To effectively remedy this, you will need a Java 11 version of Jalview. For Jalview 220.127.116.11 Java 11 is not officially supported but we are working towards that, so you can:
Problems on Windows:
If your installation of Jalview goes fine, but double clicking on the Jalview icon does not produce any error message, window or any other activity (other than the spinning blue circle) this might be caused by a space character in Jalview's installation folder. To fix this:
When Jalview is run on WIndows machines with high resolution displays (e.g. 4K, retina, etc) resolution screens, you might find that all the menus, window titles, and alignment data are really tiny. That's because on high-resolution displays, all the windows and fonts have to be magnified so that you can read them, and the fix is to ask Windows to do the same for the Jalview application.
Instructions on how to do this can be found in several places on the 'net. Your milage may vary so please let us know if you are having problems via the jalview-discuss AT jalview.org mailing list !
See https://pivotce.com/2017/12/11/fix-java-applications-for-high-dpi-display/ for the following solution which should work for launching Jalview via webstart on machines with Java 8 installed.
- Close Jalview
- Find java.exe and/or javaw.exe likely found in C:\Program Files\Java\jre(version#)\bin.
- Right click on it and select -> Properties
- Go to Compatibility tab
- Check Override high DPI scaling behavior.
- Choose System for Scaling performed by:
- Click OK
- Relaunch Jalview
1. Save your work and shut down Jalview
2. Open a Terminal window (use spotlight or the Launcher and type 'Terminal' to locate the Terminal App), and type:
defaults write -g CGFontRenderingFontSmoothingDisabled -bool NO
3. Start Jalview again and load an alignment to check that the fonts are now legible.
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=
If you are running Jalview 2.10.0 under Ubuntu or some other (possibly GTK based) Linux desktop, you may find that after opening the Sequence Fetcher, you are presented with a dialog box just showing 'OK' and 'Cancel' buttons, but nothing much else. The empty panel is due to an underlying problem with Java, but you can still choose from the list of databases with the keyboard !
If you normally launch Jalview with a local JNLP file (such as one you created to customise Jalview's memory settings), then you will find that Jalview 2.8.2 cannot export images.
To fix, simply download a new customised JNLP file via the following URL:
(change 1G to your desired memory settings - in either M or G)
1. In System Preferences, launch Java which opens Java Control Panel.
2. On the "General" pane, click "View..." which opens Java Cache Viewer
3. Select Jalview
4. Click icon for creating a shortcut. A Mac alias is installed on your Desktop. Drag it to /Applications or wherever you want it.
5. Double-click the Jalview alias file to launch.