From: Neil Rotstan <neil@bl...> - 2003-01-10 16:11:54
JGAP 0.31 is a maintenance release that fixes a serious bug that could
result in corrupted Allele state. Other minor fixes and enhancements are
also included. It is highly recommended that version 0.3 users upgrade to
version 0.31. Please see the list of changes included at the end of this
announcement for an overview of fixes and enhancements contained in this
Please note that version 0.31 is considered an alpha release and is
therefore not feature complete, not optimized, and probably contains bugs.
Version 0.31 of JGAP can be downloaded from the JGAP home page, which can
be found at http://jgap.sourceforge.net
If you run into any problems or have any questions, we encourage you to
send an email to the new jgap-users mailing list at
Thanks for trying JGAP!
--The JGAP Team
Changelog for version 0.31:
* Fixed AllelePool to discriminate between alleles intended for
different gene positions so that position-specific configurations
will be preserved. Thanks to Alexandre Freire for reporting this
* AllelePool is no longer a static class.
* The Configuration object now supports the AllelePool as an
optional configurable option, and the various JGAP components
now access the pool instance via the active Configuration. The
DefaultConfiguration utility class automatically sets up an
* The Allele.setValueFromStringRepresentation() method has been
renamed to setValueFromPersistentRepresentation() and may now throw
an UnsupportedOperationException for users who do not wish to take
advantage of XML persistence and do not want to bother providing an
implementation for this method.
* An Allele.getPersistentRepresentation() method has been added to
the Allele interface and should be implemented to provide a String
representation of the Allele that is suitable for XML persistence
and could be later used to reconstruct the Allele. Previously, the
toString() method was used for this purpose.
* IntegerAllele and BooleanAllele have been updated to conform to the
changes to the Allele interface.
* The XMLManager.getGenesFromElement() method now requires that the
active Configuration object be passed in.
* Made minor Javadoc fixes and code formatting changes, and removed
some dead code.
* Updated the README file.