From 73ab7e843ed0a215b8794b0734b9c6ed7590756e Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 16 Aug 2017 20:17:03 +0100
Subject: [PATCH] JAL-2418 whats new for 2.10.2

---
 help/html/whatsNew.html |  114 ++++++++++++++++++++++++++++-------------------
 1 file changed, 67 insertions(+), 47 deletions(-)

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 60769a4..2b792e0 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -26,56 +26,86 @@
   <p>
     <strong>What's new in Jalview 2.10.2 ?</strong>
   </p>
-  <p>
-    Full details about Jalview 2.10.2 are in the <a
-      href="releases.html#Jalview.2.10.2"> Release Notes</a>, but the
+  <p>This August 2018 release of Jalview introduces new user interface features, improved and more extensible tree and PCA analysis, more robust 3D structure viewing with UCSF Chimera and an updated service client for JABAWS. The full list of bug fixes and new features can be found in the <a
+      href="releases.html#Jalview.2.10.2"> 2.10.2 Release Notes</a>, but the
     highlights are below.
   </p>
   <ul>
-    <li><strong>New UI, and faster and more configurable
-        implementation for PCA, Neighbour-Joining and UPGMA Trees</strong><br>
-      Menu entries for calculating PCA and different types of tree have
-      been replaced by a single <em>Calculations</em> dialog box. The
-      underlying implementation for the PCA and tree calculations have
-      been made faster and more memory efficient. A new framework has
-      also been created for the score models used to calculate distances
-      between sequences. This framework allows import of substitution
-      matrices in NCBI and AAIndex format, and custom score models to be
-      created via a groovy script.</li>
+    <li><strong>New dialog and faster and more
+        configurable Tree and PCA calculations</strong><br> Menu entries for
+      calculating PCA and different types of tree have been replaced by
+      a single <a href="calculations/calculations.html"><em>Calculations</em>
+        dialog box</a>. The underlying implementation for the PCA and tree
+      calculations have been made faster and more memory efficient.</li>
+    <li><strong>Extensible score models</strong><br />A new
+      framework has also been created for the score models used to
+      calculate distances between sequences and shade alignments. This
+      framework allows import of substitution matrices in NCBI and
+      AAIndex format.<br />
+    <strong>PCA Bug Fixes</strong>. Jalview's implementation of PCA
+      differed in its treatment of gaps and non-standard residues. The
+      BLOSUM62 matrix also included a typo that affected results. See the
+      <a href="releases.html#2102scoremodelbugs">2.10.2 release note
+        about score model bugs</a> for details and how to reinstate legacy
+      behaviour.</li>
     <li><strong>Update to JABAWS 2.2</strong><br />Jalview's
       alignment, protein conservation analysis, and protein disorder and
       RNA secondary structure prediction services are now provided by <a
       href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS 2.2</a>.
-      Several of the programs provided as services have been updated, so
-      their options and parameters have changed.</li>
-    <li>New preferences for <a href="webServices/urllinks.html">opening
-        web pages for database cross-references</a> via the UK Elixir's
-      EMBL-EBI's MIRIAM database and identifiers.org services.
-    </li>
-    <li><em>Showing and hiding regions</em>
-      <ul>
-        <li><a href="menus/popupMenu.html#hideinserts">Hide
-            insertions</a> in the PopUp menu has changed its behaviour.
