Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into merge-212

diff --cc resources/lang/Messages.properties
index fdd15cd,ac9ff7a..2647c43
--- 1/resources/lang/Messages.properties
--- 2/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@@ -1400,7 -1485,4 +1485,7 @@@ label.pca = PC
  label.create_image_of = Create {0} image of {1}
  label.click_to_edit = Click to edit, right-click for menu
  label.by_annotation_tooltip = Annotation Colour is configured from the main Colour menu
 ->>>>>>> develop
 +label.show_linked_features = Show {0} features
 +label.on_top = on top
 +label.include_linked_features = Include {0} features
- label.include_linked_tooltip = Include visible {0} features<br>converted to local sequence coordinates
++label.include_linked_tooltip = Include visible {0} features<br>converted to local sequence coordinates

diff --cc resources/lang/Messages_es.properties
Simple merge

diff --cc src/jalview/analysis/AlignmentUtils.java
Simple merge

diff --cc src/jalview/appletgui/AlignFrame.java
Simple merge

diff --cc src/jalview/datamodel/Sequence.java
Simple merge

diff --cc src/jalview/gui/PopupMenu.java
index 415054e,8c87aa0..2034b3f
--- 1/src/jalview/gui/PopupMenu.java
--- 2/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@@ -31,10 -30,11 +31,11 @@@ import jalview.commands.EditCommand
  import jalview.commands.EditCommand.Action;
  import jalview.datamodel.AlignmentAnnotation;
  import jalview.datamodel.AlignmentI;
 -import jalview.datamodel.Annotation;
  import jalview.datamodel.DBRefEntry;
  import jalview.datamodel.HiddenColumns;
 +import jalview.datamodel.MappedFeatures;
  import jalview.datamodel.PDBEntry;
+ import jalview.datamodel.ResidueCount;
  import jalview.datamodel.SequenceFeature;
  import jalview.datamodel.SequenceGroup;
  import jalview.datamodel.SequenceI;

diff --cc src/jalview/io/SequenceAnnotationReport.java
Simple merge

diff --cc src/jalview/project/Jalview2XML.java
Simple merge

diff --cc src/jalview/util/MapList.java
Simple merge

diff --cc src/jalview/viewmodel/AlignmentViewport.java
Simple merge

diff --cc test/jalview/gui/AlignFrameTest.java
Simple merge

diff --cc test/jalview/gui/PopupMenuTest.java
Simple merge

diff --cc test/jalview/project/Jalview2xmlTests.java
index 5182ad4,b01556c..47b8aea
--- 1/test/jalview/project/Jalview2xmlTests.java
--- 2/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@@ -48,9 -49,9 +49,8 @@@ import jalview.datamodel.features.Featu
  import jalview.datamodel.features.FeatureMatcherSet;
  import jalview.datamodel.features.FeatureMatcherSetI;
  import jalview.gui.AlignFrame;
- import jalview.gui.AlignViewport;
  import jalview.gui.AlignmentPanel;
  import jalview.gui.Desktop;
 -import jalview.gui.FeatureRenderer;
  import jalview.gui.JvOptionPane;
  import jalview.gui.PCAPanel;
  import jalview.gui.PopupMenu;

diff --cc test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
index 6b1fbd2,c0095fe..f488c55
--- 1/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
--- 2/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
@@@ -10,7 -11,7 +11,8 @@@ import jalview.api.FeatureColourI
  import jalview.datamodel.SequenceFeature;
  import jalview.datamodel.SequenceI;
  import jalview.gui.AlignFrame;
 +import jalview.gui.AlignViewport;
+ import jalview.gui.FeatureRenderer;
  import jalview.io.DataSourceType;
  import jalview.io.FileLoader;
  import jalview.schemes.FeatureColour;