Merge branch 'Release_2_8_1_Branch' into Release_2_8_1_Branch_i18n

Conflicts:
	src/jalview/appletgui/APopupMenu.java
	src/jalview/appletgui/AlignFrame.java

diff --cc src/jalview/appletgui/APopupMenu.java
index ce1bae2,8302282..c51653d
mode 100644,100755..100644
--- 1/src/jalview/appletgui/APopupMenu.java
--- 2/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@@ -167,7 -168,11 +169,11 @@@ public class APopupMenu extends java.aw
        displayNonconserved.setState(sg.getShowNonconserved());
        if (!ap.av.getAlignment().getGroups().contains(sg))
        {
 -        menu1.setLabel("Edit New Group");
++        menu1.setLabel(MessageManager.getString("action.edit_new_group"));
          groupMenu.remove(unGroupMenuItem);
+       } else {
 -        menu1.setLabel("Edit Group");
++        menu1.setLabel(MessageManager.getString("action.edit_group"));
+         groupMenu.remove(createGroupMenuItem);
        }
  
      }
@@@ -730,15 -741,17 +741,17 @@@
  
    private void jbInit() throws Exception
    {
-     groupMenu.setLabel(MessageManager.getString("label.group"));
 -    groupMenu.setLabel("Selection");
 +    groupMenu.setLabel(MessageManager.getString("label.selection"));
      sequenceFeature.addActionListener(this);
  
      editGroupName.addActionListener(this);
 -    unGroupMenuItem.setLabel("Remove Group");
 +    unGroupMenuItem.setLabel(MessageManager.getString("action.remove_group"));
      unGroupMenuItem.addActionListener(this);
  
 -    createGroupMenuItem.setLabel("Create Group");
++    createGroupMenuItem.setLabel(MessageManager.getString("action.create_group"));
+     createGroupMenuItem.addActionListener(this);
 -    
 -    nucleotideMenuItem.setLabel("Nucleotide");
++
 +    nucleotideMenuItem.setLabel(MessageManager.getString("label.nucleotide"));
      nucleotideMenuItem.addActionListener(this);
      conservationMenuItem.addItemListener(this);
      abovePIDColour.addItemListener(this);

