Merge branch 'releases/Release_2_10_2_Branch'

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 2b792e0..3f9d76e 100755 (executable)
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -26,9 +26,13 @@
   <p>
     <strong>What's new in Jalview 2.10.2 ?</strong>
   </p>
-  <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>
+    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 dialog and faster and more
@@ -41,11 +45,11 @@
       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
+      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
@@ -69,6 +73,15 @@
       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>Gap count - a.k.a. the Occupancy
+        Annotation Row</strong><br /> Another way to filter columns according to
+      the presence of gaps is to enable the <strong>Occupancy
+        Annotation</strong> row via Jalview's Preferences. This annotation row
+      shows a histogram of the number of aligned residues at each
+      column. The <a href="features/columnFilterByAnnotation.html">Select
+        By Annotation</a> dialog now also includes a percentage threshold
+      mode, to make it easy to filter alignments to show only those
+      columns with a particular fraction of aligned sequences.</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