From 1d5d33f827ff7759334f39fcc6b0d7389c0cb4b4 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Wed, 9 Mar 2022 08:09:45 +0000
Subject: [PATCH] JAL-3746 more docs tweaking and release notes

---
 help/help/html/features/preferences.html |    7 +--
 help/help/html/releases.html             |   90 +++++++++++++++---------------
 help/help/html/whatsNew.html             |   38 +++++++------
 3 files changed, 66 insertions(+), 69 deletions(-)

diff --git a/help/help/html/features/preferences.html b/help/help/html/features/preferences.html
index 25d59bf..6708c57 100755
--- a/help/help/html/features/preferences.html
+++ b/help/help/html/features/preferences.html
@@ -213,11 +213,6 @@
     structure information read from PDB will be processed and annotation
     added to associated sequences.
   <p>
-    <em>Use RNAView for secondary structure</em> - if selected, the
-    pyRNA RNAView service (<a href="https://github.com/fjossinet/PyRNA">https://github.com/fjossinet/PyRNA</a>)
-    will be called to derive secondary structure information for RNA
-    chains.
-  <p>
     <em>Add secondary structure annotation to alignment</em> - if
     selected, <a href="http://swift.cmbi.ru.nl/gv/dssp/">Jmol's
       implementation DSSP</a> will be used to add annotation to polypeptide
@@ -228,7 +223,7 @@
     the backbone atoms in the PDB file will be extracted as annotation
     lines shown on the alignment.<br/><em>Since 2.11.2, scores from the Temperature Column for structures imported via the 3D-Beacons network may be shown instead as model quality or reliability scores.</em>
   <p>
-    <em>Default structure viewer</em> - choose Jmol, CHIMERA, CHIMERAX or PYMOL for
+    <em><strong>Default structure viewer</strong></em> - choose Jmol, CHIMERA, CHIMERAX or PYMOL for
     viewing 3D structures.
   <p>
     <em>Path to Chimera/X/Pymol program</em> - Optional, as Jalview will search
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index e02d472..aaf923d 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -59,7 +59,7 @@ 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>8/03/2022</em></strong></td>
+          <em>9/03/2022</em></strong></td>
       <td align="left" valign="top">
         <ul>
           <li>
@@ -68,10 +68,6 @@ 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>
@@ -81,15 +77,6 @@ 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
@@ -104,10 +91,8 @@ li:before {
             <!-- JAL-3863 -->Support for Canonical Uniprot IDs
           </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)
+            <!-- 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
@@ -128,6 +113,17 @@ 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
@@ -147,23 +143,31 @@ li:before {
             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- -->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.
+            <!-- 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-3728 -->Jalview logos shown for Jalview Java
-            Console and other window widgets in taskbar and dock rather
-            than anonymous 'Java' icons
+            <!-- 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)
@@ -176,19 +180,22 @@ li:before {
             <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.<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
             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>
@@ -221,20 +228,13 @@ li:before {
           <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
diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html
index c8d0fa9..57aff06 100755
--- a/help/help/html/whatsNew.html
+++ b/help/help/html/whatsNew.html
@@ -24,17 +24,13 @@
 </head>
 <body>
   <p>
-    <strong>Welcome to Jalview Version $$Version-Rel$$ !!</strong> <br />Please
-    take a look at the <a href="releases.html#Jalview.$$Version-Rel$$">release
-      notes</a> for this build. Read on for the highlights.
+    <strong>Welcome to Jalview Version $$Version-Rel$$ !!</strong><br/>
   </p>
   <p>
-    <strong>Highlights in 2.11.2</strong>
-  </p>
-  <p>
-    <strong>New features for working with 3D Structure</strong><br />
-    Jalview 2.11.2 features a number of new capabilities described
-    below.
+    This Jalview release provides support for two popular 3D structure
+    visualisation tools, new features for discovery of 3D structures,
+    improved platform integration and a new command line tool allowing
+    Jalview to be more easily called from scripts.
   </p>
 
   <p>
@@ -59,21 +55,21 @@
       href="https://doi.org/10.1093/bioinformatics/btm329">doi:10.1093/bioinformatics/btm329</a>).<br /> <br />
     The <a href="features/preferences.html#structure">Structures
       Preferences tab</a> provides new options allowing ChimeraX and
-    Pymol to be used for visualising external 3D structures. Jalview
-    2.11.2 has been tested with Pymol 2.5.0 (community) and 2.5.2
-    (incentive). For ChimeraX, we recommend using v1.3 or later.<br />Views
+    Pymol to be used for visualising external 3D structures. Views
     from all structure viewers are saved in Jalview Projects, allowing
     them to be shared with others using Jalview 2.11.2 or later,
     providing they have the same viewer installed and configured to be
-    used with Jalview.
+    used with Jalview.<br/><br/>Jalview
+    2.11.2 has been tested with <strong>Pymol 2.5.0 (community)</strong> and <strong>2.5.2
+    (incentive)</strong>. For <strong>ChimeraX, we recommend using v1.3 or later</strong>.
   </p>
   <p>Other highlights include:</p>
   <ul>
+    <li>Import of annotated DNA and RNA loci via GenBank and EMBL
+      style flatfile</li>
     <li><strong>Easier configuration of <a
         href="features/preferences.html#startup">Jalview's memory
           allocation</a></strong></li>
-    <li>Import of annotated DNA and RNA loci via GenBank and EMBL
-      style flatfile</li>
     <li>Scripts for <a href="features/commandline.html">running
         Jalview via the command line</a> on macOS, Linux/Unix and Windows.
     </li>
@@ -85,9 +81,15 @@
         href="releases.html#Jalview.2.11.2.0">the Jalview 2.11.2.0
         release notes</a>.
     </p>
-    <p>
-      <strong>Known Issues</strong>
-    </p>
+  <p>
+    <strong>Known Issues</strong> <br />The following known issues will
+    be addressed in a minor patch release.
+  
+  <ul>
+    <li>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>
     <p></p>
 </body>
 </html>
-- 
1.7.10.2