From 07addcb8a9c7904b60e19f637c5258849987c2a6 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 18 Apr 2019 13:08:26 +0100
Subject: [PATCH] JAL-3111 release notes first pass complete

---
 help/html/releases.html |  157 ++++++++++++++++++++++++++++++-----------------
 1 file changed, 102 insertions(+), 55 deletions(-)

diff --git a/help/html/releases.html b/help/html/releases.html
index 3ac1247..cffa10f 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -77,39 +77,68 @@ li:before {
     <td><div align="left">
         <ul>
           <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>
+            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
+            '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>
+            multiple groups when working with large alignments</li>
           <li>
             <!-- JAL-3200 -->Speedier import of annotation rows when
-            parsing stockholm files
-          </li>
+            parsing stockholm files</li>
           <li>
-            <!-- JAL-3018 -->Update of Ensembl Rest Client to API v9.0
-          </li>
+            <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
           <li>
-            <!-- JAL-3... -->Sequence features can be filtered and
+            <!-- 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>
+            column 9 of GFF file)</li>
           <li>
-            <!-- JAL-3139, -->More efficient sequence feature render
-            algorithm (Z-sort/transparency and filter aware)
-          </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><!--  -->
-          </li>
+            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>
         </ul>
         <em>Deprecations</em>
         <ul>
@@ -120,86 +149,104 @@ li:before {
         </ul>
         <em>Release Processes</em>
         <ul>
-          <li>Atlassian Bamboo continuous integration server for
+          <li>
+          Atlassian Bamboo continuous integration server for
             unattended Test Suite execution</li>
           <li>
             <!-- JAL-2864 -->Memory test suite to detect leaks in common
-            operations
-          </li>
+            operations</li>
           <li>
             <!-- JAL-3140 -->IntervalStoreJ (new updatable NCList
-            implementation) used for Sequence Feature collections
-          </li>
+            implementation) used for Sequence Feature collections</li>
           <li>
             <!-- JAL-3063 -->Castor library for XML marshalling and
             unmarshalling has been replaced by JAXB for Jalview projects
-            and XML based data retrieval clients
-          </li>
-          <li>
-          <!-- JAL -->
-
+            and XML based data retrieval clients</li>
         </ul>
       </div></td>
     <td><div align="left">
         <em></em>
         <ul>
           <li>
+            <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl</li>
+          <li>
             <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
-            Jalview project involving multiple views
-          </li>
+            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>
+            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>
+            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>
+            Feature Settings and Jalview Preferences panels</li>
           <li>
             <!-- JAL-2865 -->Jalview hangs when closing windows
-            or the overview updates with large alignments.
-          </li>
+            or the overview updates with large alignments</li>
           <li>
             <!-- JAL-2865 -->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>
+            and the mouse moved to the left of the first column</li>
           <li>
             <!-- JAL-2846 -->Error message for trying to load in invalid
-            URLs doesn't tell users the invalid URL
-          </li>
+            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-3161 -->Status bar updates beyond visible columns</li>
+          <li>
+            <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or 
+            printed when columns are hidden</li>
+          <li>
+            <!-- JAL-3082 -->Regular expression error 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-3002 -->Display is incorrect after Page Down and Up in wrapped mode</li>
+          <li>
+            <!-- JAL-914 -->Help page can be opened twice</li>
+          <li>
+            <!-- JAL-2839 -->Finder doesn't skip hidden regions</li>
+          <li>
+            <!-- JAL-3075 -->Column selection incorrect after scrolling out of scale panel</li>
+          <li>
+            <!-- JAL-2750 -->Tree calculation fails on a selection dragged to left of alignment</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-3125 -->Value input for graduated feature colour threshold gets 'unrounded'</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>
+            via 'Edit' sequence</li>
           <li>
             <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
             sequence features correctly when start of sequence is
-            removed (Known defect since 2.10)
-          </li>
-          <li>
-            <!-- JAL- -->
-          </li>
+            removed (Known defect since 2.10)</li>
         </ul>
         <em>New Known Defects</em>
         <ul>
           <li>
-            <!-- JAL-3178 -->Nonpositional features lose feature group
-            on export as jalview features file
-          </li>
-          <li><!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project</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>
       </div></td>
     </tr>
-- 
1.7.10.2