You can manually set it via
_Package Explorer / JRE System Library / rt.jar -> contextmenu -> properties - Attach Javadoc..
And the settings are stored in .metadata.plugins\org.eclipse.core.runtime.settings\org.eclipse.jdt.launching.prefs.
I wonder is there anyway I can programmatically specify it?
Thanks a lot!
Javadoc is here.
The method you want is IVMInstall#setJavadocLocation(URL). You need to create a VMStandin from the existing IVMInstall, modify its javadoc location, then do VMStandin#convertToRealVM() which will apply the changes.
JavaRuntime has a few methods for getting IVMInstalls.