Ewan Birney


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


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


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/DTD/seqDiff.dtd.


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.


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AUTHOR - Heikki Lehvaslaiho

Email: heikki@ebi.ac.uk Address:

     EMBL Outstation, European Bioinformatics Institute
     Wellcome Trust Genome Campus, Hinxton
     Cambs. CB10 1SD, United Kingdom


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


 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