JAL-3477 added help documentation for executable jar command line arguments -jvmmempc...

diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html
index 0d800cf..1eecfb9 100644 (file)
--- a/help/help/html/features/clarguments.html
+++ b/help/help/html/features/clarguments.html
@@ -34,6 +34,11 @@
   parameters, then include it at the beginning of the command line to
   ensure they are processed before any remaining arguments.
   <br>
+  Typical command line execution follows the following pattern:
+  <pre>
+  jalview -open &lt;Alignment File/URL&gt; [additional import arguments] [export arguments]
+  </pre>
+  
   <table width="100%" border="1" cellspacing="0" cellpadding="0">
     <tr>
       <td width="27%"><div align="center">-nodisplay</div></td>
@@ -41,7 +46,11 @@
           User Interface. (automatically disables questionnaire, version
           and usage stats checks)</div></td>
     </tr>
-
+    <tr>
+      <td><div align="center">-open FILE/URL</div></td>
+      <td><div align="left">Specify the alignment file to
+          open or process by providing additional arguments.</div></td>
+    </tr>
     <tr>
       <td><div align="center">-props FILE/URL</div></td>
       <td><div align="left">Use the given Jalview properties

diff --git a/help/help/html/features/commandline.html b/help/help/html/features/commandline.html
index e00d390..f0e04d5 100644 (file)
--- a/help/help/html/features/commandline.html
+++ b/help/help/html/features/commandline.html
@@ -65,10 +65,31 @@ open /Applications/Jalview.app --args -open ~/myalignment.fa</pre><em>(put
   </p>
   <p>
     <strong>Passing JVM Arguments to Jalview</strong><br /> If you need
-    to modify parameters for Jalview's Java Virtual Machine, then take a
-    look at the instructions for how to <a href="../memory.html#jvm">setting
-      the JVM's maximum memory</a>.
+    to modify parameters for Jalview's Java Virtual Machine, or
+    configure system properties, then take a look at the instructions
+    for how to <a href="../memory.html#jvm">setting the JVM's
+      maximum memory</a>.<br /> 
+  <p>
+    <strong>Changing Jalview's 'Look and Feel'</strong> <br />If you
+    are experiencing issues with the font size or layout of Jalview's
+    GUI, you can try changing Jalview's 'Look and feel' by
+    specifying a custom system property 'laf' on startup (see <a
+      href="../memory.html#jvm">setting the JVM's memory</a> for
+    instructions on how to do this for your platform). <br />For the
+    Jalview standalone executable jar, simply provide one of the
+    property settings before the -jar argument
   </p>
+  <ul>
+    <li>-Dlaf=system (default look and feel for the OS)</li>
+    <li>-Dlaf=crossplatform (Java's Metal Look and Feel)</li>
+    <li>-Dlaf=nimbus (Java's alternative Nimbus Look and Feel)</li>
+    <li>-Dlaf=mac (only has an effect on OSX)</li>
+    <li>-Dlaf=gtk (only has an effect on Linux)</li>
+  </ul>
+  The currently configured look and feel is logged to Jalview's console.
+  Once the look and feel has been changed, it will be stored in
+  Jalview's .jalview_properties file for future Jalview sessions.
+
   <p>&nbsp;</p>
   <p>&nbsp;</p>
 </body>

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 83a9cc3..6820883 100755 (executable)
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -66,7 +66,37 @@ li:before {
             <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
             residue in cursor mode
           </li>
-          <li></li>
+          <li>
+            <!-- JAL-3695 -->Support import of VCF 4.3 by updating
+            HTSJDK from 2.12 to 2.23
+          </li>
+          <li>
+            <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
+            optimisations and improvements suggested by Bob Hanson and
+            improved compatibility with JalviewJS
+          </li>
+          <li>
+            <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
+            alignments from Pfam and Rfam
+          </li>
+          <li>
+            <!-- JAL-2656 -->Recognise GZipped content for URLs and File
+            import (no longer based on .gz extension)
+          </li>
+          <li>
+            <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
+          </li>
+          <li>
+            <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
+            ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
+            EMBL flat file
+          </li>
+        </ul> <em>Launching Jalview</em>
+        <ul>
+          <li>
+            <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
+            through a system property
+          </li>
         </ul>
       </td>
       <td align="left" valign="top">
@@ -83,6 +113,25 @@ li:before {
             <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
             multiple EMBL gene products shown for a single contig
           </li>
+          <li>
+            <!-- JAL-3696 -->Errors encountered when processing variants
+            from VCF files yield "Error processing VCF: Format specifier
+            '%s'" on the console
+          </li>
+          <li>
+            <!-- JAL-3697 -->Count of features not shown can be wrong
+            when there are both local and complementary features mapped
+            to the position under the cursor
+          </li>
+          <li>
+            <!-- JAL-2983 -->Slider with negative range values not
+            rendered correctly in VAqua4 (Since 2.10.4)
+          </li>
+        </ul>
+        <em>New Known defects</em>
+        <ul>
+          <li><!-- JAL-3701 -->Stale build data in jalview standalone jar builds (only affects 2.11.1.1 branch)
+          </li>
         </ul>
       </td>
     </tr>