From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 7 Mar 2022 20:07:36 +0000 (+0000)
Subject: JAL-3647 release notes for JAL-1842 JAL-3509 JAL-3881, JAL-3884 JAL-3632 JAL-3633... 
X-Git-Tag: Release_2_11_2_1~26
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=392bd8b22b29e49caab9d8053ac3cf0989f77fe4;p=jalview.git

JAL-3647 release notes for JAL-1842 JAL-3509 JAL-3881, JAL-3884 JAL-3632 JAL-3633 and report JAL-3764 as a known issue
---

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index d5e5dec..e3a2a05 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -100,6 +100,16 @@ li:before {
             <!-- JAL-3863 -->Support for Canonical Uniprot IDs
           </li>
           <li>
+            <!-- JAL-3881 -->Sequence IDs split on '_' as well as other
+            non-alphanumerics when discovering database references with
+            'Fetch DB Refs'
+          </li>
+          <li>
+            <!-- JAL-3884 -->Suppressed harmless exceptions output to
+            Console whilst discovering database references for a
+            sequence
+          </li>
+          <li>
             <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
             schema
           </li>
@@ -119,6 +129,10 @@ li:before {
             textbox
           </li>
           <li>
+            <!-- JAL-3632 JAL-3633 -->support for HTTP/S access via
+            proxies that require authentication
+          </li>
+          <li>
             <!-- JAL-3837 -->GPL license info on splash screen and About
             text
           </li>
@@ -152,7 +166,10 @@ li:before {
             macOS, Linux/Unix, Windows and documentation in Help.  Installer wizard has option
             to add this to PATH, or link to it in your PATH.
           </li>
-
+          <li>
+            <!-- JAL-3633 -->Getdown launcher inherits HTTP/S proxy
+            configuration from jalview_properties
+          </li>
         </ul> <em>JalviewJS</em>
         <ul>
           <li>
@@ -257,6 +274,10 @@ li:before {
             <!-- JAL-3275 -->Can open multiple Preferences panels
           </li>
           <li>
+            <!-- JAL-3633 -->Properly configure HTTPS proxy settings
+            from Preferences
+          </li>
+          <li>
             <!-- JAL-3949 -->Standard out logging broken: messages only
             routing to stderr and appear as a raw template
           </li>
@@ -302,6 +323,14 @@ li:before {
           </li>
 
         </ul>
+        <em>Known Issues</em>
+        <ul>
+          <li>
+            <!-- JAL-3764 -->Display of RESNUM sequence features are not
+            suppressed when structures associated with a sequence are
+            viewed with an external viewer (Regression from 2.11.1 series)
+          </li>
+        </ul>
       </td>
     </tr>
     <tr>
@@ -544,6 +573,12 @@ li:before {
             <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
             when running on Linux (Requires Java 11+)
           </li>
+          <li>
+            <!-- JAL-1842 JAL-3509 -->RESNUM sequence features (the
+            green ones) are not automatically displayed when associated
+            structures are displayed or for sequences retrieved from the
+            PDB.
+          </li>
         </ul> <em>Launching Jalview</em>
         <ul>
           <li>
@@ -624,6 +659,11 @@ li:before {
             save in place.)
           </li>
           <li>
+            <!-- JAL-3509 -->Dragging a PDB file onto an alignment with
+            sequence features displayed causes displayed features to be
+            hidden.
+          </li>
+          <li>
             <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
             via command line
           </li>