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.\" ========================================================================
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.IX Title "Bio::SeqAnalysisParserI 3pm"
.TH Bio::SeqAnalysisParserI 3pm "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::SeqAnalysisParserI \- Sequence analysis output parser interface
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 6
\&    # get a SeqAnalysisParserI somehow, e.g. by
\&    my $parser = Bio::Factory::SeqAnalysisParserFactory\->get_parser(
\&                            \*(Aq\-input\*(Aq => \*(Aqinputfile\*(Aq, \*(Aq\-method\*(Aq => \*(Aqgenscan\*(Aq);
\&    while( my $feature = $parser\->next_feature() ) {
\&        print "Feature from ", $feature\->start, " to ", $feature\->end, "\en";
\&    }
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.PP
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.
.PP
See Bio::Factory::SeqAnalysisParserFactoryI and
Bio::Factory::SeqAnalysisParserFactory for interface and an implementation
of the corresponding factory.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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 the
web:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Hilmar Lapp, Jason Stajich"
.IX Header "AUTHOR - Hilmar Lapp, Jason Stajich"
Email Hilmar Lapp <hlapp@gmx.net>, Jason Stajich <jason@bioperl.org>
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "next_feature"
.IX Subsection "next_feature"
.Vb 8
\& 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
.Ve