JAL-2588 JAL-2603 JAL-2610 release notes and docs

diff --git a/help/html/features/overview.html b/help/html/features/overview.html
index ac5aecb..2a656a3 100755 (executable)
--- a/help/html/features/overview.html
+++ b/help/html/features/overview.html
@@ -27,13 +27,14 @@
     <strong>View&#8594;Overview window</strong>
   </p>
   <p>Select the overview window menu item to get a navigable image
-    of the whole alignment.</p>
+    of the whole alignment. By default, gaps are shown as dark grey, in
+    the overview (since 2.10.2b1).</p>
   <p>The red box indicates the currently viewed region of the
     alignment, this may be moved by clicking and dragging with the
     mouse.</p>
   <p>Click anywhere else in the overview to centre the view on that
     position</p>
-    <p></p>
+  <p></p>
   <p>
     <strong>Hiding hidden regions in the overview</strong>
   </p>
@@ -41,13 +42,15 @@
     Hidden sequences and columns are by default shown as dark-grey rows
     and columns in the overview. Hidden regions can also be omitted
     entirely (to make the Overview 'WYSIWIG') by <strong>Right-clicking</strong>
-    (or CMD-Clicking) to open the overview's popup menu.<br />
-    <br /> <em>The option to include/exclude hidden regions in the
+    (or CMD-Clicking) to open the overview's popup menu.<br /> <br />
+    <em>The option to include/exclude hidden regions in the
       overview was introduced in Jalview 2.10.2</em>.
   
   <p>
     <img src="overview.gif" width="407" height="137">
   </p>
   <p>&nbsp;</p>
+  <em>Previous to 2.10.2b1, gaps were white, and sequences shown as
+    dark grey unless coloured.</em>
 </body>
 </html>

diff --git a/help/html/releases.html b/help/html/releases.html
index c331ae1..8f5a024 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -77,11 +77,24 @@ li:before {
       <td><div align="left">
           <em></em>
           <ul>
+            <li>
+              <!-- JAL-2588 -->Show gaps in overview window by colouring
+              in grey (sequences used to be coloured grey, and gaps were
+              white)
+            </li>
           </ul>
         </div></td>
       <td><div align="left">
           <em></em>
           <ul>
+            <li>
+              <!-- JAL-2603 -->Overview window throws NPE if show boxes
+              format setting is unticked
+            </li>
+            <li>
+              <!-- JAL-2610 -->Groups are coloured wrongly in overview
+              if group has show boxes format setting unticked
+            </li>
           </ul>
         </div></td>
     

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index ff0fe35..92ad73f 100755 (executable)
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -30,6 +30,9 @@
     This is patch release for 2.10.2. See the <a
       href="releases.html#Jalview2.10.2b1">release notes</a>.
   </p>
+  <ul>
+    <li>Gaps are now rendered as dark grey in overview window</li>
+  </ul>
   <p>
     <strong>What's new in Jalview 2.10.2 ?</strong>
   </p>