This is Sun Java 6 beta on Vista RC1 bld 5600, IE\Web java works perfect, BUT....there are some issues that are most likely related to security restrictions or program incompatabilities as too what programs are allowed to use the explorere interface.
A protein\nucleicacid alignment program, JalView (http://www.jalview.org) that on Windows XP works flawlessly, under Vista can no longer open files from the <file open> menu, but it opens if you drag and drop a file into the program window.
You can also not save your work, as this is disabled,e.g. save button is greyed out and <save as> requires an explorer window to open.
As there are Java applications that are safe and people would like to use, are there any way to allow these to actually open and save files on the local system? Without any registry hacks or tricky workarounds!!!, e.g. something akin to an option on running a java file asking what level of system access should this spesific java program have???
Java under Vista RTM now works more or less flawlessly, the JalView application now has no issues...
So far the only "glitch" with java programs has been related to missing paths for java (think this is due to my language settings where java expects english all over and I use .no as settings for currency and such) so applications like ATVapp (http://phylogenomics.us/atv/downloads.html) a phylogenetic tool to browse trees needs to be started using a cmd line like for the latest alpha:
REM MSDOS batch file to run ATV 4.00 ALPHA 3 01.03.2007 java -cp duser.language=en -jar forester_400a3.jar
Or for an older relese:
REM MSDOS batch file to run ATVapp v1.92 java -Duser.language=en -cp ATVapp.jar ATVapp