X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=1ddc6e5ab56e912d7eaaf9a0e5353b43fa75f25e;hb=74f21ca6ca8fa17d53708e457d191e15904f8310;hp=d4cba2561c716fc28f1cb4f2b24c0994ed667e63;hpb=221d973075512e015f7c13332c77162ea6b5e7bb;p=jalview.git

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index d4cba25..1ddc6e5 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -57,8 +57,31 @@ li:before {
     </tr>
     <tr>
       <td width="60" align="center" nowrap>
-          <strong><a name="Jalview.2.11">2.11</a><br />
-            <em>27/06/2019</em></strong>
+          <strong><a name="Jalview.2.11.1">2.11.1</a><br />
+            <em>19/11/2019</em></strong>
+      </td>
+      <td align="left" valign="top">
+        <ul>
+          <li><!-- -->
+          </li>
+        </ul>
+        <em>Deprecations</em>
+      </td>
+      <td align="left" valign="top">
+        <ul>
+        </ul>
+        <em>Java 11 Compatibility issues</em>
+        <ul>
+          <li>
+            <!-- JAL-2987 -->OSX - Can't view results in PDB/Uniprot FTS
+          </li>
+        </ul>
+      </td>
+    </tr>
+    <tr>
+      <td width="60" align="center" nowrap>
+          <strong><a name="Jalview.2.11.0">2.11.0</a><br />
+            <em>04/07/2019</em></strong>
       </td>
       <td align="left" valign="top">
         <ul>
@@ -75,7 +98,7 @@ li:before {
           </li>
 					<li>
 						<!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
-						formats supported by jalview (including .jvp project files)
+						formats supported by Jalview (including .jvp project files)
 					</li>
 					<li>
 						<!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
@@ -98,17 +121,25 @@ li:before {
 						<ul>
 						          <li>
             <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
-            implementation that alows updates) used for Sequence Feature collections</li>
+            implementation that allows updates) used for Sequence Feature collections</li>
           <li>
-							<li>
-								<!-- JAL-2808,JAL-2069 -->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)
+                <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->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-2879 -->Feature Attributes and shading schemes
+                stored and restored from Jalview Projects
+              </li>
+              <li>
+								<!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
+								recognise variant features
 							</li>
 							<li>
-								<!-- JAL-2897 -->Show synonymous codon variants on peptide
-								sequences
+								<!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
+								sequences (also coloured red by default)
 							</li>
 							<li>
 								<!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
@@ -134,7 +165,7 @@ li:before {
 								<!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
 								and Viewer state saved in Jalview Project
 							</li>
-							<li>'Change parameters' option removed from viewer's
+							<li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
 								drop-down menus</li>
 							<li>
 								<!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
@@ -167,7 +198,7 @@ li:before {
 							</li>
 							<li>
 								<!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
-								what is shown)<br />Only visible region of alignment is shown by
+								what is shown)<br />Only visible regions of alignment are shown by
 								default (can be changed in user preferences)
 							</li>
 							<li>
@@ -195,7 +226,7 @@ li:before {
 								annotation
 							</li>
 							<li>
-								<!-- JAL-2814 -->Help button on Uniprot and PDB search panels
+								<!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
 							</li>
 							<li>
 								<!-- JAL-2621 -->Cursor changes over draggable box in Overview
@@ -223,40 +254,55 @@ li:before {
 				</ul>
         <em>Deprecations</em>
         <ul>
-          <li>
-            <!-- JAL-3035 -->DAS sequence retrieval and annotation
+          <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
             capabilities removed from the Jalview Desktop
           </li>
-          <li>
-            <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
+          <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
             unmarshalling has been replaced by JAXB for Jalview projects
             and XML based data retrieval clients</li>
           <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li> 
           <li><!--  -->Jalview Desktop no longer distributed via Java Web Start</li>
         </ul> <em>Documentation</em>
 				<ul>
-					<li>
-						<!-- JAL-3003 -->Added remarks about transparent rendering effects
+					<li><!-- JAL-3003 -->Added remarks about transparent rendering effects
 						not supported in EPS figure export
 					</li>
+					<li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
 				</ul> <em>Development and Release Processes</em>
         <ul>
         	<li>
-						<!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
+        	<!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
 					</li>
-					<li><!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
-					<li>
-						<!-- JAL-3225 -->Eclipse project configuration managed with
-						gradle-eclipse
-					</li>
-          <li><!-- JAL-3174,JAL-2886,JAL-2729 -->
-          Atlassian Bamboo continuous integration for
-            unattended Test Suite execution</li>
+			<li>
+			<!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
+          <li>
+          <!-- JAL-3225 -->Eclipse project configuration managed with
+            gradle-eclipse
+          </li>
+          <li>
+          <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
