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.\" ========================================================================
.\"
.IX Title "Bio::Variation::IO::xml 3pm"
.TH Bio::Variation::IO::xml 3pm "2021-12-02" "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::Variation::IO::xml \- XML sequence variation input/output stream
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Do not use this module directly.  Use it via the Bio::Variation::IO class.
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object can transform Bio::Variation::SeqDiff objects to and from \s-1XML\s0
file databases.
.PP
The \s-1XML\s0 format, although consistent, is still evolving. The current
\&\s-1DTD\s0 for it is at <http://www.ebi.ac.uk/mutations/DTDE/seqDiff.dtd>.
.SH "REQUIREMENTS"
.IX Header "REQUIREMENTS"
To use this code you need the module XML::Twig which creates an
interface to XML::Parser to read \s-1XML\s0 and modules XML::Writer and
IO::String to write \s-1XML\s0 out.
.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 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 \- Heikki Lehvaslaiho"
.IX Header "AUTHOR - Heikki Lehvaslaiho"
Email:  heikki-at-bioperl-dot-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"
.IX Subsection "next"
.Vb 5
\& Title   : next
\& Usage   : $haplo = $stream\->next()
\& Function: returns the next seqDiff in the stream
\& Returns : Bio::Variation::SeqDiff object
\& Args    : NONE
.Ve
.SS "write"
.IX Subsection "write"
.Vb 5
\& Title   : write
\& Usage   : $stream\->write(@haplos)
\& Function: writes the $seqDiff objects into the stream
\& Returns : 1 for success and 0 for error
\& Args    : Bio::Variation::SeqDiff object
.Ve