JAL-4036 JAL-4012 note about Uniprot FTS workaround in search documentation, and...

[jalview.git] / help / help / html / logging.html

diff --git a/help/help/html/logging.html b/help/help/html/logging.html
index dce1c7b..4d7e2e3 100644 (file)
--- a/help/help/html/logging.html
+++ b/help/help/html/logging.html
@@ -26,10 +26,15 @@
   <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>
@@ -45,7 +50,7 @@
     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
@@ -65,7 +70,7 @@
       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
@@ -92,6 +97,15 @@
     Jalview.</p>
 
   <p>
+    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.
+  </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:
@@ -144,7 +158,7 @@
     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