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Fuzzy fonts in the alignment view on OSX Mojave (10.14.x)

On OSX Mojave, you may notice that sequences and IDs in the Jalview alignment window are hard to read. To fix this, first:

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.

Can Jalview run with Java 9

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=

Can't see databases in Database Chooser after selecting Fetch Sequences...!

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 !

I downloaded the Jalview Installer for OSX but the install application won't run

The OSX InstallAnywhere version of Jalview is downloaded as a ZIP archive (install.zip) which is normally unpacked automatically to create an application called 'install' that you can run. If nothing happens when you double click the application, then there are a few things that could go wrong.

Installer doesn't launch because it was unpacked with a third-party archive tool

Java Web Start version of Jalview fails with error 'Unable to Launch - because JAR resources in JNLP are not signed by same certificate'

This error (and others like it) is raised when an old version of the Jalview Webstart JNLP is being used to launch the latest version of the application (for instance, because you have created your own JNLP file in order to increase the memory available to Jalview).
To fix, first make sure that you are using the latest version of the Jalview JNLP file (right-click or apple-click to save this link to a file) to launch jalview.

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