JAL-3675 update release notes for JAL-3673 and tested merge of additional patch for...

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

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 5b6180d..5d3a383 100755 (executable)
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -57,6 +57,129 @@ 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>11/08/2020</em></strong></td>
+      <td align="left" valign="top">
+        <ul>
+          <!-- -->
+          <li>
+            <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
+            residue in cursor mode
+          </li>
+          <li>
+            <!-- JAL-3695 -->Support import of VCF 4.3 by updating
+            HTSJDK from 2.12 to 2.23
+          </li>
+          <li>
+            <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
+            optimisations and improvements suggested by Bob Hanson and
+            improved compatibility with JalviewJS
+          </li>
+          <li>
+            <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
+            alignments from Pfam and Rfam
+          </li>
+          <li>
+            <!-- JAL-2656 -->Recognise GZipped content for URLs and File
+            import (no longer based on .gz extension)
+          </li>
+          <li>
+            <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
+          </li>
+          <li>
+            <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
+            ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
+            EMBL flat file
+          </li>
+          <li>
+            <!-- JAL-3677 -->Improved warning messages, debug logging
+            and fixed Retry action when Jalview encounters errors when
+            saving or making backup files.
+          </li>
+          <li>
+            <!-- JAL-3676 -->Enhanced Jalview Java Console:
+            <ul>
+              <li>Jalview's logging level can be configured</li>
+              <li>Copy to Clipboard Buttion</li>
+            </ul>
+          </li>
+          <li>
+            <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
+            when running on Linux (Requires Java 11+)
+          </li>
+        </ul> <em>Launching Jalview</em>
+        <ul>
+          <li>
+            <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
+            through a system property
+          </li>
+          <li>
+            <!-- JAL-3477 -->Improved built-in documentation and command
+            line help for configuring Jalview's memory
+          </li>
+        </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>
+          <li>
+            <!--  JAL-3680 -->Alt+Left or Right arrow in cursor mode
+            doesn't slide selected sequences, just sequence under cursor
+          </li>
+          <li>
+            <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
+            multiple EMBL gene products shown for a single contig
+          </li>
+          <li>
+            <!-- JAL-3696 -->Errors encountered when processing variants
+            from VCF files yield "Error processing VCF: Format specifier
+            '%s'" on the console
+          </li>
+          <li>
+            <!-- JAL-3697 -->Count of features not shown can be wrong
+            when there are both local and complementary features mapped
+            to the position under the cursor
+          </li>
+          <li>
+            <!-- JAL-3673 -->Sequence ID for reference sequence is
+            clipped when Right align Sequence IDs enabled
+          </li>
+          <li>
+            <!-- JAL-2983 -->Slider with negative range values not
+            rendered correctly in VAqua4 (Since 2.10.4)
+          </li>
+          <li>
+            <!-- JAL-3685 -->Single quotes not displayed correctly in
+            internationalised text for some messages and log output
+          </li>
+        </ul> <em>Developing Jalview</em>
+        <ul>
+          <li>
+            <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
+            data, causing cloverReport gradle task to fail with an
+            OutOfMemory error.
+          </li>
+        </ul> <em>New Known defects</em>
+        <ul>
+          <li>
+            <!-- JAL-3701 -->Stale build data in jalview standalone jar
+            builds (only affects 2.11.1.1 branch)
+          </li>
+          <li>
+            <!-- JAL-3667 -->Windows 10: For a minority of users, if
+            backups are not enabled, Jalview sometimes fails to
+            overwrite an existing file and raises a warning dialog.
+            Workaround is to try to save the file again, and if that
+            fails, delete the original file and save in place.
+          </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>22/04/2020</em></strong></td>
       <td align="left" valign="top">