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/DTD/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://bio.perl.org/MailList.html - About the mailing listsReporting 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 email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/AUTHOR - Heikki Lehvaslaiho
Email: heikki@ebi.ac.uk Address:
EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United KingdomAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next
Title : next
Usage : $haplo = $stream->next()
Function: returns the next seqDiff in the stream
Returns : Bio::Variation::SeqDiff object
Args : NONEwrite
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