Bio::Factory SeqAnalysisParserFactory
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Summary
Bio::Factory::SeqAnalysisParserFactory - class capable of creating
SeqAnalysisParserI compliant parsers
Package variables
No package variables defined.
Inherit
Bio::Factory::DriverFactory Bio::Factory::SeqAnalysisParserFactoryI
Synopsis
    # initialize an object implementing this interface, e.g.
$factory = Bio::Factory::SeqAnalysisParserFactory->new();
# find out the methods it knows about
print "registered methods: ",
join(', ', keys %{$factory->driver_table}), "\n";
# obtain a parser object
$parser = $factory->get_parser(-input=>$inputobj,
-params=>[@params],
-method => $method);
# $parser is an object implementing Bio::SeqAnalysisParserI
# annotate sequence with features produced by parser
while(my $feat = $parser->next_feature()) {
$seq->add_SeqFeature($feat);
}
Description
This is a factory class capable of instantiating SeqAnalysisParserI
implementing parsers.
The concept behind this class and the interface it implements
(Bio::Factory::SeqAnalysisParserFactoryI) is a generic analysis result
parsing in high-throughput automated sequence annotation
pipelines. See Bio::SeqAnalysisParserI for more documentation of this
concept.
You can always find out the methods an instance of this class knows
about by the way given in the SYNOPSIS section. By default, and
assuming that the documentation is up-to-date, this will comprise of
genscan, mzef, estscan, blast, hmmer, gff, and sim4 (all
case-insensitive).
Methods
BEGIN Code
new
No description
Code
get_parserDescriptionCode
Methods description
get_parsercode    nextTop
 Title   : get_parser
Usage : $factory->get_parser(-input=>$inputobj,
[ -params=>[@params] ],
-method => $method)
Function: Creates and returns a parser object for the given input and method.
Both file names and streams (filehandles) are allowed.
Parameters (-params argument) are passed on to the parser object and therefore are specific to the parser to be created. Example : Returns : A Bio::SeqAnalysisParserI implementing object. Exception if creation of the parser object fails. Args : input - object/file where analysis results are coming from,
params - parameter to use when parsing/running analysis
method - method of analysis
Methods code
BEGINTop
BEGIN {
    Bio::Factory::DriverFactory->register_driver
	(
	 "genscan"   => "Bio::Tools::Genscan",
	 "mzef"      => "Bio::Tools::MZEF",
	 "estscan"   => "Bio::Tools::ESTScan",
	 "hmmer"     => "Bio::Tools::HMMER::Result",
	 "gff"       => "Bio::Tools::GFF",
	 "sim4"      => "Bio::Tools::Sim4::Results",
	 "epcr"      => "Bio::Tools::EPCR", 
	 "exonerate" => "Bio::Tools::Exonerate",
	 );
}
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);

    # no per-object initialization right now - registration of default drivers
# is only done once when the module is loaded
return $self;
}
get_parserdescriptionprevnextTop
sub get_parser {
    my ($self, @args) = @_;
    my $parser;
    my $module;

    my ($input, $params, $method) =
	$self->_rearrange([qw(INPUT PARAMS METHOD)], @args);

    # retrieve module name for requested method
$method = lc $method; # method is case-insensitive
$module = $self->get_driver($method); if(! defined($module)) { $self->throw("Analysis parser driver for method $method not registered."); } # load module
$self->_load_module($module); # throws an exception on failure to load
# make sure parameters is not undef
$params = [] if( !defined $params ); # figure out input method (file or stream)
my $inputmethod = '-file'; if( ref($input) =~ /GLOB/i ) { $inputmethod = '-fh'; } # instantiate parser and return the result
$parser = $module->new($inputmethod => $input, @$params); if(! $parser->isa('Bio::SeqAnalysisParserI')) { $self->throw("Driver $module registered for method $method does not ". "implement Bio::SeqAnalyisParserI. How come?"); } return $parser;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
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 BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar Lapp, Jason StajichTop
Email Hilmar Lapp <hlapp@gmx.net>, Jason Stajich <jason@bioperl.org>
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
register_driverTop
 Title   : register_driver
Usage : $factory->register_driver("genscan", "Bio::Tools::Genscan");
Function: Registers a driver a factory class should be able to instantiate.
This method can be called both as an instance and as a class method. Returns : Args : Key of the driver (string) and the module implementing the driver (string).
driver_tableTop
 Title   : driver_table
Usage : $table = $factory->driver_table();
Function: Returns a reference to the hash table storing associations of
methods with drivers.
You use this table to look up registered methods (keys) and drivers (values). In this implementation the table is class-specific and therefore shared by all instances. You can override this in a derived class, but note that this method can be called both as an instance and a class method. This will be the table used by the object internally. You should definitely know what you're doing if you modify the table's contents. Modifications are shared by _all_ instances, those present and those yet to be created. Returns : A reference to a hash table. Args :