JAL-3065 release notes

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

diff --git a/help/html/releases.html b/help/html/releases.html
index 0ca65c0..65fbabb 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -68,6 +68,72 @@ li:before {
       </td>
     </tr>
     <tr>
+    <td width="60" nowrap>
+      <div align="center">
+        <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>4/09/2018</em></strong>
+      </div>
+    </td>
+    <td><div align="left">
+        <em></em>
+        <ul>
+            <li>
+              <!-- JAL-3065 -->Change in recommended way of starting
+              Jalview via a Java command line: add jars in lib directory
+              to CLASSPATH, rather than via the deprecated java.ext.dirs
+              property.
+            </li>
+          </ul>
+      </div></td>
+    <td><div align="left">
+        <em></em>
+        <ul>
+            <li>
+              <!-- JAL-247 -->Hidden sequence markers and representative
+              sequence bolding included when exporting alignment as EPS,
+              SVG, PNG or HTML. <em>Display of these can be
+                configured via the Format menu or in batch mode with a
+                jalview properties file.</em>
+            </li>
+            <li>
+              <!-- JAL-3087 -->Corrupted display when switching to
+              wrapped mode when sequence panel's vertical scrollbar is
+              visible.
+            </li>
+            <li>
+              <!-- JAL-3003 -->Alignment is black in exported EPS file
+              when sequences are selected in exported view.</em>
+            </li>
+            <li>
+              <!-- JAL-3059 -->Groups with different coloured borders
+              aren't rendered with correct colour.
+            </li>
+            <li>
+              <!-- JAL-3092 -->Jalview could hang when importing certain
+              types of knotted RNA secondary structure
+            </li>
+            <li>
+              <!-- JAL-3095 -->Sequence highlight and selection in
+              trimmed VARNA 2D structure is incorrect for sequences that
+              do not start at 1
+            </li>
+            <li>
+              <!-- JAL-3061 -->'.' inserted into RNA secondary structure
+              annotation when columns are inserted into an alignment
+            </li>
+            <li>
+              <!-- JAL-3061 -->'.' written into RNA secondary structure
+              annotation when writing out Stockholm format
+            </li>
+            <li>
+              <!-- JAL-3053 -->Jalview annotation rows containing upper
+              and lower-case 'E' and 'H' do not automatically get
+              treated as RNA secondary structure
+            </li>
+          </ul>
+      </div>
+    </td>
+    </tr>
+    <tr>
       <td width="60" nowrap>
         <div align="center">
           <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
@@ -78,13 +144,13 @@ li:before {
           <em></em>
           <ul>
             <li>
-              <!-- JAL-1460 -->Windows File Shortcuts can be dragged
-              onto the Jalview Desktop
-            </li>
-            <li>
               <!-- JAL-2920 -->Use HGVS nomenclature for variant
               annotation retrieved from Uniprot
             </li>
+            <li>
+              <!-- JAL-1460 -->Windows File Shortcuts can be dragged
+              onto the Jalview Desktop
+            </li>
           </ul>
         </div></td>
       <td><div align="left">
@@ -92,7 +158,7 @@ li:before {
           <ul>
             <li>
               <!-- JAL-3017 -->Cannot import features with multiple
-              variant elements
+              variant elements (blocks import of some Uniprot records)
             </li>
             <li>
               <!-- JAL-2997 -->Clustal files with sequence positions in
@@ -103,12 +169,16 @@ li:before {
               not alignment area in exported graphic
             </li>
             <li>
+              <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
+              window has input focus
+            </li>
+            <li>
               <!-- JAL-2992 -->Annotation panel set too high when
-              annotation added to view
+              annotation added to view (Windows)
             </li>
             <li>
-              <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
-              window has input focus
+              <!-- JAL-3009 -->Jalview Desktop is slow to start up when
+              network connectivity is poor
             </li>
             <li>
               <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to