X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=07ed6e89ca07452bb9ab0cbef0b05164514ea762;hb=221a20bd20c7c038f18b7f341765165e8c80ca01;hp=dfc159b193b88c5635b9628476de4f0c83836454;hpb=9c3e177b57a28975db810dd060a7f1f5f5b8f867;p=jalview.git

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index dfc159b..07ed6e8 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>04/07/2019</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>
@@ -71,22 +96,35 @@ 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
-								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
 								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 +134,23 @@ 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 +160,7 @@ 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 +175,7 @@ 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>
@@ -166,7 +204,7 @@ 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
@@ -183,13 +221,10 @@ 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 +248,43 @@ 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>
-					<li>
-						<!-- JAL-3225 -->Eclipse project configuration managed with
-						gradle-eclipse
+        	<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>
-          Atlassian Bamboo continuous integration for
-            unattended Test Suite execution</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>
+            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>
+          <li>
+            <!-- JAL-3287 -->HelpLinksChecker runs on Windows
+          </li>
+          <li>
+            <!-- JAL-3289 -->New URLs for publishing development
+            versions of Jalview
+          </li>
+          <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>          
         </ul>
       </td>
 			<td align="left" valign="top">
@@ -302,10 +344,19 @@ 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,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)
 					</li>
@@ -338,7 +389,7 @@ 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
@@ -390,16 +441,19 @@ 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
+						<!-- 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>
@@ -417,12 +471,29 @@ li:before {
 						dialog corrupts dataset sequence
 					</li>
 					<li>
-						<!-- JAL-3313 -->Codon consensus logo incorrectly scaled when
-						shown without normalisation
+						<!-- JAL-868 -->Structure colours not updated when associated tree
+						repartitions the alignment view (Regression in 2.10.5)
+					</li>
+				</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.
 					</li>
-				</ul>
-				<em>New Known Defects</em>
-				<ul>
 					<li>
 						<!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
 						is restored from a Jalview 2.11 project
@@ -446,7 +517,22 @@ li:before {
 						not shown as thresholded features in 2.11. To workaround please
 						create a Score filter instead.
 					</li>
-				</ul>
+					<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>
 			</td>
 		</tr>
     <tr>
@@ -621,6 +707,10 @@ 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>
@@ -780,7 +870,11 @@ 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>