- Jalview creates logs that can be extremely useful for diagnosing, or help to provide a workaround for, specific problems that you might encounter.
- </p>
- <p>
- The primary place to look for logs is in the <a href="#java_console">Java Console</a> which you can open from within Jalview by going to the <em>Tools</em> menu and checking the box next to <em>Show Java Console</em>. This option is stored in your Jalview preferences file and so is remembered across Jalview sessions.
- </p>
- <p>
- The Java Console will show you information about what the Jalview application is doing (often in the background) whilst it is running.
- </p>
- <p>
- However, it is possible that some early logging information from when Jalview is initially launched, is not shown in the Java Console:
- <br/>
- If you are using a standard desktop version of Jalview installed from one of our install4j installers, then Jalview's initial launch logging can be found in
+ <strong>The Java Console, Logging and Reporting Bugs<br /></strong>
+ </p>
+ <p>Like most programs, Jalview produces a series of messages
+ during its operation, often referred to as 'logs'. These logs can be
+ extremely useful for diagnosing and helping the Jalview developers
+ find a workaround for specific problems that you might encounter.</p>
+ <p>
+ The primary place to look for logs is in the <a href="#java_console">Java
+ Console</a> which you can open from within Jalview by going to the <em>Tools</em>
+ menu and checking the box next to <em>Show Java Console</em>. This
+ option is stored in your Jalview preferences file and so is
+ remembered across Jalview sessions.
+ </p>
+ <p>The Java Console will show you information about what the
+ Jalview application is doing (often in the background) whilst it is
+ running.</p>
+ <p>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:</p>
+ <p>
+ <strong>Jalview Desktop Installations</strong><br />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