Jalview uses a launcher (called getdown, see https://github.com/threerings/getdown) that runs an auto-updater for Jalview and verifies Jalview files by checking the Jalview web site. Whilst the launcher checks for existing system proxy settings, sometimes it does not find those settings. In this case it may pop up a window asking for proxy settings. If this does not happen, and proxy settings are required, you can create a file called
To effectively remedy this, you will need a Java 11 version of Jalview. For Jalview 126.96.36.199 Java 11 is not officially supported but we are working towards that, so you can:
Location: G.155, Peter Wilson Building, King's Buildings, Edinburgh, EH9 3JG
Jalview 2.11.0 introduces support for loading VCF files, and new filters and shading models for sequence features. Under the hood, we've addressed many bugs, and also made some important changes in the way the Jalview desktop is installed and launched.
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