X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=c570d0def4ba3850bf58e115b201b2a778dfd729;hb=f0aa3143af5eb4492eea8cdf67a155a2399a5552;hp=4df8ae2ffbc9c0465dd41868af3eaedd54a2371b;hpb=5bcb06fb95e9f218edaa3a1c233264cb3a86f47a;p=jalview.git

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 4df8ae2..c570d0d 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -63,7 +63,32 @@ li:before {
       <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 alows 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
@@ -86,7 +115,7 @@ 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>
@@ -95,10 +124,6 @@ li:before {
 							</li>
 						</ul>
 					</li>
-					<li>
-            <!-- JAL-3141 -->Backup files created when saving Jalview project
-            or alignment files
-          </li>
           <li><strong>Principal Components Analysis Viewer</strong>
             <ul>
 							<li>
@@ -112,7 +137,7 @@ li:before {
 								incrementally
 							</li>
 							<li>
-								<!-- JAL-2965 -->PCA plot is depth cued
+								<!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
 							</li>
 						</ul>
 					</li>
@@ -122,7 +147,7 @@ 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>
@@ -183,13 +208,10 @@ li:before {
 							
 							 
 						</ul></li>
+						<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>
@@ -215,34 +237,21 @@ li:before {
 					</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-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">
@@ -306,6 +315,10 @@ li:before {
 						export as Jalview features file
 					</li>
 					<li>
+						<!-- JAL-2816 -->Tooltips displayed for features filtered by
+						score from view
+					</li>
+					<li>
 						<!-- JAL-2060 -->'Graduated colour' option not offered for
 						manually created features (where if feature score is Float.NaN)
 					</li>
@@ -338,7 +351,7 @@ 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
@@ -394,6 +407,10 @@ li:before {
 						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
 						of report
 					</li>
@@ -417,13 +434,18 @@ 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>New Known Defects</em>
 				<ul>
 					<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>