From 0b99e0d00521ef5d567bd0233cfe4853a3aea728 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 17 Nov 2017 21:29:19 +0000
Subject: [PATCH] JAL-2698 tidy release notes and whats new

---
 help/html/releases.html |  265 +++++++++++++++++++++++++++++++++++------------
 help/html/whatsNew.html |   12 ++-
 2 files changed, 206 insertions(+), 71 deletions(-)

diff --git a/help/html/releases.html b/help/html/releases.html
index 8b90e9c..1a48340 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -70,8 +70,7 @@ li:before {
     <tr>
       <td width="60" nowrap>
         <div align="center">
-          <strong><a name="Jalview.2.10.3">2.10.3</a><br />
-            <em>17/11/2017</em></strong>
+          <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
         </div>
       </td>
       <td><div align="left">
@@ -89,93 +88,227 @@ li:before {
               <!-- JAL-2773 -->Structure views don't get updated unless
               their colours have changed
             </li>
-            <li><!-- JAL-2495 -->All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)</li>
-            <li><!-- JAL-2790 -->'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs
+            <li>
+              <!-- JAL-2495 -->All linked sequences are highlighted for
+              a structure mousover (Jmol) or selection (Chimera)
+            </li>
+            <li>
+              <!-- JAL-2790 -->'Cancel' button in progress bar for
+              JABAWS AACon, RNAAliFold and Disorder prediction jobs
+            </li>
+            <li>
+              <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
+              view from Ensembl locus cross-references
+            </li>
+            <li>
+              <!-- JAL-2685 -->Start/End limits are shown in Pairwise
+              Alignment report
+            </li>
+            <li>
+              <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
+              feature can be disabled
+            </li>
+            <li>
+              <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
+              PDB easier retrieval of sequences for lists of IDs
+            </li>
+            <li>
+              <!-- JAL-2758 -->Short names for sequences retrieved from
+              Uniprot
             </li>
-            
-            <li><!-- JAL-2617 -->Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references</li>
-            <li><!-- JAL-2685 -->Start/End limits are shown in Pairwise Alignment report</li>
-            <li><!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch' feature can be disabled</li>
-            <li><!-- JAL-2810 -->Retrieve IDs tab added for UniProt and PDB easier retrieval of sequences for lists of IDs</li>
-            <li><!-- JAL-2758 -->Short names for sequences retrieved from Uniprot</li> 
           </ul>
           <em>Scripting</em>
           <ul>
             <li>Groovy interpreter updated to 2.4.12</li>
-            <li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li>
+            <li>Example groovy script for generating a matrix of
+              percent identity scores for current alignment.</li>
           </ul>
           <em>Testing and Deployment</em>
           <ul>
-            <li><!-- JAL-2727 -->Test to catch memory leaks in Jalview UI</li>
+            <li>
+              <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
+            </li>
           </ul>
-        </div>
-      </td>
+        </div></td>
       <td><div align="left">
           <em>General</em>
           <ul>
-            <li><!-- JAL-2643 -->Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view</li>
-            <li><!-- JAL-2682 -->Race condition when parsing sequence ID strings in parallel</li>
-            <li><!-- JAL-2608 -->Overview windows are also closed when alignment window is closed</li>
-            <li><!-- JAL-2548 -->Export of features doesn't always respect group visibility</li> 
-            <li><!-- JAL-2831 -->Jumping from column 1 to column 100,000 takes a long time in Cursor mode</li>            
+            <li>
+              <!-- JAL-2643 -->Pressing tab after updating the colour
+              threshold text field doesn't trigger an update to the
+              alignment view
+            </li>
+            <li>
+              <!-- JAL-2682 -->Race condition when parsing sequence ID
+              strings in parallel
+            </li>
+            <li>
+              <!-- JAL-2608 -->Overview windows are also closed when
+              alignment window is closed
+            </li>
+            <li>
+              <!-- JAL-2548 -->Export of features doesn't always respect
+              group visibility
+            </li>
+            <li>
+              <!-- JAL-2831 -->Jumping from column 1 to column 100,000
+              takes a long time in Cursor mode
+            </li>
           </ul>
           <em>Desktop</em>
           <ul>
-            <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
-            <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
-            </li> 
-            <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
-            </li> 
-            <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
-            <li><!-- JAL-2529 -->Revised Ensembl REST API CDNA query</li>
