From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 4 Mar 2019 16:15:40 +0000 (+0000)
Subject: release notes for JAL-1767 JAL-2647 JAL-3198 JAL-3200 JAL-3018 JAL-3139 JAL-2587... 
X-Git-Tag: Release_2_11_0~17^2~16^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=522f00f76748443e71d99bb4c6c4503e1f16d36f;p=jalview.git

release notes for JAL-1767 JAL-2647 JAL-3198 JAL-3200 JAL-3018 JAL-3139 JAL-2587 JAL-2527 JAL-3140 JAL-3063 JAL-3171 JAL-3164 JAL-3158 JAL-3161 JAL-3154
---

diff --git a/help/html/releases.html b/help/html/releases.html
index 0fba08a..a08e5e1 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -71,10 +71,46 @@ li:before {
       <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>
+            <em>29/04/2019 (final due date !)</em></strong>
         </div>
       </td>
     <td><div align="left">
+        <ul>
+          <li>
+            <!-- JAL-1767,JAL-2647 -->Principal Components Analysis and
+            Viewer state is saved in Jalview Project<br />The 'Change
+            parameters' option has also been removed from the PCA
+            viewer.
+          </li>
+          <li>
+            <!-- JAL-3198 -->More efficient creation of selections and
+            multiple groups when working with large alignments
+          </li>
+          <li>
+            <!-- JAL-3200 -->Speedier import of annotation rows when
+            parsing stockholm files
+          </li>
+          <li>
+            <!-- JAL-3018 -->Update of Ensembl Rest Client to API v9.0
+          </li>
+          <li>
+            <!-- JAL-3... -->Sequence features can be filtered and
+            shaded according to any associated attributes (e.g. variant
+            attributes from VCF file, or key-value pairs imported from
+            column 9 of GFF file)
+          </li>
+          <li>
+            <!-- JAL-3139, -->More efficient sequence feature render
+            algorithm (Z-sort/transparency and filter aware)
+          </li>
+          <li>
+            <!-- JAL-2527 -->Alignment Overview now by default shows
+            only visible region of alignment (this can be changed in
+            user preferences)
+          </li>
+          <li><!--  -->
+          </li>
+        </ul>
         <em>Deprecations</em>
         <ul>
           <li>
@@ -84,14 +120,50 @@ li:before {
         </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> 
+          <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>
+          <li>
+            <!-- JAL-3140 -->IntervalStoreJ (new updatable NCList
+            implementation) used for Sequence Feature collections
+          </li>
+          <li>
+            <!-- JAL-3063 -->Castor library for XML marshalling and
+            unmarshalling has been replaced by JAXB for Jalview projects
+            and XML based data retrieval clients
+          </li>
+          <li>
+          <!-- JAL -->
+
         </ul>
       </div></td>
     <td><div align="left">
         <em></em>
         <ul>
           <li>
+            <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
+            Jalview project involving multiple views
+          </li>
+          <li>
+            <!-- JAL-3164 -->Overview for complementary view in a linked
+            CDS/Protein alignment is not updated when Hide Columns by
+            Annotation dialog hides columns
+          </li>
+          <li>
+            <!-- JAL-3158 -->Selection highlighting in the complement of
+            a CDS/Protein alignment stops working after making a
+            selection in one view, then making another selection in the
+            other view.
+          </li>
+          <li><!-- JAL-3161 -->Annotations tooltip changes beyond visible columns</li>
+          <li>
+            <!-- JAL-3154 -->Table Columns could be re-ordered in
+            Feature Settings and Jalview Preferences panels
+          </li>
+          <li>
             <!-- JAL-2865 -->Jalview hangs when closing windows
             or the overview updates with large alignments.
           </li>
@@ -127,6 +199,7 @@ li:before {
             <!-- JAL-3178 -->Nonpositional features lose feature group
             on export as jalview features file
           </li>
+          <li><!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project</li> 
         </ul>
       </div></td>
     </tr>