From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 19 Jun 2019 10:09:20 +0000 (+0100)
Subject: JAL-3111 formatting

X-Git-Tag: Release_2_11_0~7^2^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=12334155115dd7bd3d54308270db847122c76bfe;p=jalview.git

JAL-3111 formatting

---

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 7b33149..87a2f4b 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -245,128 +245,188 @@ li:before {
           <li><!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor issues resolved.</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>
+			<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 the overview updates 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-3178 -->Nonpositional features lose feature group
-            on export as Jalview features file</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 the
+						overview updates 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-3178 -->Nonpositional features lose feature group on
+						export as Jalview features file
+					</li>
 					<li>
 						<!-- JAL-2060 -->'Graduated colour' option not offered for
 						manually created features (where if 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 -->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-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>
-        <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>
+						<!-- 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 -->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-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>
+				<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>
-				</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</li> 
-          <li>
-            <!-- JAL-3213 -->Alignment panel height can be too small after 'New View'</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
+					</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
@@ -383,8 +443,8 @@ li:before {
 						create a Score filter instead.
 					</li>
 				</ul>
-      </td>
-    </tr>
+			</td>
+		</tr>
     <tr>
     <td width="60" nowrap>
       <div align="center">
@@ -590,12 +650,12 @@ li:before {
               <!-- JAL-2593 -->Improved performance when rendering lots
               of features (particularly when transparency is disabled)
             </li>
-						<li>
-							<!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
-							exchange of Jalview features and Chimera attributes made
-							generally available
-						</li>
-					</ul>
+            <li>
+              <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
+              exchange of Jalview features and Chimera attributes made
+              generally available
+            </li>
+          </ul>
           </div>
       </td>
       <td><div align="left">
@@ -1468,16 +1528,16 @@ li:before {
               <!-- JAL-2589 -->User defined gap colour not shown in
               overview when features overlaid on alignment
             </li>
-						<li>
-							<!-- JAL-2567 -->Feature settings for different views not
-							recovered correctly from Jalview project file
-						</li>
-						<li>
-							<!-- JAL-2256 -->Feature colours in overview when first opened
-							(automatically via preferences) are different to the main
-							alignment panel
-						</li>
-					</ul>
+            <li>
+              <!-- JAL-2567 -->Feature settings for different views not
+              recovered correctly from Jalview project file
+            </li>
+            <li>
+              <!-- JAL-2256 -->Feature colours in overview when first opened
+              (automatically via preferences) are different to the main
+              alignment panel
+            </li>
+          </ul>
           <em>Data import/export</em>
           <ul>
             <li>