From: Ben Soares <b.soares@dundee.ac.uk>
Date: Thu, 30 Jul 2020 13:08:06 +0000 (+0100)
Subject: Merge branch 'releases/Release_2_11_1_Branch' into merge/JAL-3628+JAL-3608+JAL-3609... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0c85e43a68ad2de5318b6e3f09bd743b7933a890;p=jalview.git

Merge branch 'releases/Release_2_11_1_Branch' into merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+JAL-3633+Release_2_11_1_Branch
---

0c85e43a68ad2de5318b6e3f09bd743b7933a890
diff --cc help/help/html/releases.html
index 8193433,3512375..8c4ba37
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@@ -67,13 -67,20 +67,28 @@@ li:before 
              residue in cursor mode
            </li>
            <li>
 +            <!-- JAL-3608 -->Set choice of Look and Feel via system property or command line option, and
 +	    force use of Metal look and feel as default on linux.
 +          </li>
 +          <li>
 +            <!-- JAL-3633 -->Preferences -&gt; Connections, Proxy server settings now allow selecting "No proxy", "System proxy settings" or custom proxy settings
 +	    which can be configured for HTTP, HTTPS and allows for an authenticated proxy server.
 +          </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></li>
          </ul>
        </td>
@@@ -92,23 -99,14 +107,24 @@@
              multiple EMBL gene products shown for a single contig
            </li>
            <li>
 +            <!-- JAL-3628 -->Unable to save update to an existing file on Windows (partially resolved)
 +	    and Backups -&gt; Single backup scheme not always saving backup file. 
 +          </li>
 +          <li>
 +            <!-- JAL-3609 -->Java 11 only: Automatically set scaling for HiDPI displays in linux.
 +          </li>
 +          <li>
 +            <!-- JAL-3632 JAL-3633 -->Proxy properties don't set HTTPS proxy for launcher or application.
 +          </li>
 +          <li>
-             <!-- JAL- -->
-           </li>
-           <li>
-             <!-- JAL- -->
+             <!-- JAL-3696 -->Errors encountered when processing variants
+             from VCF files yield "Error processing VCF: Format specifier
+             '%s'" on the console
            </li>
            <li>
-             <!-- JAL- -->
+             <!-- 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>
          </ul>
        </td>