JAL-3766 release notes for JAL-3759

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

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 685c3ee..9aec5fa 100755 (executable)
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -57,11 +57,89 @@ li:before {
     </tr>
     <tr>
       <td width="60" align="center" nowrap><strong><a
+          id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
+          <em>29/10/2020</em></strong></td>
+      <td align="left" valign="top">
+        <ul>
+
+        </ul>
+      </td>
+      <td align="left" valign="top">
+        <ul>
+          <li>
+            <!-- JAL-3765 -->Find doesn't always highlight all matching
+            positions in a sequence (bug introduced in 2.11.1.2)
+          </li>
+          <li>
+            <!-- JAL-3760 -->Alignments containing one or more protein
+            sequences can be classed as nucleotide
+          </li>
+          <li>
+            <!-- JAL-3748 -->CDS alignment doesn't match original CDS
+            sequences after alignment of protein products (known defect
+            first reported for 2.11.1.0)
+          </li>
+          <li>
+            <!-- JAL-3725 -->No tooltip or popup menu for genomic features
+            outwith CDS shown overlaid on protein
+          </li>
+          <li>
+            <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
+            correctly mapped by Jalview (e.g. affects viral CDS with
+            ribosomal slippage, since 2.9.0)
+          </li>
+          <li>
+            <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
+            CDS features
+          </li>
+          <li>
+            <!-- JAL-3700 -->Selections in CDS sequence panel don't
+            always select corresponding protein sequences
+          </li>
+          <li>
+            <!-- JAL-3759 -->
+            <em>Make groups from selection</em> for a column selection
+            doesn't always ignore hidden columns
+          </li>
+        </ul> <em>Installer</em>
+        <ul>
+          <li>
+            <!-- JAL-3611 -->Space character in Jalview install path on
+            Windows prevents install4j launching getdown
+          </li>
+        </ul> <em>Development</em>
+        <ul>
+          <li>
+            <!-- JAL-3248 -->Fixed typos and specified compatible gradle
+            version numbers in doc/building.md
+          </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.2.11.1.2">.2</a><br />
+          <em>25/09/2020</em></strong></td>
+      <td align="left" valign="top">
+        <ul>
+        </ul>
+      </td>
+      <td align="left" valign="top">
+        <ul>
+          <li>
+            <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
+            "Encountered problems opening
+            https://www.jalview.org/examples/exampleFile_2_7.jvp"
+          </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.2.11.1.1">.1</a><br />
-          <em>8/09/2020</em></strong></td>
+          <em>17/09/2020</em></strong></td>
       <td align="left" valign="top">
         <ul>
-          <!-- -->
           <li>
             <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
             residue in cursor mode
@@ -116,7 +194,7 @@ li:before {
           <li>
             <!-- JAL-3477 -->Improved built-in documentation and command
             line help for configuring Jalview's memory
-          </li>
+          </li>                   
         </ul>
       </td>
       <td align="left" valign="top">
@@ -136,6 +214,10 @@ li:before {
             doesn't slide selected sequences, just sequence under cursor
           </li>
           <li>
+            <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
+            sequence under the cursor
+          </li>
+          <li>
             <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
             multiple EMBL gene products shown for a single contig
           </li>
@@ -182,6 +264,21 @@ li:before {
             file again, and if that fails, delete the original file and
             save in place.)
           </li>
+          <li>
+            <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
+            via command line
+          </li>
+          <li>
+            <!-- JAL-3741 -->References to http://www.jalview.org in
+            program and documentation
+          </li>
+        </ul> <em>Launching Jalview</em>
+        <ul>
+          <li>
+            <!-- JAL-3718 -->Jalview application fails when launched the
+            first time for a version that has different jars to the
+            previous launched version.
+          </li>
         </ul> <em>Developing Jalview</em>
         <ul>
           <li>
@@ -196,6 +293,12 @@ li:before {
         </ul> <em>New Known defects</em>
         <ul>
           <li>
+            <!-- JAL-3748 -->CDS shown in result of submitting proteins
+            in a CDS/Protein alignment to a web service is wrong when
+            proteins share a common transcript sequence (e.g.
+            genome of RNA viruses)
+          </li>
+          <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)
@@ -213,6 +316,11 @@ li:before {
             <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
             when alignment view restored from project (since Jalview 2.11.0)
           </li>
+          <li>
+            <!-- JAL-3749 -->Duplicate CDS sequences are generated when
+            protein products for certain ENA records are repeatedly
+            shown via Calculate-&gt;Show Cross Refs
+          </li>
         </ul>
       </td>
     </tr>