X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=d9df33793b4610bb52ec13a8d6ced3dab6134f34;hb=9f01dcf165d1e3d13f9d0824fbbc60e72f408ff7;hp=65ef80aa1ce965f846a29b5c3fdf2453f04158bc;hpb=9155298ec531aa1af53e00509d29c235572373d8;p=jalview.git

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 65ef80a..d9df337 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -58,8 +58,59 @@ li:before {
     </tr>
     <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">.1</a><br />
+          <em>31/03/2022</em></strong></td>
+      <td align="left" valign="top">
+        <ul>
+          <li></li>
+        </ul>
+      </td>
+      <td align="left" valign="top">
+        <ul>
+          <li>
+            <!-- JAL-3975 -->Residue selection using keyboard input
+            stops working after first "Create sequence feature"
+          </li>
+          <li>
+            <!-- JAL-3976 -->3D Structure chooser fails to select
+            structures from 3D-beacons and pops up a 'null' dialog
+          </li>
+          <li>
+            <!-- JAL-3886 -->Pfam and Rfam alignment retrieval as
+            gzipped stockholm doesn't work on JalviewJS build of 2.11.2
+          </li>
+          <li>
+            <!-- JAL-3973 -->Cannot build Jalview 2.11.2.0 via gradle
+            from its source tarball
+          </li>
+        </ul> <em>New Known Issues</em>
+      <ul>
+          <li>
+            <!-- JAL-3873 -->Colour by->all views doesn't allow
+            colouring same structure from different views (since
+            2.11.2.0)
+          </li><li>
+          <!-- JAL-3980 -->
+          Sequence ID tooltip not showing during long running
+          retrieval/crossref operations (affects at least 2.11.1
+          onwards)
+          </li>
+          <li>
+            <!-- JAL-3972 -->Java 11 Only: Jalview 2.11.2.0 OSX install
+            not working due to VAqua requiring
+            sun.awt.image.MultiResolutionImage
+          </li>
+          <li>
+            <!-- JAL-3981 -->Sequence Details can take a long time to be
+            displayed for heavily annotated sequences (all versions)
+          </li>
+        </ul>
+      </td>
+    </tr>
+    <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>3/03/2022</em></strong></td>
+          <em>10/03/2022</em></strong></td>
       <td align="left" valign="top">
         <ul>
           <li>
@@ -77,15 +128,6 @@ li:before {
             structure mapped to positions involved in the alignment
           </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
@@ -100,6 +142,20 @@ li:before {
             <!-- JAL-3863 -->Support for Canonical Uniprot IDs
           </li>
           <li>
+            <!-- JAL-3503 -->New Preferences tab for adjusting Jalview's
+            memory settings at launch
+          </li>
+          <li>
+            <!-- JAL-3881 -->Sequence IDs split on '_' as well as other
+            non-alphanumerics when discovering database references with
+            'Fetch DB Refs'
+          </li>
+          <li>
+            <!-- JAL-3884 -->Suppressed harmless exceptions output to
+            Console whilst discovering database references for a
+            sequence
+          </li>
+          <li>
             <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
             schema
           </li>
@@ -108,6 +164,17 @@ li:before {
             disabled by default
           </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-3018 -->Updated Ensembl REST Client compatibility
+            to 15.2 and revised model organism names (rat, xenopus,
+            dmelanogaster now rattus_norvegicus, xenopus_tropicalis,
+            drosophila_melanogaster)
+          </li>
+          <li>
             <!-- JAL-3530 -->-nowebservicediscovery command line
             argument to prevent automatic discovery of analysis
             webservices on launch
@@ -118,10 +185,56 @@ li:before {
             opened by double clicking the Structure Preferences' path
             textbox
           </li>
-        </ul>
-        <em>Jalview Native App</em>
+          <li>
+            <!-- JAL-3632 JAL-3633 -->support for HTTP/S access via
+            proxies that require authentication
+          </li>
+          <li>
+            <!-- JAL-3103 -->New mechanism for opening URLs with system
+            default browser (works on OSX and Linux as well as Windows)
+          </li>
+          <li>
+            <!-- JAL-3871 JAL-3874 -->Upgraded bundled version of Jmol
+            to 14.31.53
+          </li>
+          <li>
+            <!-- JAL-3837 -->GPL license info on splash screen and About
+            text
+          </li>
+        </ul> <em>Jalview Native App</em>
         <ul>
           <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.<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>Notarized MacOS installer for compliance with latest
+            OSX releases (Monterey)</li>
+          <li>
+            <!-- JAL-3805 -->Uninstaller application for old
+            (InstallAnywhere based) Jalview installations removed from
+            the OSX disk image
+          </li>
+          <li>
+            <!-- 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>)
+          </li>
+          <li>
+            <!-- JAL-3633 -->Getdown launcher inherits HTTP/S proxy
+            configuration from jalview_properties
+          </li>
+          <li>
             <!-- JAL- -->New Jalview Develop app - making it even easier
             to get at Jalview's development builds
           </li>
@@ -137,17 +250,12 @@ 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 
-          </li>
-          <li>
-            <!-- JAL- -->
-          </li>
-          <li>
-            <!-- JAL- -->
+            <!-- JAL-3208 -->setprop commandline argument reinstated for
+            JalviewJS only
           </li>
           <li>
             <!-- JAL-3163 -->Missing message bundle keys are only
@@ -158,26 +266,28 @@ 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>
             <!--   -->First integrated JalviewJS and Jalview release
           </li>
-          <li>Updated building instructions</li>
+          <li>
+            <!-- JAL-3841,JAL-3248 -->Updated README and doc/building.md
+          </li>
           <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
@@ -187,11 +297,9 @@ li:before {
             <!-- JAL-3907 -->Improved compatibility of Jalview build
             with Java 17 (next LTS target)
           </li>
-
         </ul>
-
       </td>
-      <td>
+      <td align="left" valign="top">
         <ul>
           <li>
             <!-- JAL-3674 -->Slow structure commands can block Jalview
@@ -205,7 +313,6 @@ li:before {
           <li>
             <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
             the first SEQUENCE_GROUP defined
-
           </li>
 
           <li>
@@ -244,26 +351,29 @@ li:before {
             <!-- 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
+            <!-- JAL-3633 -->Properly configure HTTPS proxy settings
+            from Preferences
           </li>
           <li>
-            <!-- -->
+            <!-- JAL-3949 -->Standard out logging broken: messages only
+            routing to stderr and appear as a raw template
           </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
@@ -288,6 +398,14 @@ li:before {
             </ul>
           </li>
 
+        </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)
+          </li>
         </ul>
       </td>
     </tr>
@@ -531,6 +649,12 @@ li:before {
             <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
             when running on Linux (Requires Java 11+)
           </li>
+          <li>
+            <!-- JAL-1842 JAL-3509 -->RESNUM sequence features (the
+            green ones) are not automatically displayed when associated
+            structures are displayed or for sequences retrieved from the
+            PDB.
+          </li>
         </ul> <em>Launching Jalview</em>
         <ul>
           <li>
@@ -611,6 +735,11 @@ li:before {
             save in place.)
           </li>
           <li>
+            <!-- JAL-3509 -->Dragging a PDB file onto an alignment with
+            sequence features displayed causes displayed features to be
+            hidden.
+          </li>
+          <li>
             <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
             via command line
           </li>