X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=d13a435779ecab4e2126343beba8f7edd03092dc;hp=a7b2868fe6e2d10d6109339d1f89a03afeaad786;hb=a79d39451d3a2948d14f2a3152971eafae8f3b3e;hpb=63c646cffc2c9cfebdc7b9e5ea51e28bdf33dc58

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index a7b2868..d13a435 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -58,8 +58,75 @@ li:before {
     </tr>
     <tr>
       <td width="60" align="center" nowrap><strong><a
+          id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.1">.1</a><br />
+          <em>05/04/2022</em></strong></td>
+      <td align="left" valign="top">
+        <ul>
+          <li>
+            <!-- JAL-3973 -->Distribution Tarball includes git commit
+            and branch details
+          </li>
+        </ul>
+      </td>
+      <td align="left" valign="top">
+        <ul>
+          <li>
+            <!-- JAL-3975 -->Keyboard mode (F2) stops working after
+            using the "Create sequence feature" dialog
+          </li>
+          <li>
+            <!-- JAL-3976 -->3D Structure chooser fails to select
+            structures from 3D-beacons and pops up a 'null' dialog
+          </li>
+          <li>
+            <!-- JAL-3985 -->PDB FTS query results in error dialog
+            containing '414' [URL too long]
+          </li>
+          <li>
+          <!-- JAL-3980 JAL-3981 -->Sequence ID tooltip not shown during
+            long running retrieval/crossref operations (affects at least
+            2.11.1 onwards)
+          </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-3984 -->Keyboard mode (F2) stops working after
+            using the "Text Colour" dialog
+          </li>
+          <li>
+            <!-- JAL-3873 -->Colour by->all views doesn't allow
+            colouring same structure from different views (since
+            2.11.2.0)
+          </li>
+          <li>
+            <!-- JAL-3981 --> Sequence Details report can take a long
+            time to be displayed for heavily annotated sequences (such
+            as single genome contigs for highly studied organisms)
+          </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-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 +144,6 @@ 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 +158,20 @@ 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>
@@ -108,29 +180,98 @@ li:before {
             disabled by default
           </li>
           <li>
-            <!-- JAL-3530 -->-nowebservicediscovery command line argument to
-            prevent automatic discovery of analysis webservices on
-            launch
+            <!-- JAL-3144 -->Reverted to Jalview 'classic' drop-down
+            menu for selecting which database to fetch from in sequence
+            fetcher dialog.
           </li>
           <li>
-            <!-- JAL-3728 -->Jalview logos shown for Jalview Java
-            Console and other window widgets in taskbar and dock rather
-            than anonymous 'Java' icons
+            <!-- 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>
-        </ul> <em>JalviewJS</em>
+          <li>
+            <!-- JAL-3530 -->-nowebservicediscovery command line
+            argument to prevent automatic discovery of analysis
+            webservices on launch
+          </li>
+          <li>
+            <!-- JAL-3618 -->Allow 'App' directories to be opened when
+            locating Chimera, ChimeraX or Pymol binaries via filechooser
+            opened by double clicking the Structure Preferences' path
+            textbox
+          </li>
+          <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-3624 -->PDB structures mapped to Uniprot Sequences with
-            SIFTS
+            <!-- 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-3208 -->setprop commandline argument reinstated for JalviewJS only 
+            <!-- JAL-3805 -->Uninstaller application for old
+            (InstallAnywhere based) Jalview installations removed from
+            the OSX disk image
           </li>
           <li>
-            <!-- JAL- -->
+            <!-- JAL-3608 -->Options to allow user to choose the (Swing)
+            Look and Feel (LaF) used by Jalview
           </li>
           <li>
-            <!-- JAL- -->
+            <!-- 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>
+          <li>
+            <!-- JAL-3594 -->New splashscreens for Jalview, Jalview Test
+            and Jalview Develop applications.
+          </li>
+          <li>
+            <!-- JAL-3728 -->Jalview logos shown for Jalview Java
+            Console and other window widgets in taskbar and dock rather
+            than anonymous 'Java' icons
+          </li>
+        </ul> <em>JalviewJS</em>
+        <ul>
+          <li>
+            <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences
+            with SIFTS
+          </li>
+          <li>
+            <!-- JAL-3208 -->setprop commandline argument reinstated for
+            JalviewJS only
           </li>
           <li>
             <!-- JAL-3163 -->Missing message bundle keys are only
@@ -141,36 +282,40 @@ 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
             Jalview Launcher
           </li>
-
+          <li>
+            <!-- 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
@@ -184,7 +329,6 @@ li:before {
           <li>
             <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
             the first SEQUENCE_GROUP defined
-
           </li>
 
           <li>
@@ -223,26 +367,29 @@ 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
+            <!-- JAL-3633 -->Properly configure HTTPS proxy settings
+            from Preferences
           </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-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
@@ -267,6 +414,14 @@ 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>
@@ -510,6 +665,12 @@ 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>
@@ -590,6 +751,11 @@ 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>