X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=3ac124735d0c6e43ef15fba8f73abcae43bb9e4a;hb=refs%2Fheads%2Fjalview-headless;hp=0bc9e4ec480adc461f7ca078bbfbe6529619a51f;hpb=124d129cc007fbfc84039610b364df62efc72707;p=jalview.git

diff --git a/help/html/releases.html b/help/html/releases.html
index 0bc9e4e..3ac1247 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -67,10 +67,146 @@ li:before {
         </div>
       </td>
     </tr>
+    
+      <td width="60" nowrap>
+        <div align="center">
+          <strong><a name="Jalview.2.11">2.11</a><br />
+            <em>14/05/2019 (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>
+            <!-- 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>
+          <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>
+          <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>
+          <li>
+            <!-- JAL-2846 -->Error message for trying to load in invalid
+            URLs doesn't tell users the invalid URL
+          </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- -->
+          </li>
+        </ul>
+        <em>New Known Defects</em>
+        <ul>
+          <li>
+            <!-- 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>
     <tr>
     <td width="60" nowrap>
       <div align="center">
-        <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>6/09/2018</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">
@@ -111,10 +247,20 @@ 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.
@@ -146,16 +292,30 @@ li:before {
               and lower-case 'E' and 'H' do not automatically get
               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>