From 325d9af46f90ec58df53d6a0384bf3afbff6d5ab Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 10 Feb 2020 17:08:05 +0000
Subject: [PATCH] JAL-3407 JAL-3508 move to 2.11.1.0 point release versioning
 and signed off JAL-3510 JAL-3513 JAL-3388 JAL-3389 JAL-3441
 JAL-3473 JAL-3406

---
 AUTHORS                      |    2 +-
 RELEASE                      |    2 +-
 help/help/html/releases.html |  803 ++++++++++++++++++++++--------------------
 3 files changed, 423 insertions(+), 384 deletions(-)

diff --git a/AUTHORS b/AUTHORS
index 2fe3fce..68142b2 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -7,7 +7,7 @@ or might otherwise be considered author of Jalview.
 The people listed below are 'The Jalview Authors', who collectively
 own the copyright to the Jalview source code and permit it to be released under GPL.
 
-This is the authoritative list: it was correct on 5th September 2018 (or the last commit date!)
+This is the authoritative list: it was correct on the last commit date!
 
 If you are releasing a version of Jalview, please make sure any
 statement of authorship in the GUI reflects the list shown here.
diff --git a/RELEASE b/RELEASE
index f6e3b96..5a89907 100644
--- a/RELEASE
+++ b/RELEASE
@@ -1,2 +1,2 @@
 jalview.release=releases/Release_2_11_1_Branch
-jalview.version=2.11.1
+jalview.version=2.11.1.0
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 0f4dd9b..13e2ae8 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -56,28 +56,67 @@ li:before {
       <th><em>Issues Resolved</em></th>
     </tr>
     <tr>
-      <td width="60" align="center" nowrap>
-          <strong><a name="Jalview.2.11.1">2.11.1</a><br />
-            <em>16/2/2020</em></strong>
-      </td>
+      <td width="60" align="center" nowrap><strong><a
+          name="Jalview.2.11.1">2.11.1</a><a name="Jalview.2.11.1.0">.0</a><br />
+          <em>16/2/2020</em></strong></td>
       <td align="left" valign="top">
         <ul>
-          <li><!-- -->
+          <li>
+            <!-- -->
           </li>
-        </ul>
-        <em>Deprecations</em>
+        </ul> <em>Release processes</em>
+        <ul>
+          <li>
+            <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
+          </li>
+        </ul> <em>Build System</em>
+        <ul>
+          <li>
+            <!-- JAL-3510 -->Clover updated to 4.4.1
+          </li>
+          <li>
+            <!-- JAL-3513 -->Test code included in Clover coverage
+            report
+          </li>
+        </ul> <em>Deprecations</em>
       </td>
       <td align="left" valign="top">
         <ul>
-        </ul>
-        <em>Java 11 Compatibility issues</em>
+          <li>
+            <!-- -->
+          </li>
+          <li>
+            <!-- -->
+          </li>
+          <li>
+            <!-- -->
+          </li>
+          <li>
+            <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
+            ID fails with ClassCastException
+          </li>
+          <li>
+            <!-- JAL-3389 -->Chimera session not restored from Jalview
+            Project
+          </li>
+          <li>
+            <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
+            feature settings dialog also selects columns
+          </li>
+          <li>
+            <!-- JAL-3473 -->SpinnerNumberModel causing
+            IllegalArgumentException in some circumstances
+          </li>
+          <li>
+            <!-- JAL-3406 -->Credits missing some authors in Jalview
+            help documentation for 2.11.0 release
+          </li>
+        </ul> <em>Java 11 Compatibility issues</em>
         <ul>
           <li>
             <!-- JAL-2987 -->OSX - Can't view results in PDB/Uniprot FTS
           </li>
-        </ul>
-        
-        <em>Repository and Source Release</em>
+        </ul> <em>Repository and Source Release</em>
         <ul>
           <li>
             <!-- JAL-3474 -->removed redundant .gitignore files from
@@ -104,20 +143,20 @@ li:before {
             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-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>
+          <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>
@@ -125,9 +164,9 @@ li:before {
             'Translate as cDNA'</li>
           <li>
             <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
-					<li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
-						<ul>
-						          <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>
@@ -142,124 +181,124 @@ li:before {
                 stored and restored from Jalview Projects
               </li>
               <li>
-								<!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
-								recognise variant features
-							</li>
-							<li>
-								<!-- 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,JAL-1117 -->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-3205 -->Symmetric score matrices for faster
-						tree and PCA calculations
-					</li>
-					<li><strong>Principal Components Analysis Viewer</strong>
+                <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
+                recognise variant features
