Bio::Factory
SeqAnalysisParserFactoryI
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Summary
Bio::Factory::SeqAnalysisParserFactoryI - interface describing objects capable
of creating SeqAnalysisParserI compliant parsers
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
# initialize an object implementing this interface, e.g.
$factory = Bio::Factory::SeqAnalysisParserFactory->new();
# 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 an interface for factory classes capable of instantiating
SeqAnalysisParserI implementing parsers.
The concept behind the interface is a generic analysis result parsing
in high-throughput automated sequence annotation pipelines. See
Bio::SeqAnalysisParserI for more documentation of this concept.
Methods
Methods description
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.
The type of input which is suitable depends on the implementation,
but a good-style implementation should allow both file names and
streams (filehandles).
A particular implementation may not be able to create a parser for
the requested method. In this case it shall return undef.
Parameters (-params argument) are passed on to the parser object
and therefore are specific to the parser to be created. An
implementation of this interface should make this argument optional.
Example :
Returns : A Bio::SeqAnalysisParserI implementing object.
Args : input - object/file where analysis results are coming from,
params - parameter to use when parsing/running analysis
method - method of analysis |
Methods code
sub get_parser
{ my ( $self, @args) = @_;
$self->throw_not_implemented();
}
1;} | General documentation
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| AUTHOR - Hilmar Lapp, Jason Stajich | Top |
Email Hilmar Lapp <hlapp@gmx.net>, Jason Stajich <jason@bioperl.org>
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _