JAL-2920 release notes

[jalview.git] / help / html / releases.html

diff --git a/help/html/releases.html b/help/html/releases.html
index df0fe30..1ad46e3 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -70,16 +70,16 @@ li:before {
     <tr>
       <td width="60" nowrap>
         <div align="center">
-          <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>1/05/2018</em></strong>
+          <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
         </div>
       </td>
       <td><div align="left">
           <em></em>
           <ul>
             <li>
-              <!-- JAL-1847 JAL-2944 -->Structure Chooser controls to
-              control superposition of multiple structures and open
-              structures in existing views
+              <!-- 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
@@ -96,7 +96,7 @@ li:before {
             </li>
             <li>
               <!-- JAL-2593 -->Improved performance when rendering lots
-              of features
+              of features (particularly when transparency is disabled)
             </li>
           </ul>
           </div>
@@ -104,10 +104,33 @@ li:before {
       <td><div align="left">
           <ul>
             <li>
+              <!-- 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>
+              <!-- JAL-2321 -->Secondary structure and temperature
+              factor annotation not added to sequence when local PDB
+              file associated with it by drag'n'drop or structure
+              chooser
+            </li>
+            <li>
+              <!--  JAL-2984 -->Answering 'No' to PDB Autoassociate
+              dialog doesn't import PDB files dropped on an alignment
+            </li>
+            <li>
               <!-- JAL-2666 -->Linked scrolling via protein horizontal
               scroll bar doesn't work for some CDS/Protein views
             </li>
@@ -120,8 +143,8 @@ li:before {
               columns in annotation row
             </li>
             <li>
-              <!-- JAL-2913 -->Preferences panel's ID Width control is
-              honored in interactive and batch mode
+              <!-- JAL-2913 -->Preferences panel's ID Width control is not
+              honored in batch mode
             </li>
             <li>
               <!-- JAL-2945 -->Linked sequence highlighting doesn't work
@@ -142,19 +165,29 @@ li:before {
               as generated by CONSURF)
             </li>
             <li>
+              <!-- JAL-2920 -->Uniprot 'sequence variant' features
+              tooltip doesn't include a text description of mutation
+            </li>
+            <li>
+              <!-- 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><em>New Defects</em>
-            <ul>
-                <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>
+            <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>
           </ul>
           <em>Applet</em>
           <ul>
@@ -162,10 +195,33 @@ li:before {
               <!-- JAL-2926 -->Copy consensus sequence option in applet
               should copy the group consensus when popup is opened on it
             </li>
-
           </ul>
-          
-        </div></td>
+          <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>