JAL-3210 Barebones gradle/buildship/eclipse. See README

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 7b8c6c9..7d01222 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;
@@ -743,7 +743,7 @@ public class AlignViewport extends AlignmentViewport
       }
     }
 
-    ranges.setEndSeq(getAlignment().getHeight());
+    ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
     firePropertyChange("alignment", null, getAlignment().getSequences());
   }
 
@@ -771,21 +771,21 @@ public class AlignViewport extends AlignmentViewport
      * in reverse order)
      */
     JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
-            .addResponse(0, new RunResponse(0)
+            .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()