Merge branch 'bug/JAL-3333_Blurry_fonts_in_WebServiceInfo_window_title_in_macOS_mojav...

Merging in simple change from transparent image to white background and removing alpha channel in image model.

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 9b71968..d6ebd1b 100755 (executable)
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -58,7 +58,7 @@ li:before {
     <tr>
       <td width="60" align="center" nowrap>
           <strong><a name="Jalview.2.11.0">2.11.0</a><br />
-            <em>27/06/2019</em></strong>
+            <em>02/07/2019</em></strong>
       </td>
       <td align="left" valign="top">
         <ul>
@@ -101,7 +101,7 @@ li:before {
             implementation that allows updates) used for Sequence Feature collections</li>
           <li>
                                                        <li>
-                                                               <!-- JAL-2808,JAL-2069 -->Sequence features can be filtered and
+                                                               <!-- JAL-2808,JAL-2069,JAL-2820 -->Sequence features can be filtered and
                                                                shaded according to any associated attributes (e.g. variant
                                                                attributes from VCF file, or key-value pairs imported from
                                                                column 9 of GFF file)
@@ -111,8 +111,8 @@ li:before {
                                                                recognise variant features
                                                        </li>
                                                        <li>
-                                                               <!-- JAL-2897 -->Show synonymous codon variants on peptide
-                                                               sequences
+                                                               <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
+                                                               sequences (also coloured red by default)
                                                        </li>
                                                        <li>
                                                                <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
@@ -321,10 +321,6 @@ li:before {
                                                doesn't tell users the invalid URL
                                        </li>
                                        <li>
-                                               <!-- JAL-3178 -->Nonpositional features lose feature group on
-                                               export as Jalview features file
-                                       </li>
-                                       <li>
                                                <!-- JAL-2816 -->Tooltips displayed for features filtered by
                                                score from view
                                        </li>
@@ -334,8 +330,8 @@ li:before {
                                                red in original view
                                        </li>
           <li>
-            <!-- JAL-2898 -->stop_gained variants not shown correctly on
-            peptide sequence
+            <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
+            peptide sequence (computed variant shown as p.Res.null)
           </li>
                                        <li>
                                                <!-- JAL-2060 -->'Graduated colour' option not offered for
@@ -426,12 +422,15 @@ li:before {
                                                without normalisation
                                        </li>
                                        <li>
-                                               <!-- JAL-3021 -->Sequence Details report opens positioned to top
+                                               <!-- JAL-3021 -->Sequence Details report should open positioned at top
                                                of report
                                        </li>
                                        <li>
                                                <!-- JAL-914 -->Help page can be opened twice
                                        </li>
+                                 <li>
+                                 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
+                                 </li>
                                </ul> <em>Editing</em>
                                <ul>
                                        <li>
@@ -461,6 +460,8 @@ li:before {
                                        </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.
@@ -488,6 +489,10 @@ 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>

diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index 673bcc0..9ad6596 100644 (file)
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -111,6 +111,13 @@ public class CrossRefAction implements Runnable
       FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
               .getFeatureColourScheme(source);
 
+      if (dna && AlignmentUtils.looksLikeEnsembl(alignment))
+      {
+        // override default featureColourScheme so products have Ensembl variant colours
+        featureColourScheme = new SequenceFetcher()
+                .getFeatureColourScheme(DBRefSource.ENSEMBL);
+      }
+
       AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
               xrefs);
       if (!dna)