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.
- Depending on your platform you will need to take a look at the launcher.log file within the Jalview installation directory or on OSX the Jalview.app directory (opened by right clicking and selecting 'Show Contents').
'Alignment, Analysis and Visualisation with Jalview' hands-on training course at Edinburgh Genomics, University of Edinburgh
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
BBSRC Eastbio Doctoral Training Partnership PhD workshop for the students from St Andrews, Dundee, Edinburgh and Aberdeen University.
“Jalview – Dundee born and bred software to interactively visualise, analyse and present your multiple sequence alignments” by Dr Suzanne Duce & Dr Jim Procter at 11:00 – 12:00
“Dataviz’ in 30 mins: Do’s, Don’ts, and where to learn more” by Dr Jim Proctor at 12:00 – 12:30
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.