<p>
<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>
+ 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 <a
+ href="#reportingbugs">reporting bugs</a>, since they help the
+ Jalview developers diagnose and 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>
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
+ <strong>Jalview Desktop Installation Launch Logs</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
by default
</li>
</ul>
- <p><strong>Jalview Executable Jar</strong><br/>If you are using the Jalview executable jar file (also
+ <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
composer or issue tracker).
</p>
- <h3>Reporting Bugs</h3>
+ <p><strong><a name="reportingbugs">Reporting Bugs</a></strong></p>
<p>
If you come across a problem in Jalview where something is not