NAME

Bio::Variation::IO::xml - XML sequence variation input/output stream

SYNOPSIS

Do not use this module directly. Use it via the Bio::Variation::IO class.

DESCRIPTION

This object can transform Bio::Variation::SeqDiff objects to and from XML file databases.

The XML format, although consistent, is still evolving. The current DTD for it is at <http://www.ebi.ac.uk/mutations/DTDE/seqDiff.dtd>.

REQUIREMENTS

To use this code you need the module XML::Twig which creates an interface to XML::Parser to read XML and modules XML::Writer and IO::String to write XML out.

FEEDBACK

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.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

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.

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:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Heikki Lehvaslaiho

Email: heikki-at-bioperl-dot-org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

 Title   : next
 Usage   : $haplo = $stream->next()
 Function: returns the next seqDiff in the stream
 Returns : Bio::Variation::SeqDiff object
 Args    : NONE

write

 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