JAL-3675 2.11.1.1 release notes

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

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index fa70d64..c83741a 100755 (executable)
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -57,14 +57,31 @@ li:before {
     </tr>
     <tr>
       <td width="60" align="center" nowrap><strong><a
+          id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
+          <em>13/07/2020</em></strong></td>
+      <td align="left" valign="top">
+        <ul>
+        <!-- -->
+       </ul>
+      </td>
+      <td align="left" valign="top">
+        <ul>
+         <li><!-- JAL-3493 -->Escape does not clear highlights on the alignment (Since Jalview 2.10.3)</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.2.11.1.0">.0</a><br />
-          <em>27/03/2020</em></strong></td>
+          <em>22/04/2020</em></strong></td>
       <td align="left" valign="top">
         <ul>
           <li>
-            <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302 -->Map 'virtual'
-            codon features shown on protein (or vice versa) for display
-            in alignments, on structure views and for export.
+            <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
+            'virtual' codon features shown on protein (or vice versa)
+            for display in alignments, on structure views (including
+            transfer to UCSF chimera), in feature reports and for
+            export.
           </li>
           <li>
             <!-- JAL-3121 -->Feature attributes from VCF files can be
@@ -83,6 +100,10 @@ li:before {
             position if reopened
           </li>
           <li>
+            <!-- JAL-3535 -->Feature Settings dialog title includes name
+            of associated view
+          </li>
+          <li>
             <!-- JAL-3538 -->Font anti-aliasing in alignment views
             enabled by default
           </li>
@@ -94,6 +115,9 @@ li:before {
             <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
             with no feature types visible
           </li>
+          <li>
+          <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
+          </li>
         </ul><em>Jalview Installer</em>
            <ul>
           <li>
@@ -115,6 +139,9 @@ li:before {
           <li>
             <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
           </li>
+          <li>
+            <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds            
+          </li> 
         </ul> <em>Build System</em>
         <ul>
           <li>
@@ -125,20 +152,36 @@ li:before {
             report
           </li>
         </ul>
-        <ul>
-          <em>Groovy Scripts</em>
-          <ul>
-            <li>
-              <!--  JAL-3547 -->exportconsensus.groovy prints a FASTA
-              file to stdout containing the consensus sequence for each
-              alignment in a Jalview session
-            </li>
-          </ul>
+        <em>Groovy Scripts</em>
+            <ul>
+          <li>
+            <!--  JAL-3547 -->exportconsensus.groovy prints a FASTA file
+            to stdout containing the consensus sequence for each
+            alignment in a Jalview session
+          </li>
+          <li>
+            <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
+            genomic sequence_variant annotation from CDS as
+            missense_variant or synonymous_variant on protein products.
+          </li>
         </ul>
       </td>
       <td align="left" valign="top">
         <ul>
           <li>
+            <!-- JAL-3581 -->Hidden sequence markers still visible when
+            'Show hidden markers' option is not ticked
+          </li>
+          <li>
+            <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
+            PNG output when 'Automatically set ID width' is set in
+            jalview preferences or properties file
+          </li>
+          <li>
+            <!-- JAL-3571 -->Feature Editor dialog can be opened when
+            'Show Sequence Features' option is not ticked
+          </li>
+          <li>
             <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
             buttons in Feature Settings dialog are clicked when no
             features are visible
@@ -188,6 +231,11 @@ li:before {
             <!-- JAL-3406 -->Credits missing some authors in Jalview
             help documentation for 2.11.0 release
           </li>
+          <li>
+            <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
+            includes Pfam ID as sequence's accession rather than its
+            Uniprot Accession
+          </li>
         </ul> <em>Java 11 Compatibility issues</em>
         <ul>
           <li>
@@ -226,6 +274,10 @@ li:before {
             <!-- JAL-3542 -->Jalview Installation type always reports
             'Source' in console output
           </li>
+          <li>
+            <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
+            bamboo server but run fine locally.
+          </li>
         </ul>
       </td>
     </tr>