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.\" ========================================================================
.\"
.IX Title "Bio::SeqIO::bsml_sax 3pm"
.TH Bio::SeqIO::bsml_sax 3pm "2020-10-28" "perl v5.30.3" "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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.SH "NAME"
Bio::SeqIO::bsml_sax \- BSML sequence input/output stream using SAX
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\& It is probably best not to use this object directly, but rather go
\& through the SeqIO handler system. To read a BSML file:
\&
\&    $stream = Bio::SeqIO\->new( \-file => $filename, \-format => \*(Aqbsml\*(Aq);
\&
\&    while ( my $bioSeqObj = $stream\->next_seq() ) {
\&        # do something with $bioSeqObj
\&    }
\&
\& To write a Seq object to the current file handle in BSML XML format:
\&
\&    $stream\->write_seq( \-seq => $seqObj);
\&
\& If instead you would like a XML::DOM object containing the BSML, use:
\&
\&    my $newXmlObject = $stream\->to_bsml( \-seq => $seqObj);
.Ve
.SH "DEPENDENCIES"
.IX Header "DEPENDENCIES"
.Vb 1
\& In addition to parts of the Bio:: hierarchy, this module uses:
\&
\& XML::SAX
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
.Vb 2
\& This object can transform Bio::Seq objects to and from BSML (XML)
\& flatfiles.
.Ve
.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"
.Vb 3
\& 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://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason-at-bioperl-dot-org
.SH "METHODS"
.IX Header "METHODS"
.SS "next_seq"
.IX Subsection "next_seq"
.Vb 5
\& Title   : next_seq
\& Usage   : my $bioSeqObj = $stream\->next_seq
\& Function: Retrieves the next sequence from a SeqIO::bsml stream.
\& Returns : A reference to a Bio::Seq::RichSeq object
\& Args    :
.Ve