From 9dd6ed3d1c0f5ea9320a4af528127734cc0fcb8d Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 7 Aug 2017 09:49:38 +0100
Subject: [PATCH 1/1] JAL-2418 release notes

---
 help/html/releases.html |   45 ++++++++++++++++++++++++++++++++++++++-------
 1 file changed, 38 insertions(+), 7 deletions(-)

diff --git a/help/html/releases.html b/help/html/releases.html
index 307b04a..d2e41df 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -142,6 +142,11 @@ li:before {
               ungapped positions in each column of the alignment.
             </li>
             <li>
+              <!-- JAL-2533 -->File extension pruned from Sequence ID
+              for sequences derived from structure files without
+              embedded database accession
+            </li>
+            <li>
               <!-- JAL-1476 -->Status bar message shown when not enough
               aligned positions were available to create a 3D structure
               superposition.
@@ -178,6 +183,12 @@ li:before {
             <li>
             <!-- JAL-2375 -->Structure chooser automatically shows Cached Structures rather than querying the PDBe if structures are already available for sequences
             </li>
+            <li>
+              <!-- JAL-2520 -->Structures imported via URL are cached in
+              the Jalview project rather than downloaded again when the
+              project is reopened.
+            </li>
+
           </ul>
           <em>Experimental features</em>
           <ul>
@@ -203,6 +214,10 @@ li:before {
               during tests
             </li>
             <li>
+              <!-- JAL-2485, -->External service integration tests for
+              Uniprot REST Free Text Search Client
+            </li>
+            <li>
               <!--  --> <em>Scripting</em>
               <ul>
                 <li>
@@ -211,7 +226,10 @@ li:before {
                   constants)
                 </li>
                 <li>
-                  <!-- JAL- -->
+                  <!-- JAL-2228 -->FeatureCounter script refactored for efficiency when counting all displayed features (not backwards compatible with 2.10.1)  
+                </li>
+                <li>
+                
                 </li>
 
 
@@ -243,6 +261,11 @@ li:before {
               restore 2.10.2 mode
             </li>
             <li>
+              <!-- JAL-2424 -->Fixed off-by-one bug that affected scaling
+              of branch lengths for trees computed using Sequence
+              Feature Similarity.
+            </li>
+            <li>
               <!-- JAL-2346 -->Reopening Colour by annotation dialog
               doesn't reselect a specific sequence's associated
               annotation after it was used for colouring a view
@@ -354,7 +377,7 @@ li:before {
               overview when features overlaid on alignment
             </li>
             <li>
-              <!-- JAL- -->
+              <!-- JAL-2473 -->Minimum size set for Jalview windows so widgets don't permanently disappear 
             </li>
             <li>
               <!-- JAL- -->
@@ -422,10 +445,10 @@ li:before {
               when alignment view imported from project
             </li>
             <li>
-              <!-- JAL-2465 -->No mappings generated between structure
+              <!-- JAL-2520,JAL-2465 -->No mappings generated between structure
               and sequences extracted from structure files imported via
-              URL
-            </li>
+              URL and viewed in Jmol
+            </li>            
             <li>
               <!-- JAL-2520 -->Structures loaded via URL are saved in
               Jalview Projects rather than fetched via URL again when
@@ -454,7 +477,7 @@ li:before {
               proteins
             </li>
             <li>
-              <!-- JAL-2431 -->cDNA Consensus not shown
+              <!-- JAL-2482 -->SIFTs mappings not created for some structures 
             </li>
 
 
@@ -505,8 +528,16 @@ li:before {
               jalview.ws.jabaws.RNAStructExportImport setup fails
             </li>
             <li>
-              <!-- JAL- -->
+              <!-- JAL-2307 -->Unit test failure:
+              jalview.ws.sifts.SiftsClientTest due to compatibility
+              problems with deep array comparison equality asserts in
+              successive versions of TestNG
+            </li>
+            <li>
+              <!-- JAL-2479 -->Relocated StructureChooserTest and
+              ParameterUtilsTest Unit tests to Network suite
             </li>
+            
           </ul>
         </div>
     <tr>
-- 
1.7.10.2