JAL-3178 known defect in release notes

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

diff --git a/help/html/releases.html b/help/html/releases.html
index 9c4c9ed..abbc891 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -67,16 +67,82 @@ li:before {
         </div>
       </td>
     </tr>
+    
+      <td width="60" nowrap>
+        <div align="center">
+          <strong><a name="Jalview.2.11.0">2.11.0</a><br />
+            <em>29/01/2019</em></strong>
+        </div>
+      </td>
+    <td><div align="left">
+        <em>Deprecations</em>
+        <ul>
+          <li>
+            <!-- JAL-3035 -->DAS sequence retrieval and annotation
+            capabilities removed from the Jalview Desktop
+          </li>
+        </ul>
+        <em>Release Processes</em>
+        <ul>
+        <li>Atlassian Bamboo continuous integration server for unattended Test Suite execution</li>
+        <li><!-- JAL-2864 -->Memory test suite to detect leaks in common operations</li> 
+        </ul>
+      </div></td>
+    <td><div align="left">
+        <em></em>
+        <ul>
+          <li>
+            <!-- JAL-2865 -->Jalview hangs when closing windows
+            or the overview updates with large alignments.
+          </li>
+          <li>
+            <!-- JAL-2865 -->Tree and PCA calculation fails for selected
+            region if columns were selected by dragging right-to-left
+            and the mouse moved to the left of the first column.
+          </li>
+        </ul>
+        <em>Editing</em>
+        <ul>
+          <li>
+            <!-- JAL-2822 -->Start and End should be updated when
+            sequence data at beginning or end of alignment added/removed
+            via 'Edit' sequence
+          </li>
+          <li>
+            <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
+            sequence features correctly when start of sequence is
+            removed (Known defect since 2.10)
+          </li>
+          <li>
+            <!-- JAL-2846, -->Avoided use of apostrophe in dialog box
+          </li>
+          <li>
+            <!-- JAL- -->
+          </li>
+        </ul>
+        <em>New Known Defects</em>
+        <ul>
+          <li>
+            <!-- JAL-3178 -->Nonpositional features lose feature group
+            on export as jalview features file
+          </li>
+        </ul>
+      </div></td>
+    </tr>
     <tr>
     <td width="60" nowrap>
       <div align="center">
-        <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>4/09/2018</em></strong>
+        <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
       </div>
     </td>
     <td><div align="left">
         <em></em>
         <ul>
             <li>
+              <!-- JAL-3101 -->Default memory for Jalview webstart and
+              InstallAnywhere increased to 1G.
+            </li>
+            <li>
               <!-- JAL-247 -->Hidden sequence markers and representative
               sequence bolding included when exporting alignment as EPS,
               SVG, PNG or HTML. <em>Display is configured via the
@@ -85,7 +151,7 @@ li:before {
             </li>
             <li>
               <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
-              API and sequence data now imported as JSON
+              API and sequence data now imported as JSON.
             </li>
             <li>
               <!-- JAL-3065 -->Change in recommended way of starting
@@ -107,6 +173,20 @@ li:before {
         <em></em>
         <ul>
             <li>
+              <!-- JAL-3104 -->Poorly scaled bar in quality annotation
+              row shown in Feredoxin Structure alignment view of example
+              alignment.
+            </li>
+            <li>
+              <!-- JAL-2854 -->Annotation obscures sequences if lots of
+              annotation displayed.
+            </li>
+            <li>
+              <!-- JAL-3107 -->Group conservation/consensus not shown
+              for newly created group when 'Apply to all groups'
+              selected
+            </li>
+            <li>
               <!-- JAL-3087 -->Corrupted display when switching to
               wrapped mode when sequence panel's vertical scrollbar is
               visible.
@@ -121,33 +201,47 @@ li:before {
             </li>
             <li>
               <!-- JAL-3092 -->Jalview could hang when importing certain
-              types of knotted RNA secondary structure
+              types of knotted RNA secondary structure.
             </li>
             <li>
               <!-- JAL-3095 -->Sequence highlight and selection in
               trimmed VARNA 2D structure is incorrect for sequences that
-              do not start at 1
+              do not start at 1.
             </li>
             <li>
               <!-- JAL-3061 -->'.' inserted into RNA secondary structure
               annotation when columns are inserted into an alignment,
-              and when exporting as Stockolm flatfile.
+              and when exporting as Stockholm flatfile.
             </li>
             <li>
               <!-- JAL-3053 -->Jalview annotation rows containing upper
               and lower-case 'E' and 'H' do not automatically get
-              treated as RNA secondary structure
+              treated as RNA secondary structure.
+            </li>
+            <li>
+              <!-- JAL-3106 -->.jvp should be used as default extension
+              (not .jar) when saving a jalview project file.
+            </li>
+            <li>
+              <!-- JAL-3105 -->Mac Users: closing a window correctly
+              transfers focus to previous window on OSX
             </li>
           </ul>
-          <em>Java 10 Issues</em>
+          <em>Java 10 Issues Resolved</em>
           <ul>
             <li>
               <!-- JAL-2988 -->OSX - Can't save new files via the File
               or export menus by typing in a name into the Save dialog
               box.
             </li>
+            <li>
+              <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
+              of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
+              'look and feel' which has improved compatibility with the
+              latest version of OSX.
+            </li>
           </ul>
-      </div>
+        </div>
     </td>
     </tr>
     <tr>