-            <li><!-- JAL-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li> 
-            <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li> 
-            <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li> 
-            <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
-            <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
-            <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
-            <li><!-- JAL-2392 -->Jalview freezes when loading and displaying several structures</li>
-            <li><!-- JAL-2732 -->Black outlines left after resizing or moving a window</li>
-            <li><!-- JAL-1900,JAL-1625 -->Unable to minimise windows within the Jalview desktop on OSX</li>
-            <li><!-- JAL-2667 -->Mouse wheel doesn't scroll vertically when in wrapped alignment mode</li>
-            <li><!-- JAL-2636 -->Scale mark not shown when close to right hand end of alignment</li>
-            <li><!-- JAL-2684 -->Pairwise alignment of selected regions of each selected sequence do not have correct start/end positions</li>
-            <li><!-- JAL-2793 -->Alignment ruler height set incorrectly after canceling the Alignment Window's Font dialog</li>
-            <li><!-- JAL-2036 -->Show cross-references not enabled after restoring project until a new view is created</li>
-            <li><!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in URL links appears when only default EMBL-EBI link is configured (since 2.10.2b2)</li>            
-            <li><!-- JAL-2775 -->Overview redraws whole window when box position is adjusted</li>
-            <li><!-- JAL-2225 -->Structure viewer doesn't map all chains in a multi-chain structure when viewing alignment involving more than one chain (since 2.10)</li>
-            <li><!-- JAL-2811 -->Double residue highlights in cursor mode if new selection moves alignment window</li>
-            <li><!-- JAL-2837,JAL-2840 -->Alignment vanishes when using arrow key in cursor mode to pass hidden column marker</li>
-            <li><!-- JAL-2679 -->Ensembl Genomes example ID changed to one that produces correctly annotated transcripts and products</li>
-            <li><!-- JAL-2776 -->Toggling a feature group after first time doesn't update associated structure view</li>
-           </ul>
-          ><em>Applet</em><br/>
-           <ul>
-            <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li> 
+            <li>
+              <!-- JAL-2777 -->Structures with whitespace chainCode
+              cannot be viewed in Chimera
+            </li>
+            <li>
+              <!-- JAL-2728 -->Protein annotation panel too high in
+              CDS/Protein view
+            </li>
+            <li>
+              <!-- JAL-2757 -->Can't edit the query after the server
+              error warning icon is shown in Uniprot and PDB Free Text
+              Search Dialogs
+            </li>
+            <li>
+              <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
+            </li>
+            <li>
+              <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
+            </li>
+            <li>
+              <!-- JAL-2739 -->Hidden column marker in last column not
+              rendered when switching back from Wrapped to normal view
+            </li>
+            <li>
+              <!-- JAL-2768 -->Annotation display corrupted when
+              scrolling right in unwapped alignment view
+            </li>
+            <li>
+              <!-- JAL-2542 -->Existing features on subsequence
+              incorrectly relocated when full sequence retrieved from
+              database
+            </li>
+            <li>
+              <!-- JAL-2733 -->Last reported memory still shown when
+              Desktop->Show Memory is unticked (OSX only)
+            </li>
+            <li>
+              <!-- JAL-2658 -->Amend Features dialog doesn't allow
+              features of same type and group to be selected for
+              amending
+            </li>
+            <li>
+              <!-- JAL-2524 -->Jalview becomes sluggish in wide
+              alignments when hidden columns are present
+            </li>
+            <li>
+              <!-- JAL-2392 -->Jalview freezes when loading and
+              displaying several structures
+            </li>
+            <li>
+              <!-- JAL-2732 -->Black outlines left after resizing or
+              moving a window
+            </li>
+            <li>
+              <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
+              within the Jalview desktop on OSX
+            </li>
+            <li>
+              <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
+              when in wrapped alignment mode
+            </li>
+            <li>
+              <!-- JAL-2636 -->Scale mark not shown when close to right
+              hand end of alignment
+            </li>
+            <li>
+              <!-- JAL-2684 -->Pairwise alignment of selected regions of
+              each selected sequence do not have correct start/end
+              positions
+            </li>
+            <li>
+              <!-- JAL-2793 -->Alignment ruler height set incorrectly
+              after canceling the Alignment Window's Font dialog
