From: Jim Procter <j.procter@dundee.ac.uk>
Date: Wed, 15 Sep 2021 15:16:15 +0000 (+0100)
Subject: JAL-3816 bump version number and cut release notes
X-Git-Tag: Release_2_11_2_0~34^2~2^2~4
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=ad31864f13259c7063cd598d4693b64b4c5fce92

JAL-3816 bump version number and cut release notes

 Conflicts:
	RELEASE
	doc/building.html
---

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 0e3e652..4c72658 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -55,19 +55,92 @@ li:before {
       <th><em>New Features</em></th>
       <th><em>Issues Resolved</em></th>
     </tr>
+    <td width="60" align="center" nowrap><strong><a
+        id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
+        <em>08/02/2021</em></strong></td>
+    <td align="left" valign="top"><em>Improved control of
+        Jalview's use of network services</em>
+      <ul>
+        <li>
+          <!-- JAL-3814 -->New .jalview_properties token controlling
+          launch of the news browser (like -nonews argument)
+        </li>
+        <li>
+          <!-- JAL-3813 -->New .jalview_properties token controlling
+          download of linkout URLs from
+          www.jalview.org/services/identifiers
+        </li>
+        <li>
+          <!-- JAL-3812 -->New .jalview_properties token controlling
+          download of BIOJSHTML templates
+        </li>
+        <li>
+          <!-- JAL-3811 -->New 'Discover Web Services' option to trigger
+          a one off JABAWS discovery if autodiscovery was disabled
+        </li>
+      </ul></td>
+    <td align="left" valign="top">
+      <ul>
+        <li></li>
+      </ul>
+    </td>
+    </tr>
     <tr>
       <td width="60" align="center" nowrap><strong><a
           id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
-          <em>27/10/2020</em></strong></td>
+          <em>29/10/2020</em></strong></td>
       <td align="left" valign="top">
         <ul>
+
         </ul>
       </td>
       <td align="left" valign="top">
         <ul>
           <li>
             <!-- JAL-3765 -->Find doesn't always highlight all matching
-            positions in a sequence
+            positions in a sequence (bug introduced in 2.11.1.2)
+          </li>
+          <li>
+            <!-- JAL-3760 -->Alignments containing one or more protein
+            sequences can be classed as nucleotide
+          </li>
+          <li>
+            <!-- JAL-3748 -->CDS alignment doesn't match original CDS
+            sequences after alignment of protein products (known defect
+            first reported for 2.11.1.0)
+          </li>
+          <li>
+            <!-- JAL-3725 -->No tooltip or popup menu for genomic
+            features outwith CDS shown overlaid on protein
+          </li>
+          <li>
+            <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
+            correctly mapped by Jalview (e.g. affects viral CDS with
+            ribosomal slippage, since 2.9.0)
+          </li>
+          <li>
+            <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
+            CDS features
+          </li>
+          <li>
+            <!-- JAL-3700 -->Selections in CDS sequence panel don't
+            always select corresponding protein sequences
+          </li>
+          <li>
+            <!-- JAL-3759 --> <em>Make groups from selection</em> for a
+            column selection doesn't always ignore hidden columns
+          </li>
+        </ul> <em>Installer</em>
+        <ul>
+          <li>
+            <!-- JAL-3611 -->Space character in Jalview install path on
+            Windows prevents install4j launching getdown
+          </li>
+        </ul> <em>Development</em>
+        <ul>
+          <li>
+            <!-- JAL-3248 -->Fixed typos and specified compatible gradle
+            version numbers in doc/building.md
           </li>
         </ul>
       </td>
@@ -272,6 +345,11 @@ li:before {
             <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
             when alignment view restored from project (since Jalview 2.11.0)
           </li>
+          <li>
+            <!-- JAL-3749 -->Duplicate CDS sequences are generated when
+            protein products for certain ENA records are repeatedly
+            shown via Calculate-&gt;Show Cross Refs
+          </li>
         </ul>
       </td>
     </tr>
diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html
index a448aaa..bee8380 100755
--- a/help/help/html/whatsNew.html
+++ b/help/help/html/whatsNew.html
@@ -26,46 +26,22 @@
   <p>
     <strong>Jalview 2.11.1.3</strong>
   </p>
-  <p>Jalview 2.11.1.3 is the third patch release, fixing a bug
-    introduced in last weeks Jalview 2.11.1.1 release affecting display
-    of Jalview's example project for some users. Together, these
-    releases include fixes for a number of critical bugs, and also contains a
-    handful of new features suggested by the Jalview community.</p>
+  <p>Jalview 2.11.1.3 is the third patch release in the 2.11.1
+    series. Critical bugs resolved in this release include:</p>
   <ul>
-    <li>Shift+arrow keys navigate to next gap or residue in cursor
-      mode (enable with F2)</li>
-    <li>Support import of VCF 4.3 by updating HTSJDK from 2.12 to
-      2.23</li>
-    <li>Improved recognition of GZipped files from local disk or
-      retrieved via the web</li>
-    <li>EMBL and EMBL CDS database records retrieved from the
-      European Nucleotide Archive's Data API as 'EMBL Flatfile' records</li>
-    <li>Improved <a href="logging.html">Java Console and
-        logging</a> to help track down problems
-    </li>
-    <li>Improved support for Hi-DPI (4K) screens when running on
-      Linux (Requires Java 11+)</li>
-  </ul>
-  <p>Critical bug fixes include</p>
-  <ul>
-    <li>Jalview runs correctly when launched with Turkish language
-      settings</li>
-    <li>Peptide-to-CDS tracking broken when multiple EMBL gene
-      products shown for a single contig (such as viral genomes)</li>
-    <li>Errors encountered when processing variants from VCF files
-      yield "Error processing VCF: Format specifier '%s'" on the console</li>
-    <li>Count of features not shown can be wrong when there are
-      both DNA and Protein features mapped to the position under
-      the cursor</li>
-    <li>Sequence ID for reference sequence is clipped when Right
-      align Sequence IDs enabled</li>
-    <li>Find doesn't report matches that span hidden gapped columns</li>
-    <li>Jalview ignores file format parameter specifying output
-      format when exporting an alignment via the command line</li>
+    <li>Find doesn't highlight all motif matches for a sequence.</li>
+    <li>Mouse over highlighting, CDS reconstruction and problems
+      with virtual feature popups when working with linked CDS/Protein
+      alignments.</li>
+    <li>Result of aligning protein sequences linked to CDS results
+      in incorrect CDS alignment.</li>
+    <li>Jalview installer doesn't correctly install Jalview on
+      paths containing spaces.</li>
   </ul>
   <p>
-    For the full release notes, see <a href="releases.html#Jalview.2.11.1.1">the
-      Jalview 2.11.1.1 release notes</a>.
+    For the full release notes, see <a
+      href="releases.html#Jalview.2.11.1.3">the Jalview 2.11.1.3
+      release notes</a>.
   </p>
   <p>
     <strong>Known Issues</strong>
@@ -80,7 +56,7 @@
       v2.11.1.0)</li>
     <li>Drag and drop of alignment file onto alignment window when
       in a HiDPI scaled mode in Linux only works for the top left
-      quadrant of the alignment window</li>
+      quadrant of the alignment window.</li>
   </ul>
 </body>
 </html>