+ <p><strong>Jalview Executable Jar Launch Logs</strong><br/>If you are using the Jalview executable jar file (also
+ used by bioconda and OSX homebrew installations) then the default run class (
+ <em>jalview.bin.Launcher</em> -- a minimised launcher that will set
+ memory and linux dpi settings before re-launching
+ <em>jalview.bin.Jalview</em>), will output logging information to
+ STDOUT and STDERR.
+ </p>
+
+ <p><strong>
+ <a name="java_console">Java Console and Log Level</a>
+ </strong></p>
+ <p>
+ The Java Console is opened by selecting <strong>Tools
+ → Show Java Console</strong>. The visibility of the console is stored
+ in your preferences, so if you quit Jalview with the console open,
+ it will be shown the next time you start Jalview. You can close the
+ console by selecting the same menu option again, or just closing the
+ console window.
+ </p>
+ <p>The Java Console's text display always shows information about
+ your system and Jalview installation details. The rest are the most
+ recent messages output during your Jalview session. Some messages
+ are only captured by the console when it is open, so to get a full
+ log for debugging a problem, enable the console and then restart
+ Jalview.</p>
+
+ <p>
+ You can temporarily control the detail of what appears as output by
+ selecting a <em>Log level</em> using the drop-down list at the
+ bottom left of the console. There are several levels to choose from:
+ The most verbose is TRACE, followed by DEBUG, INFO, WARN. When the
+ Console is opened, the default level will be chosen (INFO).
+ </p>
+ <p>
+ <strong>Note! If you change the log level in the Java
+ Console, this change will only persist for as long as the console
+ is open. Once you close the console the log level will revert back
+ to what it had been when you opened the console (usually INFO).</strong>
+ </p>
+ <p><strong>Permanently changing Jalview's default log level</strong><br/>
+ You can change the default log level by editing the Jalview
+ preferences file, <em>.jalview_properties</em>, found in your home
+ directory (on Windows: %HOMEPATH%, or the folder above 'My
+ Documents'; on macOS: ~ or /Users/<em>username</em>; on linux/unix:
+ ~ or /home/<em>username</em>), and setting the property <em>logs.Jalview.level</em>
+ to the log level you prefer, e.g.
+ <pre>
+ logs.Jalview.level=DEBUG
+ </pre>
+ You can also set the property
+ <pre>
+ logs.Axis.level=DEBUG
+ </pre>
+ <p>to get debug information for Jalview's JPred service. The Axis log
+ level cannot be set from within the Java Console.
+ </p>
+ <p>
+ You can also set the <em>logs.jalview.level</em> property to a log level
+ not usually presented in the Java Console (though restricted to log
+ levels used by Apache Log4j -- see <a
+ href="https://logging.apache.org/log4j/2.x/manual/customloglevels.html">Log4j
+ Custom Log Levels</a> for details of the standard log levels
+ available). Jalview does not currently define any custom log levels.
+ If you do set the property with a log level that is normally not
+ visible in the Java Console this should be respected and visibly
+ selected when you open the console.
+ </p>
+ <p>
+ The <em>Clear</em> button at the bottom of the console will clear
+ all logging messages except for the initial system information which
+ is rewritten to the console.
+ </p>
+ <p>
+ The <em>Copy to clipboard</em> button at the bottom right of the
+ console will copy all of the text in the console to your system
+ clipboard, ready to paste into another application (e.g. email
+ composer or issue tracker).
+ </p>