JAL-3407 group together ‘virtual feature’ related features in release notes

[jalview.git] / help / help / html / releases.html

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index d7f3ee1..67f6fc1 100755 (executable)
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -57,25 +57,62 @@ li:before {
     </tr>
     <tr>
       <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>25/2/2020</em></strong></td>
+          id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
+          <em>27/03/2020</em></strong></td>
       <td align="left" valign="top">
         <ul>
           <li>
-            <!-- JAL-3376 -->Record &quot;fixed column&quot; values POS,
-            ID, QUAL, FILTER from VCF as Feature Attributes
+            <!-- JAL-3187 -->Option to show 'virtual' codon features on
+            protein (or vice versa)
+            <ul>
+              <li>
+                <!-- JAL-3304 -->Option to export virtual features if
+                shown
+              </li>
+              <li>
+                <!-- JAL-3302 -->Option to transfer virtual features to
+                Chimera
+              </li>
+            </ul>
+          </li>
+          <li>
+          <!-- JAL-3121 -->Feature attributes from VCF files can be exported and re-imported as GFF3 files
+          </li>
+          <li>
+            <!-- JAL-3376 -->Capture VCF &quot;fixed column&quot; values POS,
+            ID, QUAL, FILTER as Feature Attributes
+          </li>
+          <li>
+            <!-- JAL-3375 -->More robust VCF numeric data field validation while parsing
+          </li>
+          <li>
+            <!-- JAL-3533 -->Feature Settings dialog keeps same screen position if reopened 
+           </li>
+          <li>
+            <!-- JAL-3538 -->Font anti-aliasing in alignment views enabled by default
+           </li>
+          <li>
+            <!-- JAL-3468 -->Very long feature descriptions truncated in tooltips and menus
+           </li>
+          <li>
+            <!-- JAL-3549 -->Warn if Sort by Score or Density attempted with no feature types visible 
           </li>
+        </ul><em>Jalview Installer</em>
+           <ul>
           <li>
-            <!-- JAL-3375 -->More robust VCF numeric data field
-            validation while parsing (e.g. AF* attributes)
+            <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
+            in console (may be null when Jalview launched as executable jar or via conda)
           </li>
           <li>
-            <!-- JAL-3538 -->Font anti-aliasing in alignment views
-            enabled by default
+           <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
           </li>
           <li>
-          <!-- JAL -->
+           <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
           </li>
+             <li>
+               <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
+             <li>
+               <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
         </ul> <em>Release processes</em>
         <ul>
           <li>
@@ -90,12 +127,15 @@ li:before {
             <!-- JAL-3513 -->Test code included in Clover coverage
             report
           </li>
-        </ul> <em>Deprecations</em>
+        </ul>
       </td>
       <td align="left" valign="top">
         <ul>
           <li>
-            <!-- -->
+            <!-- JAL-3412 -->ID margins for CDS and Protein views not equal when split frame is first opened
+          </li>
+          <li>
+            <!-- JAL-3296 -->Sequence position numbers in status bar not correct after editing a sequence's start position
           </li>
           <li>
             <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
@@ -119,23 +159,35 @@ li:before {
             feature settings dialog also selects columns
           </li>
           <li>
-            <!-- JAL-3473 -->SpinnerNumberModel causing
+            <!-- JAL-3473 -->SpinnerNumberModel causes
             IllegalArgumentException in some circumstances
           </li>
           <li>
+            <!-- JAL-3534 -->Multiple feature settings dialogs can be opened for a view
+          </li>
+          <li>
+            <!-- JAL-2764 -->Feature Settings dialog is orphaned if alignment window is closed
+          </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
+            <!-- JAL-2987 -->OSX - Can't view some search results in PDB/Uniprot search panel
+          </li>
+       </ul> <em>Installer</em>
+        <ul>
+          <li><!-- JAL-3447 -->Jalview should not create file associations for 3D structure files (.pdb, .mmcif. .cif)
           </li>
         </ul> <em>Repository and Source Release</em>
         <ul>
           <li>
-            <!-- JAL-3474 -->removed redundant .gitignore files from
-            repository
+            <!-- JAL-3474 -->removed obsolete .cvsignore files from repository
+          </li>
+          <li>
+            <!-- JAL-3541 -->Clover report generation running out of memory
           </li>
         </ul>
         <em>New Known Issues</em>
@@ -150,6 +202,9 @@ li:before {
             clipped in headless figure export when Right Align option
             enabled
           </li>
+          <li>
+            <!-- JAL-3542 -->Jalview Installation type always reports 'Source' in console output
+          </li>
         </ul>
       </td>
     </tr>