+              </li>
+              <li>
+                <!-- 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,JAL-1117 -->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-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><!-- 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, JAL-1285 -->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-2185,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 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
-								what is shown)<br />Only visible regions of alignment are 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 a graph or histogram
-								annotation
-							</li>
-							<li>
-								<!-- JAL-2814,JAL-437 -->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>
-							<li>
-							<!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
-							<li>
-							<!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
-							
-							 
-						</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>
-								<!--  -->OSX GUI integrations for App menu's 'About' entry and
-								trapping CMD-Q
-							</li>
-						</ul></li>
-				</ul>
+              <li>
+                <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
+                and Viewer state saved in Jalview Project
+              </li>
+              <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, JAL-1285 -->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-2185,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 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
+                what is shown)<br />Only visible regions of alignment are 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 a graph or histogram
+                annotation
+              </li>
+              <li>
+                <!-- JAL-2814,JAL-437 -->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>
+              <li>
+              <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
+              <li>
+              <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
+              
+               
+            </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>
+                <!--  -->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
@@ -271,18 +310,18 @@ li:before {
           <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li> 
           <li><!--  -->Jalview Desktop no longer distributed via Java Web Start</li>
         </ul> <em>Documentation</em>
-				<ul>
-					<li><!-- 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-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>
+        <ul>
+          <li><!-- 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-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
@@ -313,194 +352,194 @@ li:before {
           </li>
         </ul>
       </td>
-			<td align="left" valign="top">
-				<ul>
-					<li>
-						<!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
-					</li>
-					<li>
-						<!-- JAL-3244 -->'View [Structure] Mappings' and structure
-						superposition in Jmol fail on Windows
-					</li>
-					<li>
-						<!-- JAL-3286 -->Blank error dialog is displayed when discovering
-						structures for sequences with lots of PDB structures
-					</li>
-					<li>
-						<!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
-						monospaced font
-					</li>
-					<li>
-						<!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
-						project involving multiple views
-					</li>
-					<li>
-						<!-- JAL-3164 -->Overview for complementary view in a linked
-						CDS/Protein alignment is not updated when Hide Columns by
-						Annotation dialog hides columns
-					</li>
-					<li>
-						<!-- JAL-3158 -->Selection highlighting in the complement of a
-						CDS/Protein alignment stops working after making a selection in
-						one view, then making another selection in the other view
-					</li>
-					<li>
-						<!-- JAL-3161 -->Annotations tooltip changes beyond visible
-						columns
-					</li>
-					<li>
-						<!-- JAL-3154 -->Table Columns could be re-ordered in Feature
-						Settings and Jalview Preferences panels
-					</li>
-					<li>
-						<!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
-						overview with large alignments
-					</li>
-					<li>
-						<!-- 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>
-					<li>
-						<!-- 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>
+      <td align="left" valign="top">
+        <ul>
+          <li>
+            <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
+          </li>
+          <li>
+            <!-- JAL-3244 -->'View [Structure] Mappings' and structure
+            superposition in Jmol fail on Windows
+          </li>
+          <li>
+            <!-- JAL-3286 -->Blank error dialog is displayed when discovering
+            structures for sequences with lots of PDB structures
+          </li>
+          <li>
+            <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
+            monospaced font
+          </li>
+          <li>
+            <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
