X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=15fdd37d60d5dd43062c6514da49301b77d92d37;hb=ae5a45158724104362a6abaab8b3eefdde9a6c6a;hp=e6f23b2f3956175edf9019ae87ba83d5d806b1a3;hpb=a84a61e465c49e5e279ff78884004815dcd18367;p=jalview.git

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index e6f23b2..15fdd37 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -59,27 +59,197 @@ li:before {
     <tr>
       <td width="60" align="center" nowrap><strong><a
           id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
-          <em>01/02/2022</em></strong></td>
+          <em>3/03/2022</em></strong></td>
       <td align="left" valign="top">
         <ul>
           <li>
-            <!-- -->
+            <!-- JAL-3616 JAL-3551 JAL-2322 -->Support for viewing 3D
+            structures with ChimeraX and Pymol in addition to Jmol and
+            Chimera.
+          </li>
+          <li>
+            <!-- JAL-3503 -->New Preferences tab for adjusting Jalview's
+            memory settings at launch
+          </li>
+          <li>
+            <!-- JAL-3144 -->Reverted to Jalview 'classic' drop-down
+            menu for selecting which database to fetch from in sequence
+            fetcher dialog.
+          </li>
+          <li>
+            <!-- JAL-2226 -->Structure annotation rows for all mapped
+            chains in 3D structures are included in the 'Reference
+            Annotation' for a sequence
+          </li>
+          <li>
+            <!-- JAL-1260 -->Import Genbank and EMBL format flatfiles 
+          </li>
+          <li>
+            <!-- JAL-3821 -->ENA record's mol_type honoured so RNA
+            molecules imported from ENA records are shown as RNA
+          <li>
+            <!-- JAL-3863 -->Support for Canonical Uniprot IDs
+          </li>
+          <li>
+            <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
+            schema
+          </li>
+          <li>
+            <!-- JAL-3926 -->Uniprot and PDBe autosearch option is disabled by default
+          </li>
+          <li>
+            <!-- JAL- -->
+          </li>
+          <li>
+          </li>
+        </ul> <em>JalviewJS</em>
+        <ul>
+          <li>
+            <!-- 3624 -->PDB structures mapped to Uniprot Sequences with
+            SIFTS
+          </li>
+          <li>
+            <!-- JAL- -->
+          </li>
+          <li>
+            <!-- JAL- -->
           </li>
-        </ul> <!-- <em>Development</em>
+          <li>
+            <!-- JAL- -->
+          </li>
+          <li>
+            <!-- JAL-3163 -->Missing message bundle keys are only
+            reported once per key (avoids excessive log output in js
+            console)
+          </li>
+          <li>
+            <!-- JAL-3168 -->Feature type is included in the title of
+            the Feature Settings' Colour Chooser dialog
+          </li>
+          <li></li>
+        </ul> <em>Development</em>
         <ul>
+          <li>
+            <!--   -->First integrated JalviewJS and Jalview release
+          </li>
           <li>Updated building instructions</li>
-        </ul> -->
+          <li>
+            <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
+            process, added support for system package provided eclipse
+            installs on linux
+          </li>
+          <li>Install4j 9.0.x used for installer packaging</li>
+          <li>Notarized MacOS installer for compatibility with Big
+            Sur and Monterey</li>
+          <li>
+            <!-- JAL-3805 -->Uninstaller application for old
+            (InstallAnywhere based) Jalview installations removed from
+            the DMG
+          </li>
+          <li>
+            <!-- JAL-3930 -->Improved use of installers for unattended
+            installation with a customizedId of "JALVIEW" in install4j's
+            Jalview Launcher
+          </li>
+
+        </ul>
 
       </td>
       <td>
         <ul>
+                  <li>
+            <!-- JAL-3674 -->Slow structure commands can block Jalview
+            execution
+          </li>
+        <li>
+            <!-- JAL-3904 -->Structure window's viewer-specific menu
+            disappears when only one structure is shown (and many
+            sequences:one chain mappings are present)
+          </li>
+          <li>
+            <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
+            the first SEQUENCE_GROUP defined
+
+          </li>
+        
+          <li>
+            <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
+            propagated between Linked CDS - Protein alignments and their
+            trees (known defect from 2.11.1.3)
+          </li>
+          <li>
+            <!-- JAL-3761  -->Not all codon positions highlighted for
+            overlapping exon splice sites (e.g due to RNA slippage)
+          </li>
+                    <li>
+            <!-- JAL-3794 -->X was not being recognised as the unknown base
+            in DNA sequences
+          </li>
           <li>
             <!-- JAL-3915 -->Removed RNAview checkbox and logic from
             Structure Preferences
           </li>
+          <li>
+            <!--  JAL-3583 -->Tooltip behaviour improved (slightly)
+          </li>
+          <li>
+            <!-- JAL-3162 -->Can edit a feature so that start &gt; end
+          </li>
+          <li>
+            <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
+            modified graduated colour
+          </li>
+          <li>
+            <!-- JAL-3788 -->New View with automatic 'Show Overview'
+            preference enabled results in Null Pointer Exceptions when
+            clustal colouring is enabled
+          </li>
+          <li><!-- JAL-3275 -->Can open multiple Preferences panels</li>
+          <li>
+            <!-- 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>
+            <!-- -->
+          </li>
+          <li>
+            <!-- -->
+          </li>
+          <li>
+            <!-- -->
+          </li>
+          <li>
+            <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
+            via Info.args when there are arguments on the URL
+          </li>
+          <li>
+            <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
+          </li>
+          <li>
+            <!-- JAL-3603 -->Annotation file fails to load from URL in
+            JalviewJS
+          </li>
         </ul> <em>Development</em>
         <ul>
-          <li>Fixed non-fatal gradle errors during build</li>
+          <li>Gradle
+            <ul>
+              <li>Fixed non-fatal gradle errors during build</li>
+              <li>
+                <!--  JAL-3745 -->Updated build.gradle for use with
+                Gradle v.6.6+
+              </li>
+            </ul>
+          </li>
+
         </ul>
       </td>
     </tr>
@@ -88,18 +258,20 @@ li:before {
           id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
           <em>18/01/2022</em></strong></td>
       <td></td>
-      <td align="left" valign="top"><em>Security</em>
+      <td align="left" valign="top">
         <ul>
           <li>
-            <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
-            certificates.
-          </li>
-          <li>
-            <!-- JAL-3702, JAL-3935 -->Files open in Jalview cannot be
+            <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
             updated by Jalview or other applications (Windows, other non
             Unix/BSD OSs)
           </li>
-        </ul></td>
+        </ul> <em>Security</em>
+        <ul>
+          <li>
+            <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
+            certificates.
+          </li>
+        </ul>
     </tr>
     <tr>
       <td width="60" align="center" nowrap><strong><a