From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 2 Jul 2019 22:35:18 +0000 (+0100)
Subject: JAL-3111 updated what’s new… still more to come !
X-Git-Tag: Release_2_11_0~2^2~5
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=e6322a597de6a9d28819a643a598f5e7d60c0242

JAL-3111 updated what’s new… still more to come !
---

diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html
index f7df4c2..aaef948 100755
--- a/help/help/html/whatsNew.html
+++ b/help/help/html/whatsNew.html
@@ -33,17 +33,25 @@
   <ul>
     <li><em>VCF Support</em>. Proteins and genomic contigs with
       chromosomal location annotation (such as protein coding genes
-      retrieved from Ensembl) can be annotated with variants imported
-      from a local VCF file.</li>
+      retrieved from Ensembl) can be annotated with variants <a
+      href="features/importvcf.html">imported from a local VCF file</a>.</li>
     <li><em>The Jalview Launcher and Update System</em><br />
       Jalview's new installation model means you'll only need to
       download and install Jalview once. After installation, Jalview
       will automatically keep itself up to date. The launcher also sets
       Jalview's memory automatically, so you'll never again have to
-      manually configure Java's memory settings.<br />We are grateful to
-      Install4J who provided us with a free license for their
+      manually configure Java's memory settings.<br />We are grateful
+      to Install4J who provided us with a free license for their
       installation system, and Jalview's over the air update system is
-      via Getdown.</li>
+      based on Three Rings' Getdown system.</li>
+    <li><em>Backup files</em><br />Jalview will automatically
+      create backups when overwriting existing files, and - unlike with
+      earlier versions, should Jalview crash during a save, the original
+      file will be unaffected.</li>
+    <li><em>PCA plots stored in Jalview Projects</em><br />The PCA
+      viewer has also been enhanced and the user interface revised.</li>
+    <li>
+    </li>
   </ul>
   <p>
     The full list of bugs fixed in this release can be found in the <a
@@ -52,20 +60,10 @@
   <p>
     <strong>Jalview and Java 11, 13, and onwards</strong>
   </p>
-  <p>Java 11 provides improved performance and better OS
-    integration, so we now recommend users select our Java 11 Jalview
-    distribution rather than the legacy Java 8 build.</p>
-  <em>Known Issues - update for 211 </em>
-  <ul>
-    <li>OSX: The 'Open File' dialog for Jalview's Groovy Console
-      appears with the title 'Save As', and attempting to select a file
-      to load yields a FileNotFound exception.</br>The workaround is to first
-      clear the 'Untitled' filename before selecting the file you wish
-      to load.
-    </li>
-    <li>OSX: Links don't open when clicked on or via the Sequence
-      or Alignment window popup menu.</li>
-    <li>OSX (Webstart): Jalview only displays old news feed items</li>
-  </ul>
+  <p>The Jalview application comes bundled with its own independent
+    Java installation which will be updated automatically from
+    www.jalview.org. Version 2.11.0 includes an AdoptOpenJDK Java 1.8
+    runtime, but installations will be migrated to the latest Java
+    release once remaining issues have been addressed.</p>
 </body>
 </html>