JAL-3675 JAL-3561 documented 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 dfbbde5..f0516e9 100755 (executable)
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -58,7 +58,7 @@ li:before {
     <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>
+          <em>11/08/2020</em></strong></td>
       <td align="left" valign="top">
         <ul>
           <!-- -->
@@ -76,12 +76,47 @@ li:before {
             improved compatibility with JalviewJS
           </li>
           <li>
-          <!-- JAL-3615 -->Retrieve GZipped stockholm formatted alignments from Pfam and Rfam
+            <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
+            alignments from Pfam and Rfam
           </li>
           <li>
-          <!-- JAL-2656 -->Recognise GZipped content fetched via URL
+            <!-- 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-3667 -->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>
-          <li></li>
         </ul>
       </td>
       <td align="left" valign="top">
@@ -92,7 +127,7 @@ li:before {
           </li>
           <li>
             <!--  JAL-3680 -->Alt+Left or Right arrow in cursor mode
-            doesn't slide selected sequences
+            doesn't slide selected sequences, just sequence under cursor
           </li>
           <li>
             <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
@@ -108,6 +143,61 @@ li:before {
             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>
+          <li>
+            <!-- JAL-3490 -->Find doesn't report matches that span
+            hidden gapped columns
+          </li>
+          <li>
+            <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
+            panels, Alignment viewport and annotation renderer.
+          </li>
+          <li>
+            <!-- JAL-3561 -->Jalview ignores file format parameter
+            specifying output format when exporting an alignment via the
+            command line
+          </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-3576 -->Co-located features exported and re-imported
+            are ordered differently when shown on alignment and in
+            tooltips. (Also affects v2.11.1.0)
+          </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>
+          <li>
+            <!-- JAL-3702 -->Drag and drop of alignment file onto
+            alignment window not working correctly when in a HiDPI
+            scaled mode in Linux
+          </li>
+          <li>
+            <!-- JAL-3701 -->Stale build data in jalview standalone jar
+            builds (only affects 2.11.1.1 branch)
+          </li>
         </ul>
       </td>
     </tr>