Merge branch 'releases/Release_2_10_4_Branch' of http://source.jalview.org/git/jalvie...

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

diff --git a/help/html/releases.html b/help/html/releases.html
index 3c59031..dd2bb62 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -70,25 +70,145 @@ li:before {
     <tr>
       <td width="60" nowrap>
         <div align="center">
-          <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>27/02/2018</em></strong>
+          <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>8/05/2018</em></strong>
         </div>
       </td>
       <td><div align="left">
           <em></em>
           <ul>
             <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-2759 -->Improved performance for large alignments
+              and lots of hidden columns
+            </li>
+            <li>
+              <!-- JAL-2593 -->Improved performance when rendering lots
+              of features (particularly when transparency is disabled)
+            </li>
           </ul>
           </div>
       </td>
       <td><div align="left">
           <ul>
             <li>
-              <!-- JAL-2778 -->Slow redraw when Overview panel shown operlapping 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-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>
           </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>