The Java Console, Logging and Reporting Bugs

Like most programs, Jalview contains bugs, despite our best efforts. However, Jalview also produces a series of messages during its operation, often referred to as 'logs'. These logs provide a record of Jalview's operation. They can also be extremely useful when reporting bugs, since they help the Jalview developers diagnose and find a workaround for specific problems that you might encounter.

The primary place to look for logs is in the Java Console which you can open from within Jalview by going to the Tools menu and checking the box next to Show Java Console. This option is stored in your Jalview preferences file and so is remembered across Jalview sessions.

The Java Console will show you information about what the Jalview application is doing (often in the background) whilst it is running.

However, when tracking down problems preventing Jalview from starting up properly, you need to look at the startup logs - which are not shown in the Jalview Console. The location of these depends on how you launched Jalview:

Jalview Desktop Installation Launch Logs
If you are using a standard desktop version of Jalview installed from one of our install4j installers, then messages about Jalview's initial launch can be found in

JALVIEW_APP_DIR/launcher.log

• In Windows this is %APPDATA%\Local\Jalview by default
• In macOS this is /Applications/Jalview.app/Contents/Resources/app by default
• In Linux and other Unix OSes this is ~/opt/jalview by default

Jalview Executable Jar Launch Logs
If you are using the Jalview executable jar file (also used by bioconda and OSX homebrew installations) then the default run class ( jalview.bin.Launcher -- a minimised launcher that will set memory and linux dpi settings before re-launching jalview.bin.Jalview), will output logging information to STDOUT and STDERR.

Java Console and Log Level

The Java Console is opened by selecting Tools → Show Java Console. 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.

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.

Jalview logging will automatically scroll the text in the Java Console but if you want to examine a particular part of the logs whilst logging is still going on you can click on any part of the text area to stop this behaviour. A border should appear arround the text area to signify that autoscroll has been turned off. You can toggle the autoscroll behaviour on and off by clicking again on the text area.

You can temporarily control the detail of what appears as output by selecting a Log level 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).

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).

Permanently changing Jalview's default log level
You can change the default log level by editing the Jalview preferences file, .jalview_properties, found in your home directory (on Windows: %HOMEPATH%, or the folder above 'My Documents'; on macOS: ~ or /Users/username; on linux/unix: ~ or /home/username), and setting the property logs.Jalview.level to the log level you prefer, e.g.

  logs.Jalview.level=DEBUG
  

  logs.Axis.level=DEBUG
  

to get debug information for Jalview's JPred service. The Axis log level cannot be set from within the Java Console.

You can also set the logs.jalview.level property to a log level not usually presented in the Java Console (though restricted to log levels used by Apache Log4j -- see Log4j Custom Log Levels 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.

The Clear button at the bottom of the console will clear all logging messages except for the initial system information which is rewritten to the console.

The Copy to clipboard 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).

Reporting Bugs

If you come across a problem in Jalview where something is not working as described, or how you think it should, you should first check the Jalview FAQ to see if this is a known problem and if there is a suggested workaround.

If there is no FAQ answer covering your problem then you can submit a bug report on the Jalview Issue Tracker. It is good practice to search the issue tracker first to see if the issue has already been reported. If an issue already exists please continue to add your own comments to the issue which may well help narrow down the problem, if not then you can create an account and submit a new bug report:

Make sure that you set Project to Jalview (JAL), and Issue Type to Bug or New Feature or Improvement appropriately.
Give a one line summary of the issue in the Summary.
In the Environment text box you can describe the system you are using. This is usually most easily done by opening the Java Console, clicking the Clear button, and then immediately on the Copy to clipboard button, and then pasting the clipboard into the text box.

You can then give more detailed information about how to recreate the problem in the Description text box. If you want to attach any screenshots or example alignment files that demonstrate the problem then you can drag them to the Create Issue dialog in your browser, or use the Attachment browse facility to locate them on your computer.

To help the Jalview team with diagnosing a particular issue, it is really helpful if you can also add more detailed logs output whilst re-creating the problem. To do this, open the Java Console, click the Clear button and select TRACE in the Log level drop down list.
Whilst leaving the console open, perform the task in Jalview that re-creates the problem.
Then you can copy the debug information in the Java Console by clicking on the Copy to clipboard button and then paste that into the Description, or a Comment of your issue.

For other queries or comments about Jalview, remember you can contact the Jalview team using email via the Jalview Discussion Forum, on Twitter @Jalview, or for technical discussions, via the Jalview developer's chatroom at https://gitter.im/jalview/developers.