+            project involving multiple views
+          </li>
+          <li>
+            <!-- JAL-3164 -->Overview for complementary view in a linked
+            CDS/Protein alignment is not updated when Hide Columns by
+            Annotation dialog hides columns
+          </li>
+          <li>
+            <!-- JAL-3158 -->Selection highlighting in the complement of a
+            CDS/Protein alignment stops working after making a selection in
+            one view, then making another selection in the other view
+          </li>
+          <li>
+            <!-- JAL-3161 -->Annotations tooltip changes beyond visible
+            columns
+          </li>
+          <li>
+            <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
+            Settings and Jalview Preferences panels
+          </li>
+          <li>
+            <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
+            overview with large alignments
+          </li>
+          <li>
+            <!-- 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>
+          <li>
+            <!-- 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 feature score is Float.NaN)
-					</li>
-					<li>
-						<!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
-						when columns are hidden
-					</li>
-					<li>
-						<!-- JAL-3082 -->Regular expression error for '(' in Select
-						Columns by Annotation description
-					</li>
-					<li>
-						<!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
-						out of Scale or Annotation Panel
-					</li>
-					<li>
-						<!-- JAL-3075 -->Column selection incorrect after scrolling out of
-						scale panel
-					</li>
-					<li>
-						<!-- JAL-3074 -->Left/right drag in annotation can scroll
-						alignment down
-					</li>
-					<li>
-						<!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
-						scale panel
-					</li>
-					<li>
-						<!-- JAL-3002 -->Column display is out by one after Page Down,
-						Page Up in wrapped mode
-					</li>
-					<li>
-						<!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
-					</li>
-					<li>
-						<!-- JAL-2932 -->Finder searches in minimised alignments
-					</li>
-					<li>
-						<!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
-						on opening an alignment
-					</li>
-					<li>
-						<!-- JAL-3180 -->'Colour by Annotation' not marked selected in
-						Colour menu
-					</li>
-					<li>
-						<!-- JAL-3201 -->Per-group Clustal colour scheme changes when
-						different groups in the alignment are selected
-					</li>
-					<li>
-						<!-- JAL-2717 -->Internationalised colour scheme names not shown
-						correctly in menu
-					</li>
-					<li>
-						<!-- JAL-3206 -->Colour by Annotation can go black at min/max
-						threshold limit
-					</li>
-					<li>
-						<!-- JAL-3125 -->Value input for graduated feature colour
-						threshold gets 'unrounded'
-					</li>
-					<li>
-						<!-- JAL-2982 -->PCA image export doesn't respect background
-						colour
-					</li>
-					<li>
-						<!-- JAL-2963 -->PCA points don't dim when rotated about y axis
-					</li>
-					<li>
-						<!-- JAL-2959 -->PCA Print dialog continues after Cancel
-					</li>
-					<li>
-						<!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
-						Tree font
-					</li>
-					<li>
-						<!-- JAL-2964 -->Associate Tree with All Views not restored from
-						project file
-					</li>
-					<li>
-						<!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
-						shown in complementary view
-					</li>
-					<li>
-						<!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
-						without normalisation
-					</li>
-					<li>
-						<!-- 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>
-						<!-- JAL-2822 -->Start and End should be updated when sequence
-						data at beginning or end of alignment added/removed via 'Edit'
-						sequence
-					</li>
-					<li>
-						<!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
-						relocate sequence features correctly when start of sequence is
-						removed (Known defect since 2.10)
-					</li>
-					<li>
-						<!-- 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>Datamodel</em>
+          <li>
+            <!-- JAL-2060 -->'Graduated colour' option not offered for
+            manually created features (where feature score is Float.NaN)
+          </li>
+          <li>
+            <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
+            when columns are hidden
+          </li>
+          <li>
+            <!-- JAL-3082 -->Regular expression error for '(' in Select
+            Columns by Annotation description
+          </li>
+          <li>
+            <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
+            out of Scale or Annotation Panel
+          </li>
+          <li>
+            <!-- JAL-3075 -->Column selection incorrect after scrolling out of
+            scale panel
+          </li>
+          <li>
+            <!-- JAL-3074 -->Left/right drag in annotation can scroll
+            alignment down
+          </li>
+          <li>
+            <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
