Result parsing

SYNOPSIS

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# do not use this object directly it is an interface # See Bio::SearchIO::SearchResultEventBuilder for an implementation

    use Bio::SearchIO::SearchResultEventBuilder;
    my $handler = Bio::SearchIO::SearchResultEventBuilder->new();

DESCRIPTION

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This interface describes the basic methods needed to handle Events thrown from parsing a Search Result such as FASTA, BLAST, or HMMer.

FEEDBACK

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Mailing Lists

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/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

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 the web:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich

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Email jason-at-bioperl.org

APPENDIX

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

start_result

 Title   : start_result
 Usage   : $handler->start_result($data)
 Function: Begins a result event cycle
 Returns : none 
 Args    : Type of Result

end_result

 Title   : end_result
 Usage   : $handler->end_result($data)
 Function: Ends a result event cycle
 Returns : Bio::Search::Result::ResultI object
 Args    : none

start_hsp

 Title   : start_hsp
 Usage   : $handler->start_hsp($data)
 Function: Start a HSP event cycle
 Returns : none
 Args    : type of element
           associated hashref

end_hsp

 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

start_hit

 Title   : start_hit
 Usage   : $handler->start_hit()
 Function: Starts a Hit event cycle
 Returns : none
 Args    : type of event and associated hashref

end_hit

 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

start_iteration

 Title   : start_iteration
 Usage   : $handler->start_iteration()
 Function: Starts an Iteration event cycle
 Returns : none
 Args    : type of event and associated hashref

end_iteration

 Title   : end_iteration
 Usage   : $handler->end_iteration()
 Function: Ends an Iterationevent cycle
 Returns : Bio::Search::Iteration::IterationI object
 Args    : type of event and associated hashref

register_factory

 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

factory

 Title   : factory
 Usage   : my $f = $handler->factory('TYPE');
 Function: Retrieves the associated factory for requested 'TYPE'
 Returns : a Bio::Factory::ObjectFactoryI
 Throws  : Bio::Root::BadParameter if none registered for the supplied type
 Args    : name of factory class to retrieve

See Bio::Factory::ObjectFactoryI for more information

Bio::Event::EventHandlerI methods

will_handle

 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

SAX methods

See Bio::Event::EventHandlerI for the additional SAX methods.

BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::SearchIO::EventHandlerI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code



# Let the code begin...


package Bio::SearchIO::EventHandlerI;
use strict;
use Carp;


use base qw(Bio::Event::EventHandlerI);


sub start_result {
    my ($self) = @_;
    $self->throw_not_implemented();
}


sub end_result{
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}


sub start_hsp{
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}


sub end_hsp{
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}


sub start_hit {
   my ($self,@args) = @_;
   $self->throw_not_implemented
}


sub end_hit {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}


sub start_iteration {
   my ($self,@args) = @_;
   $self->throw_not_implemented
}


sub end_iteration {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}


sub register_factory{
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}



sub factory{
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}




1;