JAL-3253 ApplicationSingletonProvider replaces Instance

[jalview.git] / src / jalview / gui / AlignViewport.java

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 7b8c6c9..1ebf584 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -48,7 +48,6 @@ import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.util.MessageManager;
-import jalview.util.dialogrunner.RunResponse;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.params.AutoCalcSetting;
 
@@ -291,7 +290,7 @@ public class AlignViewport extends AlignmentViewport
               ResidueColourScheme.NONE);
     }
     ColourSchemeI colourScheme = ColourSchemeProperty
-            .getColourScheme(alignment, schemeName);
+            .getColourScheme(this, alignment, schemeName);
     residueShading = new ResidueShader(colourScheme);
 
     if (colourScheme instanceof UserColourScheme)
@@ -305,6 +304,7 @@ public class AlignViewport extends AlignmentViewport
     {
       residueShading.setConsensus(hconsensus);
     }
+    setColourAppliesToAllGroups(true);
   }
 
   boolean validCharWidth;
@@ -383,9 +383,8 @@ public class AlignViewport extends AlignmentViewport
      */
     if (align != null)
     {
-      StructureSelectionManager ssm = StructureSelectionManager
-              .getStructureSelectionManager(Desktop.instance);
-      ssm.registerMappings(align.getCodonFrames());
+      Desktop.getInstance().getStructureSelectionManager()
+              .registerMappings(align.getCodonFrames());
     }
 
     /*
@@ -405,8 +404,8 @@ public class AlignViewport extends AlignmentViewport
       List<AlignedCodonFrame> mappings = al.getCodonFrames();
       if (mappings != null)
       {
-        StructureSelectionManager ssm = StructureSelectionManager
-                .getStructureSelectionManager(Desktop.instance);
+        StructureSelectionManager ssm = Desktop.getInstance()
+                .getStructureSelectionManager();
         for (AlignedCodonFrame acf : mappings)
         {
           if (noReferencesTo(acf))
@@ -531,12 +530,10 @@ public class AlignViewport extends AlignmentViewport
   @Override
   public void sendSelection()
   {
-    jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance)
-            .sendSelection(new SequenceGroup(getSelectionGroup()),
-                    new ColumnSelection(getColumnSelection()),
-                    new HiddenColumns(getAlignment().getHiddenColumns()),
-                    this);
+    Desktop.getInstance().getStructureSelectionManager().sendSelection(
+            new SequenceGroup(getSelectionGroup()),
+            new ColumnSelection(getColumnSelection()),
+            new HiddenColumns(getAlignment().getHiddenColumns()), this);
   }
 
   /**
@@ -577,8 +574,7 @@ public class AlignViewport extends AlignmentViewport
   @Override
   public StructureSelectionManager getStructureSelectionManager()
   {
-    return StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance);
+    return Desktop.getInstance().getStructureSelectionManager();
   }
 
   @Override
@@ -743,7 +739,7 @@ public class AlignViewport extends AlignmentViewport
       }
     }
 
-    ranges.setEndSeq(getAlignment().getHeight());
+    ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
     firePropertyChange("alignment", null, getAlignment().getSequences());
   }
 
@@ -770,22 +766,22 @@ public class AlignViewport extends AlignmentViewport
      * dialog responses 0, 1, 2 (even though JOptionPane shows them
      * in reverse order)
      */
-    JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
-            .addResponse(0, new RunResponse(0)
+    JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane())
+            .setResponseHandler(0, new Runnable()
             {
               @Override
               public void run()
               {
                   addDataToAlignment(al);
               }
-            }).addResponse(1, new RunResponse(1)
+            }).setResponseHandler(1, new Runnable()
             {
               @Override
               public void run()
               {
                 us.openLinkedAlignmentAs(al, title, true);
               }
-            }).addResponse(2, new RunResponse(2)
+            }).setResponseHandler(2, new Runnable()
             {
               @Override
               public void run()