From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 24 Oct 2016 14:24:54 +0000 (+0100)
Subject: Merge branch 'develop' into releases/Release_2_10_0_Branch
X-Git-Tag: Release_2_10_0b1~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bc059a21e8d7949157f436dc706fb8d0335b3874;hp=ea3d24d953af89ca95d4480371149b70abbfcc67;p=jalview.git

Merge branch 'develop' into releases/Release_2_10_0_Branch
---

diff --git a/help/html/editing/index.html b/help/html/editing/index.html
index 471e520..fd8c5a3 100755
--- a/help/html/editing/index.html
+++ b/help/html/editing/index.html
@@ -49,9 +49,8 @@
     right to insert gaps and remove gaps.<br> If the current
     selection is a group over all sequences in the alignment, or a group
     over some sequences or all columns in the alignment, then hold down
-    either &quot;Control&quot; key (or the &quot;Alt;&quot; on OSX if
-    &quot;Control&quot; does not work) and drag the residue left or
-    right to edit all sequences in the defined group at once.
+    &quot;Control&quot; key (&quot;Cmd&quot; key on OSX) and drag the residue 
+    left or right to edit all sequences in the defined group at once.
   </p>
   <p>
     <em>Copy/paste/cut/delete</em> - any sequences which are in the
diff --git a/help/html/releases.html b/help/html/releases.html
index 5718926..7d34557 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -53,30 +53,51 @@
       </td>
       <td><em>Application</em>
         <ul>
-          <li>3D Structure chooser opens with 'Cached structures' view if structures already loaded</li>
-          <li>Progress bar reports models as they are loaded to structure views</li> 
+          <li>3D Structure chooser opens with 'Cached structures'
+            view if structures already loaded</li>
+          <li>Progress bar reports models as they are loaded to
+            structure views</li>
         </ul></td>
       <td>
         <div align="left">
           <em>General</em>
           <ul>
-            <li>Colour by conservation always enabled and no tick shown in menu when PID shading applied</li>
+            <li>Colour by conservation always enabled and no tick
+                shown in menu when BLOSUM or PID shading applied</li>
           </ul>
           <em>Application</em>
           <ul>
-            <li>Jalview projects with views of local PDB structure files saved on Windows cannot be opened on OSX</li>
-            <li>Multiple structure views can be opened and superposed without timeout for structures with multiple models or multiple sequences in alignment</li>
-            <li>Cannot import or associated local PDB files without a PDB ID HEADER line</li>
-            <li>RMSD is not output in Jmol console when superposition is performed</li> 
-            <li>Drag and drop of URL from Browser fails for Linux and OSX versions earlier than El Capitan</li>
+            <li>Jalview projects with views of local PDB structure
+              files saved on Windows cannot be opened on OSX</li>
+            <li>Multiple structure views can be opened and
+              superposed without timeout for structures with multiple
+              models or multiple sequences in alignment</li>
+            <li>Cannot import or associated local PDB files without
+              a PDB ID HEADER line</li>
+            <li>RMSD is not output in Jmol console when
+              superposition is performed</li>
+            <li>Drag and drop of URL from Browser fails for Linux
+              and OSX versions earlier than El Capitan</li>
             <li>ENA client ignores invalid content from ENA server</li>
-            <li>Exceptions are not raised in console when ENA client attempts to fetch non-existent IDs via Fetch DB Refs UI option</li>
-            <li>Exceptions are not raised in console when a new view is created on the alignment</li>
+            <li>Exceptions are not raised in console when ENA
+              client attempts to fetch non-existent IDs via Fetch DB
+              Refs UI option</li>
+            <li>Exceptions are not raised in console when a new
+              view is created on the alignment</li>
+            <li>OSX right-click fixed for group selections:
+              CMD-click to insert/remove gaps in groups and CTRL-click
+              to open group pop-up menu</li>
           </ul>
-          <em>New Known Issues</em>
-          <ul><li>Drag and drop from URL links in browsers do not work on Windows</li></ul>
           <em>Build and deployment</em>
-          <ul><li>URL link checker now copes with multi-line anchor tags</li></ul>
+          <ul>
+            <li>URL link checker now copes with multi-line anchor
+              tags</li>
+          </ul>
+          <em>New Known Issues</em>
+          <ul>
+            <li>Drag and drop from URL links in browsers do not
+              work on Windows</li>
+          </ul>
         </div>
       </td>
     </tr>
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index bae80db..3266fab 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -616,13 +616,14 @@ public class SeqPanel extends JPanel implements MouseListener,
       return;
     }
 
-    if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
+    boolean isControlDown = Platform.isControlDown(evt);
+    if (evt.isShiftDown() || isControlDown)
     {
-      if (evt.isAltDown() || evt.isControlDown())
+      editingSeqs = true;
+      if (isControlDown)
       {
         groupEditing = true;
       }
-      editingSeqs = true;
     }
     else
     {
diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index d7b26b0..00c52ed 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -338,11 +338,9 @@ public class AlignViewportTest
     /*
      * test for JAL-2283 don't inadvertently turn on colour by conservation
      */
-    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
-            Boolean.TRUE.toString());
-    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
-            Boolean.FALSE.toString());
     Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "NONE");
+    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+            Boolean.TRUE.toString());
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", FormatAdapter.FILE);
     ColourSchemeI cs = new PIDColourScheme();