X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=2b835454dd1e0c58ad453357a68a07332272a624;hb=06fb1b18865c75aa78186970e74392058444fde4;hp=8f98369269001b45959045b729392f344a982755;hpb=614f50a40e2ef7913219ae26874510ac8b47b8ad;p=jalview.git

diff --git a/help/html/releases.html b/help/html/releases.html
index 8f98369..2b83545 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -77,12 +77,26 @@ li:before {
           <em></em>
           <ul>
             <li>
-              <!-- JAL-984 -->Mouse cursor changes to indicate Sequence ID and annotation area margins can be click-dragged to adjust them.</li> 
+              <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
+              for disabling automatic superposition of multiple
+              structures and open structures in existing views
+            </li>
+            <li>
+              <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
+              ID and annotation area margins can be click-dragged to
+              adjust them.
+            </li>
+            <li>
+              <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
+              Ensembl services
+            </li>
             <li>
-            <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and Ensembl services 
+              <!-- JAL-2759 -->Improved performance for large alignments
+              and lots of hidden columns
             </li>
             <li>
-            <!-- JAL-2759 -->Improved performance for large alignments and lots of hidden columns
+              <!-- JAL-2593 -->Improved performance when rendering lots
+              of features (particularly when transparency is disabled)
             </li>
           </ul>
           </div>
@@ -90,20 +104,111 @@ li:before {
       <td><div align="left">
           <ul>
             <li>
-              <!-- JAL-2778 -->Slow redraw when Overview panel shown overlapping alignment panel
+              <!-- JAL-2899 -->Structure and Overview aren't updated
+              when Colour By Annotation threshold slider is adjusted
+            </li>
+            <li>
+              <!-- JAL-2778 -->Slow redraw when Overview panel shown
+              overlapping alignment panel
+            </li>
+            <li>
+              <!--  JAL-2929 -->overview doesn't show end of unpadded
+              sequence as gaps
+            </li>
+            <li>
+              <!-- JAL-2789, JAL-2893 -->Cross-reference handling improved: CDS not handled correctly if transcript has no UTR
+            </li>
+            <li>
+            
+            </li>
+            <li>
+              <!-- JAL-2666 -->Linked scrolling via protein horizontal
+              scroll bar doesn't work for some CDS/Protein views
+            </li>
+            <li>
+              <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
+              Java 1.8u153 onwards and Java 1.9u4+.
+            </li>
+            <li>
+              <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
+              columns in annotation row
+            </li>
+            <li>
+              <!-- JAL-2913 -->Preferences panel's ID Width control is
+              honored in interactive and batch mode
+            </li>
+            <li>
+              <!-- JAL-2945 -->Linked sequence highlighting doesn't work
+              for structures added to existing Jmol view
+            </li>
+            <li>
+              <!-- JAL-2223 -->'View Mappings' includes duplicate
+              entries after importing project with multiple views
+            </li>
+            <li>
+              <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
+              protein sequences via SIFTS from associated PDB entries
+              with negative residue numbers or missing residues fails
+            </li>
+            <li>
+              <!-- JAL-2952 -->Exception when shading sequence with negative
+              Temperature Factor values from annotated PDB files (e.g.
+              as generated by CONSURF)
             </li>
             <li>
-              <!-- JAL-2666 -->Linked scrolling via protein horizontal scroll bar doesn't work for some CDS/Protein views 
+              <!-- JAL-2922 -->Invert displayed features very slow when
+              structure and/or overview windows are also shown
+            </li>
+            <li>
+              <!-- JAL-2954 -->Selecting columns from highlighted regions
+              very slow for alignments with large numbers of sequences
+            </li>
+            <li>
+              <!-- JAL-2925 -->Copy Consensus fails for group consensus
+              with 'StringIndexOutOfBounds'
+            </li>
+            <li>
+              <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
+              platforms running Java 10
+            </li>
+            <li>
+              <!-- JAL-2960 -->Adding a structure to existing structure
+              view appears to do nothing because the view is hidden behind the alignment view
             </li>
-            <li><!-- JAL-2930 -->Trackpad scrolling is broken on OSX on Java 1.8u153 onwards and Java 1.9u4+.</li>
-            <li><!-- JAL-2924 -->Tooltip shouldn't be displayed for empty columns in annotation row</li>
-            <li><!-- JAL-2913 -->Preferences panel's ID Width control is honored in interactive and batch mode</li>
-            </ul><em>Applet</em><ul>
-            <li><!-- JAL-2926 -->Copy consensus sequence option in applet should copy the group consensus when popup is opened on it</li>
-             
           </ul>
-      </div>
-      </td>
+          <em>Applet</em>
+          <ul>
+            <li>
+              <!-- JAL-2926 -->Copy consensus sequence option in applet
+              should copy the group consensus when popup is opened on it
+            </li>
+          </ul>
+          <em>Batch Mode</em>
+          <ul>
+          <li>
+            <!-- JAL-2913 -->Fixed ID width preference is not respected
+          </li>
+          </ul>
+          <em>New Known Defects</em>
+          <ul>
+            <li>
+              <!-- JAL-2973 --> Exceptions occasionally raised when
+              editing a large alignment and overview is displayed
+            </li>
+            <li>
+              <!-- JAL-2974 -->'Overview updating' progress bar is shown
+              repeatedly after a series of edits even when the overview
+              is no longer reflecting updates
+            </li>
+            <li>
+              <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
+              structures for protein subsequence (if 'Trim Retrieved
+              Sequences' enabled) or Ensembl isoforms (Workaround in
+              2.10.4 is to fail back to N&amp;W mapping)
+            </li>
+          </ul>
+        </div>
+          </td>
     </tr>
     <tr>
       <td width="60" nowrap>