diff --cc src/jalview/appletgui/AlignFrame.java
index 865f0d4,bf04268..564f28c
--- 1/src/jalview/appletgui/AlignFrame.java
--- 2/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@@ -3036,61 -3047,63 +3045,63 @@@ public class AlignFrame extends Embmenu
                                       // provided
      tcoffeeColour.addActionListener(this);
      avDistanceTreeBlosumMenuItem
 -            .setLabel("Average Distance Using BLOSUM62");
 +            .setLabel(MessageManager.getString("label.average_distance_bloslum62"));
      avDistanceTreeBlosumMenuItem.addActionListener(this);
 -    njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
 +    njTreeBlosumMenuItem.setLabel(MessageManager.getString("label.neighbour_blosum62"));
      njTreeBlosumMenuItem.addActionListener(this);
 -    annotationPanelMenuItem.setLabel("Show Annotations");
 +    annotationPanelMenuItem.setLabel(MessageManager.getString("label.show_annotations"));
      annotationPanelMenuItem.addItemListener(this);
 -    colourTextMenuItem.setLabel("Colour Text");
 +    colourTextMenuItem.setLabel(MessageManager.getString("label.colour_text"));
      colourTextMenuItem.addItemListener(this);
 -    displayNonconservedMenuItem.setLabel("Show nonconserved");
 +    displayNonconservedMenuItem.setLabel(MessageManager.getString("label.show_non_conversed"));
      displayNonconservedMenuItem.addItemListener(this);
      alProperties.addActionListener(this);
 -    overviewMenuItem.setLabel("Overview Window");
 +    overviewMenuItem.setLabel(MessageManager.getString("label.overview_window"));
      overviewMenuItem.addActionListener(this);
      undoMenuItem.setEnabled(false);
 -    undoMenuItem.setLabel("Undo");
 +    undoMenuItem.setLabel(MessageManager.getString("action.undo"));
      undoMenuItem.addActionListener(this);
      redoMenuItem.setEnabled(false);
 -    redoMenuItem.setLabel("Redo");
 +    redoMenuItem.setLabel(MessageManager.getString("action.redo"));
      redoMenuItem.addActionListener(this);
 -    conservationMenuItem.setLabel("by Conservation");
 +    conservationMenuItem.setLabel(MessageManager.getString("action.by_conservation"));
      conservationMenuItem.addItemListener(this);
 -    noColourmenuItem.setLabel("None");
 +    noColourmenuItem.setLabel(MessageManager.getString("label.none"));
      noColourmenuItem.addActionListener(this);
 -    wrapMenuItem.setLabel("Wrap");
 +    wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
      wrapMenuItem.addItemListener(this);
 -    renderGapsMenuItem.setLabel("Show Gaps");
 +    renderGapsMenuItem.setLabel(MessageManager.getString("action.show_gaps"));
      renderGapsMenuItem.setState(true);
      renderGapsMenuItem.addItemListener(this);
 -    findMenuItem.setLabel("Find...");
 +    findMenuItem.setLabel(MessageManager.getString("action.find"));
      findMenuItem.addActionListener(this);
 -    abovePIDThreshold.setLabel("Above Identity Threshold");
 +    abovePIDThreshold.setLabel(MessageManager.getString("label.above_identity_threshold"));
      abovePIDThreshold.addItemListener(this);
 -    nucleotideColour.setLabel("Nucleotide");
 +    nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
      nucleotideColour.addActionListener(this);
 -    deleteGroups.setLabel("Undefine Groups");
 +    deleteGroups.setLabel(MessageManager.getString("action.undefine_groups"));
      deleteGroups.addActionListener(this);
 -    grpsFromSelection.setLabel("Make Groups For Selection");
 +    grpsFromSelection.setLabel(MessageManager.getString("action.make_groups_selection"));
      grpsFromSelection.addActionListener(this);
 -    createGroup.setLabel("Create Group");
 -    unGroup.setLabel("Remove Group");
 -    copy.setLabel("Copy");
++    createGroup.setLabel(MessageManager.getString("action.create_group"));
++    unGroup.setLabel(MessageManager.getString("action.remove_group"));
 +    copy.setLabel(MessageManager.getString("action.copy"));
      copy.addActionListener(this);
 -    cut.setLabel("Cut");
 +    cut.setLabel(MessageManager.getString("action.cut"));
      cut.addActionListener(this);
 -    delete.setLabel("Delete");
 +    delete.setLabel(MessageManager.getString("action.delete"));
      delete.addActionListener(this);
 -    pasteMenu.setLabel("Paste");
 -    pasteNew.setLabel("To New Alignment");
 +    pasteMenu.setLabel(MessageManager.getString("action.paste"));
 +    pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
      pasteNew.addActionListener(this);
 -    pasteThis.setLabel("Add To This Alignment");
 +    pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
      pasteThis.addActionListener(this);
 -    applyToAllGroups.setLabel("Apply Colour To All Groups");
 +    applyToAllGroups.setLabel(MessageManager.getString("label.apply_colour_to_all_groups"));
      applyToAllGroups.setState(true);
      applyToAllGroups.addItemListener(this);
 -    font.setLabel("Font...");
 +    font.setLabel(MessageManager.getString("action.font"));
      font.addActionListener(this);
 -    scaleAbove.setLabel("Scale Above");
 +    scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
      scaleAbove.setState(true);
      scaleAbove.setEnabled(false);
      scaleAbove.addItemListener(this);

diff --cc src/jalview/gui/AlignFrame.java
index 423f7b9,d15f742..e2fe90c
mode 100644,100755..100644
--- 1/src/jalview/gui/AlignFrame.java
--- 2/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -75,9 -76,9 +76,10 @@@ import jalview.schemes.TaylorColourSche
  import jalview.schemes.TurnColourScheme;
  import jalview.schemes.UserColourScheme;
  import jalview.schemes.ZappoColourScheme;
 +import jalview.util.MessageManager;
  import jalview.ws.jws1.Discoverer;
  import jalview.ws.jws2.Jws2Discoverer;
+ import jalview.ws.jws2.jabaws2.Jws2Instance;
  import jalview.ws.seqfetcher.DbSourceProxy;
  
  import java.awt.BorderLayout;

diff --cc src/jalview/gui/AnnotationPanel.java
Simple merge

diff --cc src/jalview/gui/Desktop.java
Simple merge

diff --cc src/jalview/gui/SeqPanel.java
Simple merge

diff --cc src/jalview/gui/TreeCanvas.java
Simple merge

diff --cc src/jalview/jbgui/GAlignFrame.java
Simple merge