From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 7 Aug 2017 10:56:01 +0000 (+0100)
Subject: JAL-2418 release notes
X-Git-Tag: Release_2_10_3b1~132^2~15^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=cc0b6158d11333a9ee0b5cf57fbe890d5309e510;hp=50c521fe300eae13190e22811e418d38693e1271;p=jalview.git

JAL-2418 release notes
---

diff --git a/help/html/releases.html b/help/html/releases.html
index d2e41df..351b055 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -151,6 +151,10 @@ li:before {
               aligned positions were available to create a 3D structure
               superposition.
             </li>
+            <li>
+            <!-- JAL-2507 -->More robust per-sequence positional annotation input/output via stockholm flatfile
+            </li>
+            
           </ul>
           <em>Application</em>
           <ul>
@@ -380,13 +384,53 @@ li:before {
               <!-- JAL-2473 -->Minimum size set for Jalview windows so widgets don't permanently disappear 
             </li>
             <li>
-              <!-- JAL- -->
+              <!-- JAL-2503 -->Cannot select or filter quantitative
+              annotation that are shown only as column labels (e.g.
+              T-Coffee column reliability scores)
             </li>
             <li>
-              <!-- JAL- -->
+              <!-- JAL-2589 -->Gap colours in user-defined colourschemes are not shown   
             </li>
+            <li><!-- JAL-2594 -->Exception thrown if trying to create a sequence feature on gaps only</li>
             <li>
-              <!-- JAL- -->
+              <!-- JAL-2544 --> Sort by features includes features to
+              right of selected region when gaps present on right-hand
+              boundary
+            </li>
+            <li>
+              <!-- JAL-2504 -->Features created with 'New feature'
+              button from a Find inherit previously defined feature type
+              rather than the Find query string
+            </li>
+            <li>
+              <!-- JAL-2423  -->incorrect title in output window when
+              exporting tree calculated in Jalview
+            </li>
+            <li>
+            <!-- JAL-2507 -->Per-sequence RNA secondary structures added after a sequence was imported are not written to Stockholm File
+            </li>
+            <li>
+            <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost when importing RNA secondary structure via Stockholm 
+            </li>
+            <li>
+            <!-- JAL-2509 -->Secondary structure arrows for [] and {} not shown in correct direction for simple pseudoknots 
+            </li>
+            <li>
+            <!-- JAL-2437 -->Hiding sequences at bottom of alignment and then revealing them reorders sequences on the alignment 
+            </li><li>
+            <!-- JAL-964 -->Group panel in sequence feature settings doesn't update to reflect available set of groups after interactively adding or modifying features
+            </li>
+            <li>
+            <!-- JAL-2225 -->Sequence Database chooser unusable on Linux  
+            </li>
+            <li>
+            <!-- JAL --> 
+            </li>
+            <li>
+            <!-- JAL --> 
+            </li>
+            <li>
+            <!-- JAL --> 
             </li>
           </ul>
           <strong>Documentation</strong>
@@ -395,10 +439,16 @@ li:before {
               <!-- JAL-2339 -->Release notes reformatted for readibility
               with the built-in Java help viewer
             </li>
+            <li><!-- JAL-1644 -->Find documentation updated with 'search sequence description' option</li>
           </ul>
           <em>Application</em>
           <ul>
             <li>
+            <!-- JAL-2225 -->Sequence Database chooser doesn't show available databases panel on Linux  
+            </li>
+            <li><!-- JAL-2519 -->EnsemblGenomes example failing after release of Ensembl v.88</li>
+            <li><!-- JAL-2361 -->User Defined Colours not added to Colour menu</li>
+            <li>
               <!-- JAL-2401 -->Easier creation of colours for all 'Lower
               case' residues (button in colourscheme editor debugged and
               new documentation and tooltips added)
@@ -412,6 +462,10 @@ li:before {
               new features are added to alignment
             </li>
             <li>
+            <!-- JAL-2532 -->Cancel in feature settings reverts changes to feature colours via the Amend features dialog
+            </li>
+            <li><!-- JAL-2506 -->Null pointer exception when attempting to edit graduated feature colour via amend features dialog box</li>
+            <li>
               <!-- JAL-2436 -->Structure viewer's View -> Colour By view
               selection menu changes colours of alignment views
             </li>