+            scale panel
+          </li>
+          <li>
+            <!-- JAL-3002 -->Column display is out by one after Page Down,
+            Page Up in wrapped mode
+          </li>
+          <li>
+            <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
+          </li>
+          <li>
+            <!-- JAL-2932 -->Finder searches in minimised alignments
+          </li>
+          <li>
+            <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
+            on opening an alignment
+          </li>
+          <li>
+            <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
+            Colour menu
+          </li>
+          <li>
+            <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
+            different groups in the alignment are selected
+          </li>
+          <li>
+            <!-- JAL-2717 -->Internationalised colour scheme names not shown
+            correctly in menu
+          </li>
+          <li>
+            <!-- JAL-3206 -->Colour by Annotation can go black at min/max
+            threshold limit
+          </li>
+          <li>
+            <!-- JAL-3125 -->Value input for graduated feature colour
+            threshold gets 'unrounded'
+          </li>
+          <li>
+            <!-- JAL-2982 -->PCA image export doesn't respect background
+            colour
+          </li>
+          <li>
+            <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
+          </li>
+          <li>
+            <!-- JAL-2959 -->PCA Print dialog continues after Cancel
+          </li>
+          <li>
+            <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
+            Tree font
+          </li>
+          <li>
+            <!-- JAL-2964 -->Associate Tree with All Views not restored from
+            project file
+          </li>
+          <li>
+            <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
+            shown in complementary view
+          </li>
+          <li>
+            <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
+            without normalisation
+          </li>
+          <li>
+            <!-- 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>
+            <!-- JAL-2822 -->Start and End should be updated when sequence
+            data at beginning or end of alignment added/removed via 'Edit'
+            sequence
+          </li>
+          <li>
+            <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
+            relocate sequence features correctly when start of sequence is
+            removed (Known defect since 2.10)
+          </li>
+          <li>
+            <!-- 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>Datamodel</em>
         <ul>
           <li>
             <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
@@ -514,41 +553,41 @@ li:before {
           </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>
-				<li>
-					<!-- JAL-3213 -->Alignment panel height can be too small after
-					'New View'
-				</li>
-				<li>
-					<!-- JAL-3240 -->Display is incorrect after removing gapped
-					columns within hidden columns
-				</li>
-				<li>
-					<!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
-					window after dragging left to select columns to left of visible
-					region
-				</li>
-				<li>
-					<!-- JAL-2876 -->Features coloured according to their description
-					string and thresholded by score in earlier versions of Jalview are
-					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>
+        <!-- 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>
+        <li>
+          <!-- JAL-3213 -->Alignment panel height can be too small after
+          'New View'
+        </li>
+        <li>
+          <!-- JAL-3240 -->Display is incorrect after removing gapped
+          columns within hidden columns
+        </li>
+        <li>
+          <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
+          window after dragging left to select columns to left of visible
+          region
+        </li>
+        <li>
+          <!-- JAL-2876 -->Features coloured according to their description
+          string and thresholded by score in earlier versions of Jalview are
+          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>
           <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
           alignments with multiple views can close views unexpectedly
@@ -562,7 +601,7 @@ li:before {
             </li>
         </ul>
       </td>
-		</tr>
+    </tr>
     <tr>
     <td width="60" nowrap>
       <div align="center">
@@ -898,11 +937,11 @@ li:before {
               Sequences' enabled) or Ensembl isoforms (Workaround in
               2.10.4 is to fail back to N&amp;W mapping)
             </li>
-						<li>
-							<!-- JAL-2990 -->Export Annotations from File Menu with CSV
-							option gives blank output
-						</li>
-					</ul>
+            <li>
+              <!-- JAL-2990 -->Export Annotations from File Menu with CSV
+              option gives blank output
+            </li>
+          </ul>
         </div>
           </td>
     </tr>
-- 
1.7.10.2