X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=b64c24caee5b6d43cfc15c855f13f810f834a66a;hb=32deb2b9a173873736b62c2999b9145cb63f84b2;hp=87a2f4b89fd8674e0f503d8d3c9ca77ac5a3b5c4;hpb=12334155115dd7bd3d54308270db847122c76bfe;p=jalview.git

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 87a2f4b..b64c24c 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -57,13 +57,38 @@ li:before {
     </tr>
     <tr>
       <td width="60" align="center" nowrap>
-          <strong><a name="Jalview.2.11">2.11</a><br />
-            <em>20/06/2019</em></strong>
+          <strong><a name="Jalview.2.11.0">2.11.0</a><br />
+            <em>02/07/2019</em></strong>
       </td>
       <td align="left" valign="top">
         <ul>
           <li>
+            <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
+            Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
+            source project) rather than InstallAnywhere
+          </li>
+          <li>
+            <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
+            settings, receive over the air updates and launch specific
+            versions via (<a href="https://github.com/threerings/getdown">Three
+              Rings' GetDown</a>)
+          </li>
+					<li>
+						<!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
+						formats supported by jalview (including .jvp project files)
+					</li>
+					<li>
+						<!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
+						arguments and switch between different getdown channels
+					</li>
+					<li>
+						<!-- JAL-3141 -->Backup files created when saving Jalview project
+						or alignment files
+					</li>
+
+					<li>
             <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
+            <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li> 
           <li>
             <!-- JAL-2620 -->Alternative genetic code tables for
             'Translate as cDNA'</li>
@@ -71,6 +96,10 @@ li:before {
             <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
 					<li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
 						<ul>
+						          <li>
+            <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
+            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
@@ -78,6 +107,10 @@ li:before {
 								column 9 of GFF file)
 							</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
 							</li>
@@ -86,7 +119,7 @@ li:before {
 								details
 							</li>
 							<li>
-								<!-- JAL-3139,JAL-2816 -->More efficient sequence feature render
+								<!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
 								algorithm (Z-sort/transparency and filter aware)
 							</li>
 							<li>
@@ -96,23 +129,23 @@ li:before {
 						</ul>
 					</li>
 					<li>
-            <!-- JAL-3141 -->Backup files created when saving Jalview project
-            or alignment files
-          </li>
-          <li><strong>Principal Components Analysis Viewer</strong>
+						<!-- JAL-3205 -->Symmetric score matrices for faster
+						tree and PCA calculations
+					</li>
+					<li><strong>Principal Components Analysis Viewer</strong>
             <ul>
 							<li>
 								<!-- 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
 								incrementally
 							</li>
 							<li>
-								<!-- JAL-2965 -->PCA plot is depth cued
+								<!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
 							</li>
 						</ul>
 					</li>
@@ -122,7 +155,7 @@ li:before {
 					<li><strong>Speed and Efficiency</strong>
 					<ul>
 							<li>
-								<!-- JAL-3198 -->More efficient creation of selections and
+								<!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
 								multiple groups when working with large alignments
 							</li>
 							<li>
@@ -137,7 +170,7 @@ li:before {
 								view
 							</li>
 							<li>
-								<!-- JAL-2527 -->Alignment Overview now WYSIWIS (What you see is
+								<!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
 								what is shown)<br />Only visible region of alignment is shown by
 								default (can be changed in user preferences)
 							</li>
@@ -183,13 +216,10 @@ li:before {
 							
 							 
 						</ul></li>
-					<li><strong>Java 11 Support</strong>
+						<li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li> 
+					<li><strong>Java 11 Support (not yet on general release)</strong>
 						<ul>
 							<li>
-								<!-- JAL- -->Java 11 Native Desktop installer, standalone JAR
-								and getdown release channels
-							</li>
-							<li>
 								<!--  -->OSX GUI integrations for App menu's 'About' entry and
 								trapping CMD-Q
 							</li>
@@ -213,36 +243,25 @@ li:before {
 						<!-- 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-3007 -->Jalview Native Application and
-						Installers built with Install4j (licensed to the Jalview open
-						source project) rather than InstallAnywhere
-					</li>
-					<li>
-						<!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
-						settings, receive over the air updates and launch specific
-						versions via (<a href="https://github.com/threerings/getdown">Three
-							Rings' GetDown</a>)
-					</li>
-					<li>
-						<!-- JAL-3196,JAL-3179 -->Build system migrated from Ant to Gradle
+        	<li>
+						<!-- 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>
+          <li><!-- JAL-3174,JAL-2886,JAL-2729 -->
           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-3140 JAL-2446 -->IntervalStoreJ (NCList
-            implementation that alows updates) used for Sequence Feature collections</li>
-          <li><!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor issues resolved.</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>          
         </ul>
       </td>
 			<td align="left" valign="top">
@@ -302,9 +321,18 @@ li:before {
 						doesn't tell users the invalid URL
 					</li>
 					<li>
-						<!-- JAL-3178 -->Nonpositional features lose feature group on
-						export as Jalview features file
+						<!-- 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 -->stop_gained variants not shown correctly on
+            peptide sequence
+          </li>
 					<li>
 						<!-- JAL-2060 -->'Graduated colour' option not offered for
 						manually created features (where if feature score is Float.NaN)
@@ -338,7 +366,7 @@ li:before {
 						Page Up in wrapped mode
 					</li>
 					<li>
-						<!-- JAL-2839 -->Finder doesn't skip hidden regions
+						<!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
 					</li>
 					<li>
 						<!-- JAL-2932 -->Finder searches in minimised alignments
@@ -390,8 +418,8 @@ li:before {
 						shown in complementary view
 					</li>
 					<li>
-						<!-- JAL-2898 -->stop_gained variants not shown correctly on
-						peptide sequence
+						<!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
+						without normalisation
 					</li>
 					<li>
 						<!-- JAL-3021 -->Sequence Details report opens positioned to top
@@ -416,10 +444,26 @@ li:before {
 						<!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
 						dialog corrupts dataset sequence
 					</li>
+					<li>
+						<!-- 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>
+				<em>Datamodel</em>
 				<ul>
 					<li>
+						<!-- JAL-2986 -->Sequence.findIndex returns wrong value when
+						sequence's End is greater than its length
+					</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.
+					</li>
+					<li>
 						<!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
 						is restored from a Jalview 2.11 project
 					</li>
@@ -442,6 +486,17 @@ li:before {
 						not shown as thresholded features in 2.11. To workaround please
 						create a Score filter instead.
 					</li>
+					<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><strong>Java 11 Specific defects</strong>
+            <ul>
+              <li>
+              <!-- JAL-3235 -->Jalview Properties file is not sorted alphabetically when saved</li>
+              
+            </ul></li>
+					
 				</ul>
 			</td>
 		</tr>
@@ -617,6 +672,10 @@ li:before {
                 open URL in the browser can be dropped onto Jalview.</em>
             </li>
           </ul>
+          <em>New Known Defects</em>
+          <ul>
+            <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
+          </ul>
         </div></td>
     </tr>
     <tr>
@@ -776,7 +835,11 @@ li:before {
               Sequences' enabled) or Ensembl isoforms (Workaround in
               2.10.4 is to fail back to N&amp;W mapping)
             </li>
-          </ul>
+						<li>
+							<!-- JAL-2990 -->Export Annotations from File Menu with CSV
+							option gives blank output
+						</li>
+					</ul>
         </div>
           </td>
     </tr>