+            </li>
+            <li>
+              <!-- JAL-2036 -->Show cross-references not enabled after
+              restoring project until a new view is created
+            </li>
+            <li>
+              <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
+              URL links appears when only default EMBL-EBI link is
+              configured (since 2.10.2b2)
+            </li>
+            <li>
+              <!-- JAL-2775 -->Overview redraws whole window when box
+              position is adjusted
+            </li>
+            <li>
+              <!-- JAL-2225 -->Structure viewer doesn't map all chains
+              in a multi-chain structure when viewing alignment
+              involving more than one chain (since 2.10)
+            </li>
+            <li>
+              <!-- JAL-2811 -->Double residue highlights in cursor mode
+              if new selection moves alignment window
+            </li>
+            <li>
+              <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
+              arrow key in cursor mode to pass hidden column marker
+            </li>
+            <li>
+              <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
+              that produces correctly annotated transcripts and products
+            </li>
+            <li>
+              <!-- JAL-2776 -->Toggling a feature group after first time
+              doesn't update associated structure view
+            </li>
+          </ul>
+          <em>Applet</em><br />
+          <ul>
+            <li>
+              <!-- JAL-2687 -->Concurrent modification exception when
+              closing alignment panel
+            </li>
           </ul>
-          <em>BioJSON</em><br/>
+          <em>BioJSON</em><br />
           <ul>
-          <li>
-            <!-- JAL-2546 -->BioJSON export does not preserve non-positional features
-          </li>
+            <li>
+              <!-- JAL-2546 -->BioJSON export does not preserve
+              non-positional features
+            </li>
           </ul>
-          <strong>New Known Issues</strong>
+          <em>New Known Issues</em>
           <ul>
-          <li><!-- JAL-2541 -->Delete/Cut selection doesn't relocate sequence features correctly (for many previous versions of Jalview)</li>
-          <li><!-- JAL-2841 -->Cursor mode unexpectedly scrolls when using cursor in wrapped panel other than top</li>
-          <li><!-- JAL-2791 -->Select columns containing feature ignores graduated colour threshold</li>
-          <li><!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't always preserve numbering and sequence features</li>
+            <li>
+              <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
+              sequence features correctly (for many previous versions of
+              Jalview)
+            </li>
+            <li>
+              <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
+              using cursor in wrapped panel other than top
+            </li>
+            <li>
+              <!-- JAL-2791 -->Select columns containing feature ignores
+              graduated colour threshold
+            </li>
+            <li>
+              <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
+              always preserve numbering and sequence features
+            </li>
           </ul>
-          <strong>Known Java 9 Issues</strong>
+          <em>Known Java 9 Issues</em>
           <ul>
-            <li><!-- JAL-2902 -->Groovy Console very slow to open and is 
-            not responsive when entering characters (Webstart, Java 9.01, 
-            OSX 10.10)
+            <li>
+              <!-- JAL-2902 -->Groovy Console very slow to open and is
+              not responsive when entering characters (Webstart, Java
+              9.01, OSX 10.10)
             </li>
           </ul>
-          </div>
-      </td>
+        </div></td>
     </tr>
     <tr>
       <td width="60" nowrap>
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 6901f61..4bf1cec 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -27,10 +27,11 @@
     <strong>What's new in Jalview 2.10.3 ?</strong>
   </p>
   <p>
-    Version 2.10.3 was released in November 2017. The full list of
-    bug fixes and new features can be found in the <a
-      href="releases.html#Jalview.2.10.3"> 2.10.3 Release Notes</a>, but
-    the highlights are below.
+    Version 2.10.3 was released in November 2017. The major focus was to
+    improve Jalview's sequence features datamodel and the scalability of
+    the alignment rendering system. The full list of bug fixes and new
+    features can be found in the <a href="releases.html#Jalview.2.10.3">2.10.3
+      Release Notes</a>. Key improvements include:
   </p>
   <ul>
     <li>Faster and more responsive UI when importing and working
@@ -43,6 +44,7 @@
       IDs.
     </li>
     <li>Short names assigned to sequences retrieved from UniProt</li>
+    <li>Groovy console upgraded to 2.4.12 (improved support for Java 9)</li>
   </ul>
   <p>
     <strong><a name="experimental">Experimental Features</a></strong>
@@ -58,6 +60,6 @@
         the Chimera viewer's Chimera menu</a> allow positional annotation to
       be exchanged between Chimera and Jalview.</li>
   </ul>
-
+  
 </body>
 </html>
-- 
1.7.10.2