Bio::SeqAnalysisParserI - Sequence analysis output parser interface # 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"; } 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.

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Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ Email Hilmar Lapp <hlapp@gmx.net>, Jason Stajich <jason@chg.mc.duke.edu> The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Remark : Classes implementing this interface are expected to implement recognition of at least the following named parameters: -file input file (alternative to -fh) -fh input stream (alternative to -file)

next_feature
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