From 2acfca153f47a42f2e2ba6db01acb1846d9d7848 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 20 Jun 2019 14:47:33 +0100
Subject: [PATCH] =?utf8?q?JAL-3111=20signed=20off=20=E2=80=99done=E2=80=99=20?=
 =?utf8?q?issues=20in=20Jira=20as=20of=20now:=20JAL-1059,JAL-1117,JAL-1285,J?=
 =?utf8?q?AL-1793,JAL-1839,JAL-1929,JAL-2069,JAL-2185,JAL-2360,JAL-2416,JAL-?=
 =?utf8?q?2446,JAL-2620,JAL-2647,JAL-2671,JAL-2729,JAL-2753,JAL-2808,JAL-281?=
 =?utf8?q?6,JAL-2839,JAL-2864,JAL-2886,JAL-2898,JAL-2932,JAL-2965,JAL-3007,J?=
 =?utf8?q?AL-3018,JAL-3021,JAL-3139,JAL-3140,JAL-3141,JAL-3174,JAL-3179,JAL-?=
 =?utf8?q?3196,JAL-3198,JAL-3225,JAL-3232,JAL-3236,JAL-3248,JAL-3254,JAL-326?=
 =?utf8?q?0,JAL-3313,JAL-781,JAL-868=E2=80=A8?=
MIME-Version: 1.0
Content-Type: text/plain; charset=utf8
Content-Transfer-Encoding: 8bit

---
 help/help/html/releases.html |   82 +++++++++++++++++++++++++-----------------
 1 file changed, 50 insertions(+), 32 deletions(-)

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 4df8ae2..7d9d7c9 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">
@@ -338,7 +347,7 @@ 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 +403,10 @@ 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 +430,18 @@ 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>
-- 
1.7.10.2