Bio SeqAnalysisParserI
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Summary
Bio::SeqAnalysisParserI - Sequence analysis output parser interface
Package variables
No package variables defined.
Included modules
Carp
Inherit
Bio::Root::RootI
Synopsis
    # get a SeqAnalysisParserI somehow, e.g. by
my $parser = Bio::Factory::SeqAnalysisParserFactory->get_parser(
'-input' => 'inputfile', '-method' => 'genscan');
while( my $feature = $parser->next_feature() ) {
print "Feature from ", $feature->start, " to ", $feature->end, "\n";
}
Description
SeqAnalysisParserI is a generic interface for describing sequence analysis
result parsers. Sequence analysis in this sense is a search for similarities
or the identification of features on the sequence, like a databank search or a
a gene prediction result.
The concept behind this interface is to have a generic interface in sequence
annotation pipelines (as used e.g. in high-throughput automated
sequence annotation). This interface enables plug-and-play for new analysis
methods and their corresponding parsers without the necessity for modifying
the core of the annotation pipeline. In this concept the annotation pipeline
has to rely on only a list of methods for which to process the results, and a
factory from which it can obtain the corresponding parser implementing this
interface.
See Bio::Factory::SeqAnalysisParserFactoryI and
Bio::Factory::SeqAnalysisParserFactory for interface and an implementation
of the corresponding factory.
Methods
next_featureDescriptionCode
Methods description
next_featurecode    nextTop
 Title   : next_feature
Usage : $seqfeature = $obj->next_feature();
Function: Returns the next feature available in the analysis result, or
undef if there are no more features.
Example :
Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
more features.
Args : none
Methods code
next_featuredescriptionprevnextTop
sub next_feature {
    my ($self) = shift;
    $self->throw_not_implemented();
}

1;
}
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 _