From 6875edc608179e9710388439099542296f263c15 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 29 Oct 2020 20:01:45 +0000
Subject: [PATCH] =?utf8?q?JAL-3766=20what=E2=80=99s=20new=20and=20release=20?=
 =?utf8?q?notes=20for=202.11.1.3?=
MIME-Version: 1.0
Content-Type: text/plain; charset=utf8
Content-Transfer-Encoding: 8bit

---
 help/help/html/releases.html |    9 ++++----
 help/help/html/whatsNew.html |   52 ++++++++++++------------------------------
 2 files changed, 18 insertions(+), 43 deletions(-)

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 9aec5fa..ec4f041 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -80,8 +80,8 @@ li:before {
             first reported for 2.11.1.0)
           </li>
           <li>
-            <!-- JAL-3725 -->No tooltip or popup menu for genomic features
-            outwith CDS shown overlaid on protein
+            <!-- JAL-3725 -->No tooltip or popup menu for genomic
+            features outwith CDS shown overlaid on protein
           </li>
           <li>
             <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
@@ -97,9 +97,8 @@ li:before {
             always select corresponding protein sequences
           </li>
           <li>
-            <!-- JAL-3759 -->
-            <em>Make groups from selection</em> for a column selection
-            doesn't always ignore hidden columns
+            <!-- JAL-3759 --> <em>Make groups from selection</em> for a
+            column selection doesn't always ignore hidden columns
           </li>
         </ul> <em>Installer</em>
         <ul>
diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html
index a448aaa..bee8380 100755
--- a/help/help/html/whatsNew.html
+++ b/help/help/html/whatsNew.html
@@ -26,46 +26,22 @@
   <p>
     <strong>Jalview 2.11.1.3</strong>
   </p>
-  <p>Jalview 2.11.1.3 is the third patch release, fixing a bug
-    introduced in last weeks Jalview 2.11.1.1 release affecting display
-    of Jalview's example project for some users. Together, these
-    releases include fixes for a number of critical bugs, and also contains a
-    handful of new features suggested by the Jalview community.</p>
+  <p>Jalview 2.11.1.3 is the third patch release in the 2.11.1
+    series. Critical bugs resolved in this release include:</p>
   <ul>
-    <li>Shift+arrow keys navigate to next gap or residue in cursor
-      mode (enable with F2)</li>
-    <li>Support import of VCF 4.3 by updating HTSJDK from 2.12 to
-      2.23</li>
-    <li>Improved recognition of GZipped files from local disk or
-      retrieved via the web</li>
-    <li>EMBL and EMBL CDS database records retrieved from the
-      European Nucleotide Archive's Data API as 'EMBL Flatfile' records</li>
-    <li>Improved <a href="logging.html">Java Console and
-        logging</a> to help track down problems
-    </li>
-    <li>Improved support for Hi-DPI (4K) screens when running on
-      Linux (Requires Java 11+)</li>
-  </ul>
-  <p>Critical bug fixes include</p>
-  <ul>
-    <li>Jalview runs correctly when launched with Turkish language
-      settings</li>
-    <li>Peptide-to-CDS tracking broken when multiple EMBL gene
-      products shown for a single contig (such as viral genomes)</li>
-    <li>Errors encountered when processing variants from VCF files
-      yield "Error processing VCF: Format specifier '%s'" on the console</li>
-    <li>Count of features not shown can be wrong when there are
-      both DNA and Protein features mapped to the position under
-      the cursor</li>
-    <li>Sequence ID for reference sequence is clipped when Right
-      align Sequence IDs enabled</li>
-    <li>Find doesn't report matches that span hidden gapped columns</li>
-    <li>Jalview ignores file format parameter specifying output
-      format when exporting an alignment via the command line</li>
+    <li>Find doesn't highlight all motif matches for a sequence.</li>
+    <li>Mouse over highlighting, CDS reconstruction and problems
+      with virtual feature popups when working with linked CDS/Protein
+      alignments.</li>
+    <li>Result of aligning protein sequences linked to CDS results
+      in incorrect CDS alignment.</li>
+    <li>Jalview installer doesn't correctly install Jalview on
+      paths containing spaces.</li>
   </ul>
   <p>
-    For the full release notes, see <a href="releases.html#Jalview.2.11.1.1">the
-      Jalview 2.11.1.1 release notes</a>.
+    For the full release notes, see <a
+      href="releases.html#Jalview.2.11.1.3">the Jalview 2.11.1.3
+      release notes</a>.
   </p>
   <p>
     <strong>Known Issues</strong>
@@ -80,7 +56,7 @@
       v2.11.1.0)</li>
     <li>Drag and drop of alignment file onto alignment window when
       in a HiDPI scaled mode in Linux only works for the top left
-      quadrant of the alignment window</li>
+      quadrant of the alignment window.</li>
   </ul>
 </body>
 </html>
-- 
1.7.10.2