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.\" ========================================================================
.\"
.IX Title "Bio::SeqIO::swissdriver 3pm"
.TH Bio::SeqIO::swissdriver 3pm "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
Bio::SeqIO::swissdriver \- SwissProt/UniProt handler\-based push parser
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&  #It is probably best not to use this object directly, but
\&  #rather go through the SeqIO handler:
\&
\&  $stream = Bio::SeqIO\->new(\-file => $filename,
\&                            \-format => \*(Aqswissdriver\*(Aq);
\&
\&  while ( my $seq = $stream\->next_seq() ) {
\&      # do something with $seq
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object can transform Bio::Seq objects to and from UniProt flat file
databases. The key difference between this parser and the tried-and-true
Bio::SeqIO::swiss parser is this version separates the parsing and data
manipulation into a 'driver' method (next_seq) and separate object handlers
which deal with the data passed to it.
.SS "The Driver"
.IX Subsection "The Driver"
The main purpose of the driver routine, in this case \fBnext_seq()\fR, is to carve out
the data into meaningful chunks which are passed along to relevant handlers (see
below).
.PP
Each chunk of data in the has a \s-1NAME\s0 tag attached to it, similar to that for \s-1XML\s0
parsing. This designates the type of data passed (annotation type or seqfeature)
and the handler to be called for processing the data.
.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 \- Bioperl Project"
.IX Header "AUTHOR - Bioperl Project"
bioperl-l at 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_seq"
.IX Subsection "next_seq"
.Vb 5
\& Title   : next_seq
\& Usage   : $seq = $stream\->next_seq()
\& Function: returns the next sequence in the stream
\& Returns : Bio::Seq object
\& Args    : none
.Ve
.SS "write_seq"
.IX Subsection "write_seq"
.Vb 5
\& Title   : write_seq
\& Usage   : $stream\->write_seq($seq)
\& Function: writes the $seq object (must be seq) to the stream
\& Returns : 1 for success and 0 for error
\& Args    : array of 1 to n Bio::SeqI objects
.Ve
.SS "seqhandler"
.IX Subsection "seqhandler"
.Vb 5
\& Title   : seqhandler
\& Usage   : $stream\->seqhandler($handler)
\& Function: Get/Set the Bio::Seq::HandlerBaseI object
\& Returns : Bio::Seq::HandlerBaseI 
\& Args    : Bio::Seq::HandlerBaseI
.Ve