JAL-3010 getColumnClass() never return null

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

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 35215b4..7b8eae4 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
 import jalview.api.FeatureSettingsControllerI;
 import jalview.datamodel.AlignmentI;
@@ -520,7 +521,7 @@ public class FeatureSettings extends JPanel
       {
         fr.setGroupVisibility(check.getText(), check.isSelected());
         resetTable(new String[] { grp });
-        af.alignPanel.paintAlignment(true, true);
+        refreshDisplay();
       }
     });
     groupPanel.add(check);
@@ -1078,7 +1079,7 @@ public class FeatureSettings extends JPanel
 
     if (fr.setFeaturePriority(rowData, visibleNew))
     {
-      af.alignPanel.paintAlignment(true, true);
+      refreshDisplay();
     }
   }
 
@@ -1253,7 +1254,7 @@ public class FeatureSettings extends JPanel
         if (!inConstruction)
         {
           fr.setTransparency((100 - transparency.getValue()) / 100f);
-          af.alignPanel.paintAlignment(true, true);
+          refreshDisplay();
         }
       }
     });
@@ -1265,6 +1266,7 @@ public class FeatureSettings extends JPanel
     boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
     showComplement = new JCheckBox(
             "Show " + (nucleotide ? "protein" : "CDS") + " features");
+    showComplement.setSelected(af.getViewport().isShowComplementFeatures());
     showComplement.addActionListener(new ActionListener()
     {
       @Override
@@ -1272,6 +1274,7 @@ public class FeatureSettings extends JPanel
       {
         af.getViewport()
                 .setShowComplementFeatures(showComplement.isSelected());
+        refreshDisplay();
       }
     });
 
@@ -1307,6 +1310,22 @@ public class FeatureSettings extends JPanel
     this.add(settingsPane);
   }
 
+  /**
+   * Repaints alignment, structure and overview (if shown). If there is a
+   * complementary view which is showing this view's features, then also
+   * repaints that.
+   */
+  void refreshDisplay()
+  {
+    af.alignPanel.paintAlignment(true, true);
+    AlignViewportI complement = af.getViewport().getCodingComplement();
+    if (complement != null && complement.isShowComplementFeatures())
+    {
+      AlignFrame af2 = Desktop.getAlignFrameFor(complement);
+      af2.alignPanel.paintAlignment(true, true);
+    }
+  }
+
   // ///////////////////////////////////////////////////////////////////////
   // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
   // ///////////////////////////////////////////////////////////////////////
@@ -1365,13 +1384,22 @@ public class FeatureSettings extends JPanel
     }
 
     /**
-     * Answers the class of the object in column c of the first row of the table
+     * Answers the class of column c of the table
      */
     @Override
     public Class<?> getColumnClass(int c)
     {
-      Object v = getValueAt(0, c);
-      return v == null ? null : v.getClass();
+      switch (c)
+      {
+      case TYPE_COLUMN:
+        return String.class;
+      case COLOUR_COLUMN:
+        return FeatureColour.class;
+      case FILTER_COLUMN:
+        return FeatureMatcherSet.class;
+      default:
+        return Boolean.class;
+      }
     }
 
     @Override