Jalview is compatible with Java 9, but only via webstart, or with a modified command-line launch script. If you use the InstallAnywhere version of Jalview it will recommend you install Java 8.
If you have installed Jalview via InstallAnywhere and you cannot access JABAWS services (a dialog box appears after you start Jalview about this), then you can patch the Jalview installation.
On OSX: - Add two lines to the Jalview.app/Contents/Info.plist file after the line starting <string>-Xdock:icon=
<string>--add-modules=java.se.ee</string>
<string>--illegal-access=warn</string>
On Windows: Open the Jalview.lax file in Notepad (or another editor) # and locate and replace the existing lax.nl.java.option.additional line with
lax.nl.java.option.additional=--add-modules=java.se.ee --illegal-access=warn
Launching Jalview from the command line on Java 9
To run Jalview 2.10.3 on Java 9, you need to add two additional JVM command line arguments:
--add-modules=java.se.ee --illegal-access=warn
Java 9 also ignores the 'java.ext.dirs' property so instead we recommend launching jalview via a script like:
# set install path of jalview
JALVIEWDIR=$DIR; # change $DIR to where you built Jalview
# compile the classpath
CLASSPATH=`echo $JALVIEWDIR/*.jar | sed -e 's/r /r:/g'`
# launch Jalview
# you might also want --Xmx<memory in GB>G
java -classpath $CLASSPATH --add-modules=java.se.ee --illegal-access=warn jalview.bin.Jalview ${@};