-          Prior to 2.10.2, columns were only shown or hidden according
-          to gaps in the sequence under the popup menu. Now, only
-          columns that are gapped in all selected sequences as well as
-          the sequence under the popup menu are hidden, and column
-          visibility outside the selected region is left as is. This
-          makes it easy to filter insertions from the alignment view
-          (just select the region containing insertions to remove)
-          without affecting the rest of the hidden columns.</li>
-      </ul></li>
-    <li>Recent search histories for <a
+      Several of the programs provided as JABAWS 2.2 services have been
+      updated, so their options and parameters have changed.</li>
+    <li><strong>URL linkouts to other bioinformatics
+        databases</strong><br />New preferences for <a
+      href="webServices/urllinks.html">opening web pages for
+        database cross-references</a> via the UK Elixir's EMBL-EBI's MIRIAM
+      database and identifiers.org services.</li>
+    <li><strong>Showing and hiding regions</strong> <br /> <a
+      href="menus/popupMenu.html#hideinserts">Hide insertions</a> in the
+      PopUp menu has changed its behaviour. Prior to 2.10.2, columns
+      were only shown or hidden according to gaps in the sequence under
+      the popup menu. Now, only columns that are gapped in all selected
+      sequences as well as the sequence under the popup menu are hidden,
+      and column visibility outside the selected region is left as is.
+      This makes it easy to filter insertions from the alignment view
+      (just select the region containing insertions to remove) without
+      affecting the rest of the hidden columns.</li>
+    <li><strong>Recent search history for Find, PDBe and
+        Uniprot</strong><br />Easily repeat a previous search for <a
       href="features/search.html#queryhistory">Find</a> and the free
       text search system (for querying Uniprot and the PDBe).</li>
+    <li><strong>Improved Overview Window</strong><br />The <a
+      href="features/overview.html">alignment overview</a> is now easier
+      to use when working with alignments of more than 5000 rows and
+      columns, and features a new pop-up menu that allows hidden regions
+      to be excluded from the overview. It also works with CDS/Protein
+      alignments and MSA views in wrapped mode.</li>
+    <li><strong>3D Structure</strong><br />Jalview's communication
+      with UCSF Chimera has been made more robust, particularly when
+      working with many structures and long sequences. Regions in
+      structures that correspond to hidden regions in an alignment view
+      are now left un-coloured, making it easier to highlight specific
+      features in 3D. See below for <a href="#experimental">experimental
+        features for exchanging annotation between Chimera and Jalview.</a></li>
   </ul>
   <p>
+    <strong>Scripting</strong><br />New <a
+      href="http://www.jalview.org/examples/groovy">groovy examples</a>
+    demonstrate Jalview 2.10.2 APIs for creation of data-driven
+    colourschemes, and custom alignment file handlers. The <a
+      href="groovy/featuresCounter.html">FeatureAnnotationWorker</a>
+    introduced in Jalview 2.10 has also been refactored to allow
+    efficient counting across multiple feature types. Please be aware
+    that feature counter scripts created for earlier versions will not
+    execute in Jalview 2.10.2.
+  </p>
+  <p>
     <strong><a name="experimental">Experimental Features</a></strong>
   </p>
   <p>
-    This release of Jalview includes a new option in the Jalview Desktop
-    that allows you to try out features that are still in development.
-    To access the features described below, please first enable the <strong>Tools&#8594;Enable
+    This release of Jalview introduces an <em>Experimental Features</em>
+    option in the Jalview Desktop's <em>Tools</em> menu that allows you
+    to try out features that are still in development. To access the
+    experimental features below - first enable the <strong>Tools&#8594;Enable
       Experimental Features</strong> option, and then restart Jalview.
   </p>
   <ul>
@@ -84,16 +114,6 @@
         the Chimera viewer's Chimera menu</a> allow positional annotation to
       be exchanged between Chimera and Jalview.</li>
   </ul>
-  <p>
-    <strong>Scripting</strong><br />New <a
-      href="http://www.jalview.org/examples/groovy">groovy examples</a>
-    demonstrate Jalview 2.10.2 APIs for creation of data-driven
-    colourschemes, and custom alignment file handlers. The <a
-      href="groovy/featuresCounter.html">FeatureAnnotationWorker</a>
-    introduced in Jalview 2.10 has also been refactored to allow
-    efficient counting across multiple feature types. Please be aware
-    that feature counter scripts created for earlier versions will not
-    execute in Jalview 2.10.2.
-  </p>
+
 </body>
 </html>
-- 
1.7.10.2