X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=e02d472b33e5bf0b3e3020e479525d9057bde148;hp=2f9c09653bea5452c61235674051f92baa1d560c;hb=e7338a61f3ce96dadf44ac80b2b32cc5ba4b94c8;hpb=ca74027f55fb1f8af9fef0d77348449a07a1b5d5

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 2f9c096..e02d472 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -68,6 +68,10 @@ li:before {
             Chimera.
           </li>
           <li>
+            <!-- JAL-3871 JAL-3874 -->Upgraded bundled version of Jmol
+            to 14.31.53
+          </li>
+          <li>
             <!-- JAL-3829 -->Discover 3D structure data for sequences
             with Uniprot references via 3D-Beacons
           </li>
@@ -101,8 +105,9 @@ li:before {
           </li>
           <li>
             <!-- JAL-3018 -->Updated Ensembl REST Client compatibility
-            to 15.2 and revised model organism names (rat, xenopus, dmelanogaster now
-            rattus_norvegicus, xenopus_tropicalis, drosophila_melanogaster)
+            to 15.2 and revised model organism names (rat, xenopus,
+            dmelanogaster now rattus_norvegicus, xenopus_tropicalis,
+            drosophila_melanogaster)
           </li>
           <li>
             <!-- JAL-3881 -->Sequence IDs split on '_' as well as other
@@ -145,8 +150,7 @@ li:before {
             <!-- JAL-3837 -->GPL license info on splash screen and About
             text
           </li>
-        </ul>
-        <em>Jalview Native App</em>
+        </ul> <em>Jalview Native App</em>
         <ul>
           <li>
             <!-- JAL- -->New Jalview Develop app - making it even easier
@@ -162,18 +166,24 @@ li:before {
             than anonymous 'Java' icons
           </li>
           <li>
-            <!-- JAL-3608 -->Options to allow user to choose the (Swing) Look and Feel (LaF) used by Jalview
+            <!-- JAL-3608 -->Options to allow user to choose the (Swing)
+            Look and Feel (LaF) used by Jalview
           </li>
           <li>
-            <!-- JAL-3552, JAL-3609 -->Metal LaF used to improved operation on Linux Ubuntu with
-            HiDPI display in Java 11 (still known issues with HiDPI screens in java
-            8 and 11. see <a
-            href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>)
+            <!-- JAL-3552, JAL-3609 -->Metal LaF used to improved
+            operation on Linux Ubuntu with HiDPI display in Java 11
+            (still known issues with HiDPI screens in java 8 and 11. see
+            <a href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>)
           </li>
           <li>
-            <!-- JAL-3830 -->New command line launcher scripts (.sh, .ps1, .bat) usable on
-            macOS, Linux/Unix, Windows and documentation in Help.  Installer wizard has option
-            to add this to PATH, or link to it in your PATH.
+            <!-- JAL-3830 -->New command line launcher scripts (.sh,
+            .ps1, .bat) usable on macOS, Linux/Unix, Windows and
+            documentation in Help. Installer wizard has option to add
+            this to PATH, or link to it in your PATH.<br /> <em>This
+              is the recommended workaround for known issue about
+              working directory preservation when running native
+              application from command line. <!-- JAL-3523 -->
+          </em>
           </li>
           <li>
             <!-- JAL-3633 -->Getdown launcher inherits HTTP/S proxy
@@ -182,11 +192,12 @@ li:before {
         </ul> <em>JalviewJS</em>
         <ul>
           <li>
-            <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences with
-            SIFTS
+            <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences
+            with SIFTS
           </li>
           <li>
-            <!-- JAL-3208 -->setprop commandline argument reinstated for JalviewJS only 
+            <!-- JAL-3208 -->setprop commandline argument reinstated for
+            JalviewJS only
           </li>
           <li>
             <!-- JAL-3163 -->Missing message bundle keys are only
@@ -197,7 +208,14 @@ li:before {
             <!-- JAL-3168 -->Feature type is included in the title of
             the Feature Settings' Colour Chooser dialog
           </li>
-          <li></li>
+          <li>
+            <!-- JAL-3279 -->Build details reported in About window
+          </li>
+          <li>
+            <!-- JAL-3038 JAL-3071 JAL-3263 JAL-3084 -->Numerous minor
+            GUI additions and improvements in sync with Java
+            application.
+          </li>
         </ul> <em>Development</em>
         <ul>
           <li>
@@ -226,9 +244,7 @@ li:before {
             <!-- JAL-3907 -->Improved compatibility of Jalview build
             with Java 17 (next LTS target)
           </li>
-
         </ul>
-
       </td>
       <td>
         <ul>
@@ -244,7 +260,6 @@ li:before {
           <li>
             <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
             the first SEQUENCE_GROUP defined
-
           </li>
 
           <li>
@@ -290,23 +305,22 @@ li:before {
             <!-- JAL-3949 -->Standard out logging broken: messages only
             routing to stderr and appear as a raw template
           </li>
-        </ul> <em>JalviewJS</em>
-        <ul>
-          <li>
-            <!-- JAL-3202 -->Consensus profile may include zero (rounded
-            down) percentage values causing a divide by zero
-          </li>
-          <li>
-            <!-- -->
-          </li>
           <li>
-            <!-- -->
+            <!-- JAL-3739 -->Entering web service parameter values in
+            numerical field doesn't update the value of the parameter
+            until return is pressed.
           </li>
           <li>
-            <!-- -->
+            <!-- JAL-3749 -->Resolved known issue (from 2.11.1.1)
+            concerning duplicate CDS sequences generated when protein
+            products for certain ENA records are repeatedly shown via
+            Calculate-&gt;Show Cross Refs
           </li>
+        </ul> <em>JalviewJS</em>
+        <ul>
           <li>
-            <!-- -->
+            <!-- JAL-3202 -->Consensus profile may include zero (rounded
+            down) percentage values causing a divide by zero
           </li>
           <li>
             <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
@@ -331,13 +345,13 @@ li:before {
             </ul>
           </li>
 
-        </ul>
-        <em>Known Issues</em>
+        </ul> <em>Known Issues</em>
         <ul>
           <li>
             <!-- JAL-3764 -->Display of RESNUM sequence features are not
             suppressed when structures associated with a sequence are
-            viewed with an external viewer (Regression from 2.11.1 series)
+            viewed with an external viewer (Regression from 2.11.1
+            series)
           </li>
         </ul>
       </td>