+            Bamboo continuous integration for unattended Test Suite
+            execution
+          </li>
+          <li>
+          <!-- JAL-2864 -->Memory test suite to detect leaks in common
+            operations
+          </li>
           <li>
-            <!-- JAL-2864 -->Memory test suite to detect leaks in common
-            operations</li>
-          <li><!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor issues resolved.</li>
-          <li><!-- JAL-3248 -->Developer documentation migrated to markdown (with HTML rendering)</li>          
+          <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
+            issues resolved
+          </li>
+          <li>
+          <!-- JAL-3248 -->Developer documentation migrated to
+            markdown (with HTML rendering)
+          </li>
+          <li>
+          <!-- JAL-3287 -->HelpLinksChecker runs on Windows
+          </li>
+          <li>
+          <!-- JAL-3289 -->New URLs for publishing development
+            versions of Jalview
+          </li>
         </ul>
       </td>
 			<td align="left" valign="top">
@@ -299,8 +345,8 @@ li:before {
 						Settings and Jalview Preferences panels
 					</li>
 					<li>
-						<!-- JAL-2865 -->Jalview hangs when closing windows or the
-						overview updates with large alignments
+						<!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
+						overview with large alignments
 					</li>
 					<li>
 						<!-- JAL-2750 -->Tree and PCA calculation fails for selected
@@ -316,16 +362,21 @@ li:before {
 						doesn't tell users the invalid URL
 					</li>
 					<li>
-						<!-- JAL-3178 -->Nonpositional features lose feature group on
-						export as Jalview features file
-					</li>
-					<li>
 						<!-- JAL-2816 -->Tooltips displayed for features filtered by
 						score from view
 					</li>
 					<li>
+						<!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
+						show cross references or Fetch Database References are shown in
+						red in original view
+					</li>
+          <li>
+            <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
+            peptide sequence (computed variant shown as p.Res.null)
+          </li>
+					<li>
 						<!-- JAL-2060 -->'Graduated colour' option not offered for
-						manually created features (where if feature score is Float.NaN)
+						manually created features (where feature score is Float.NaN)
 					</li>
 					<li>
 						<!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
@@ -408,20 +459,19 @@ li:before {
 						shown in complementary view
 					</li>
 					<li>
-						<!-- JAL-2898 -->stop_gained variants not shown correctly on
-						peptide sequence
-					</li>
-					<li>
 						<!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
 						without normalisation
 					</li>
 					<li>
-						<!-- JAL-3021 -->Sequence Details report opens positioned to top
+						<!-- JAL-3021 -->Sequence Details report should open positioned at top
 						of report
 					</li>
 					<li>
 						<!-- JAL-914 -->Help page can be opened twice
 					</li>
+				  <li>
+				  <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
+				  </li>
 				</ul> <em>Editing</em>
 				<ul>
 					<li>
@@ -442,10 +492,23 @@ li:before {
 						<!-- JAL-868 -->Structure colours not updated when associated tree
 						repartitions the alignment view (Regression in 2.10.5)
 					</li>
-
-				</ul>
-				<em>New Known Defects</em>
-				<ul>
+				</ul> <em>Datamodel</em>
+        <ul>
+          <li>
+            <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
+            sequence's End is greater than its length
+          </li>
+        </ul> <em>Bugs fixed for Java 11 Support (not yet on
+          general release)</em>
+        <ul>
+          <li>
+            <!-- JAL-3288 -->Menus work properly in split-screen
+          </li>
+        </ul> <em>New Known Defects</em>
+        <ul>
+				<li>
+				<!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
+				</li>
 					<li>
 						<!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
 						regions of protein alignment.
@@ -473,14 +536,23 @@ li:before {
 						not shown as thresholded features in 2.11. To workaround please
 						create a Score filter instead.
 					</li>
-					 <li><strong>Java 11 Specific defects</strong>
+					<li>
+					<!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li> 
+					<li>
+					<!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
+					</li>
+          <li>
+            <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
+            alignments with multiple views can close views unexpectedly
+          </li>
+          </ul>
+          <em>Java 11 Specific defects</em>
             <ul>
               <li>
-              <!-- JAL-3235 -->Jalview Properties file is not sorted alphabetically when saved</li>
-              
-            </ul></li>
-					
-				</ul>
+                <!-- JAL-3235 -->Jalview Properties file is not sorted
+                alphabetically when saved
+              </li>
+          </ul>
 			</td>
 		</tr>
     <tr>
@@ -500,7 +572,7 @@ li:before {
               <!-- 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
-                Format menu, or for command-line use via a jalview
+                Format menu, or for command-line use via a Jalview
                 properties file.</em>
             </li>
             <li>
@@ -574,7 +646,7 @@ li:before {
             </li>
             <li>
               <!-- JAL-3106 -->.jvp should be used as default extension
-              (not .jar) when saving a jalview project file.
+              (not .jar) when saving a Jalview project file.
             </li>
             <li>
               <!-- JAL-3105 -->Mac Users: closing a window correctly