JAL-3111 JAL-3340 JAL-3184 JAL-3338 new known defects

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

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index d4cba25..f75a177 100755 (executable)
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -57,8 +57,8 @@ li:before {
     </tr>
     <tr>
       <td width="60" align="center" nowrap>
-          <strong><a name="Jalview.2.11">2.11</a><br />
-            <em>27/06/2019</em></strong>
+          <strong><a name="Jalview.2.11.0">2.11.0</a><br />
+            <em>02/07/2019</em></strong>
       </td>
       <td align="left" valign="top">
         <ul>
@@ -98,7 +98,7 @@ li:before {
                                                <ul>
                                                          <li>
             <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
-            implementation that alows updates) used for Sequence Feature collections</li>
+            implementation that allows updates) used for Sequence Feature collections</li>
           <li>
                                                        <li>
                                                                <!-- JAL-2808,JAL-2069 -->Sequence features can be filtered and
@@ -107,6 +107,10 @@ li:before {
                                                                column 9 of GFF file)
                                                        </li>
                                                        <li>
+                                                               <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
+                                                               recognise variant features
+                                                       </li>
+                                                       <li>
                                                                <!-- JAL-2897 -->Show synonymous codon variants on peptide
                                                                sequences
                                                        </li>
@@ -134,7 +138,7 @@ li:before {
                                                                <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
                                                                and Viewer state saved in Jalview Project
                                                        </li>
-                                                       <li>'Change parameters' option removed from viewer's
+                                                       <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
                                                                drop-down menus</li>
                                                        <li>
                                                                <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
@@ -239,6 +243,7 @@ li:before {
                                                <!-- JAL-3003 -->Added remarks about transparent rendering effects
                                                not supported in EPS figure export
                                        </li>
+                                       <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
                                </ul> <em>Development and Release Processes</em>
         <ul>
                <li>
@@ -324,6 +329,15 @@ li:before {
                                                score from view
                                        </li>
                                        <li>
+                                               <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
+                                               show cross references or Fetch Database References are shown in
+                                               red in original view
+                                       </li>
+          <li>
+            <!-- JAL-2898 -->stop_gained variants not shown correctly on
+            peptide sequence
+          </li>
+                                       <li>
                                                <!-- JAL-2060 -->'Graduated colour' option not offered for
                                                manually created features (where if feature score is Float.NaN)
                                        </li>
@@ -408,10 +422,6 @@ li:before {
                                                shown in complementary view
                                        </li>
                                        <li>
-                                               <!-- JAL-2898 -->stop_gained variants not shown correctly on
-                                               peptide sequence
-                                       </li>
-                                       <li>
                                                <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
                                                without normalisation
                                        </li>
@@ -442,11 +452,18 @@ li:before {
                                                <!-- JAL-868 -->Structure colours not updated when associated tree
                                                repartitions the alignment view (Regression in 2.10.5)
                                        </li>
-
                                </ul>
-                               <em>New Known Defects</em>
+                               <em>Datamodel</em>
                                <ul>
                                        <li>
+                                               <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
+                                               sequence's End is greater than its length
+                                       </li>
+                               </ul> <em>New Known Defects</em>
+                               <ul>
+                               <li><!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
+                               </li>
+                                       <li>
                                                <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
                                                regions of protein alignment.
                                        </li>
@@ -473,6 +490,10 @@ li:before {
                                                not shown as thresholded features in 2.11. To workaround please
                                                create a Score filter instead.
                                        </li>
+                                       <li><!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li> 
+                                       <li>
+                                       <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
+                                       </li>
                                         <li><strong>Java 11 Specific defects</strong>
             <ul>
               <li>