X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=88b0fd76d39efb81877489f093c09fe55936ea04;hb=d4e1d57420f851da08da04f2a82efd5f7a580664;hp=a98b060296b1f4b9236c26bffa0b14e52ace3b16;hpb=65f6d20fc14e4fd410084bd3ffefa52e54341077;p=jalview.git

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index a98b060..88b0fd7 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -58,106 +58,179 @@ li:before {
     <tr>
       <td width="60" align="center" nowrap>
           <strong><a name="Jalview.2.11">2.11</a><br />
-            <em>14/05/2019 (final due date !)</em></strong>
+            <em>20/06/2019</em></strong>
       </td>
       <td align="left" valign="top">
         <ul>
           <li>
             <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
           <li>
-            <!-- JAL-3141 -->Optional automatic backups when saving
-            Jalview project or alignment files</li>
-          <li>
-            <!-- JAL-1767,JAL-2647 -->Principal Components Analysis and
-            Viewer state is saved in Jalview Project<br />The 'Change
-            parameters' option has also been removed from the PCA viewer</li>
-          <li>
-            <!-- JAL-3127 -->New 'Colour by Sequence ID' (subgroup) option</li>
-          <li>
-            <!-- JAL-2620 -->Alternative genetic code tables supported for
+            <!-- JAL-2620 -->Alternative genetic code tables for
             'Translate as cDNA'</li>
           <li>
-            <!-- JAL-2933 -->Finder panel remembers last position in each view</li>
-          <li>
-            <!-- JAL-3198 -->More efficient creation of selections and
-            multiple groups when working with large alignments</li>
-          <li>
-            <!-- JAL-3200 -->Speedier import of annotation rows when
-            parsing stockholm files</li>
-          <li>
             <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</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)</li>
-          <li>
-            <!-- JAL-2897 -->Show synonymous codon variants on peptide sequences</li>
-          <li>
-            <!-- JAL-2792 -->Popup report of a selected sequence feature's details</li>
-          <li>
-            <!-- JAL-3139,JAL-2816 -->More efficient sequence feature render
-            algorithm (Z-sort/transparency and filter aware)</li>
-          <li>
-            <!-- JAL-2527 -->Alignment Overview now by default shows
-            only visible region of alignment (this can be changed in
-            user preferences)</li>
-          <li>
-            <!-- JAL-3169 -->File Chooser stays open after Cancel overwrite</li>
-          <li>
-            <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when
-          all sequences are hidden</li>
-          <li>
-            <!-- JAL-1244 -->Status bar shows bounds when dragging a selection
-          region, and gap count when inserting or deleting gaps</li>
-          <li>
-            <!-- JAL-3132 -->Status bar updates over sequence and annotation labels</li>
-          <li>
-            <!-- JAL-3093 -->Show annotation tooltips and popup menus in wrapped mode</li>
-          <li>
-            <!-- JAL-3073 -->Can select columns by dragging left/right in annotations</li>
-          <li>
-            <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings dialog</li>
-          <li>
-            <!-- JAL-2814 -->Help button on Uniprot and PDB search panels</li>
-          <li> 
-            <!-- JAL-2621 -->Cursor changes over draggable box in Overview panel</li>
-          <li>
-            <!-- JAL-3203  -->Overview panel default changed to not show hidden regions</li>
-          <li>
-            <!-- JAL-3181 -->Consistent ordering of links in sequence id popup menu</li>
-          <li>
-            <!-- JAL-3021 -->Sequence Details report opens positioned to top of report</li>
-          <li>
-            <!-- JAL-3218 -->Scale panel popup menu allows Hide selected columns adjacent 
-            to a hidden column marker</li>
-          <li>
-            <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image incrementally</li>
-          <li>
-            <!-- JAL-2965 -->PCA depth queuing with graduated colours</li>
-        </ul>
+					<li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
+						<ul>
+							<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)
+							</li>
+							<li>
+								<!-- JAL-2897 -->Show synonymous codon variants on peptide
+								sequences
+							</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
+								algorithm (Z-sort/transparency and filter aware)
+							</li>
+							<li>
+								<!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
+								dialog
+							</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>
+								<!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
+								and Viewer state saved in Jalview Project
+							</li>
+							<li>'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
+							</li>
+						</ul>
+					</li>
+					<li>
+						<!-- JAL-3127 -->New 'Colour by Sequence ID' option
+					</li>
+					<li><strong>Speed and Efficiency</strong>
+					<ul>
+							<li>
+								<!-- JAL-3198 -->More efficient creation of selections and
+								multiple groups when working with large alignments
+							</li>
+							<li>
+								<!-- JAL-3200 -->Speedier import of annotation rows when parsing
+								Stockholm files
+							</li>
+						</ul>
+					<li><strong>User Interface</strong>
+					<ul>
+							<li>
+								<!-- JAL-2933 -->Finder panel remembers last position in each
+								view
+							</li>
+							<li>
+								<!-- JAL-2527 -->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>
+							<li>
+								<!-- JAL-3169 -->File Chooser stays open after responding Cancel
+								to the Overwrite Dialog
+							</li>
+							<li>
+								<!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
+								sequences are hidden
+							</li>
+							<li>
+								<!-- JAL-1244 -->Status bar shows bounds when dragging a
+								selection region, and gap count when inserting or deleting gaps
+							</li>
+							<li>
+								<!-- JAL-3132 -->Status bar updates over sequence and annotation
+								labels
+							</li>
+							<li>
+								<!-- JAL-3093 -->Annotation tooltips and popup menus are shown
+								when in wrapped mode
+							</li>
+							<li>
+								<!-- JAL-3073 -->Can select columns by dragging left/right in
+								annotations
+							</li>
+							<li>
+								<!-- JAL-2814 -->Help button on Uniprot and PDB search panels
+							</li>
+							<li>
+								<!-- JAL-2621 -->Cursor changes over draggable box in Overview
+								panel
+							</li>
+							<li>
+								<!-- JAL-3181 -->Consistent ordering of links in sequence id
+								popup menu
+							</li>
+						</ul></li>
+					<li><strong>Java 11 Support</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>
+						</ul></li>
+				</ul>
         <em>Deprecations</em>
         <ul>
           <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
+            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>Release Processes</em>
+        <em>Development and Release Processes</em>
         <ul>
-          <li>
-          Atlassian Bamboo continuous integration server for
+					<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>
+          <li>
+          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 -->IntervalStoreJ (new updatable NCList
-            implementation) used for Sequence Feature collections</li>
-          <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>
+            <!-- JAL-3140 -->IntervalStoreJ (NCList
+            implementation that alows updates) used for Sequence Feature collections</li>          
         </ul>
       </td>
     <td align="left" valign="top">
@@ -192,6 +265,9 @@ li:before {
             <!-- JAL-2750 -->Tree and PCA calculation fails for selected
             region if columns were selected by dragging right-to-left
             and the mouse moved to the left of the first column</li>
+            <li>
+            <!-- JAL-3218 -->Couldn't hide selected columns adjacent 
+            to a hidden column marker via scale popup menu</li>
           <li>
             <!-- JAL-2846 -->Error message for trying to load in invalid
             URLs doesn't tell users the invalid URL</li>
@@ -247,6 +323,8 @@ li:before {
           <li>
             <!-- JAL-2898 -->stop_gained variants not shown correctly on peptide sequence</li>
           <li>
+            <!-- JAL-3021 -->Sequence Details report opens positioned to top of report</li>
+          <li>
             <!-- JAL-914 -->Help page can be opened twice</li>
         </ul>
         <em>Editing</em>