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 dbe3317..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;
@@ -150,6 +151,8 @@ public class FeatureSettings extends JPanel
 
   JSlider transparency = new JSlider();
 
+  JCheckBox showComplement;
+
   /*
    * when true, constructor is still executing - so ignore UI events
    */
@@ -518,7 +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);
@@ -1076,7 +1079,7 @@ public class FeatureSettings extends JPanel
 
     if (fr.setFeaturePriority(rowData, visibleNew))
     {
-      af.alignPanel.paintAlignment(true, true);
+      refreshDisplay();
     }
   }
 
@@ -1251,7 +1254,7 @@ public class FeatureSettings extends JPanel
         if (!inConstruction)
         {
           fr.setTransparency((100 - transparency.getValue()) / 100f);
-          af.alignPanel.paintAlignment(true, true);
+          refreshDisplay();
         }
       }
     });
@@ -1260,6 +1263,21 @@ public class FeatureSettings extends JPanel
     transparency.setToolTipText(
             MessageManager.getString("label.transparency_tip"));
 
+    boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
+    showComplement = new JCheckBox(
+            "Show " + (nucleotide ? "protein" : "CDS") + " features");
+    showComplement.setSelected(af.getViewport().isShowComplementFeatures());
+    showComplement.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        af.getViewport()
+                .setShowComplementFeatures(showComplement.isSelected());
+        refreshDisplay();
+      }
+    });
+
     JPanel transPanel = new JPanel(new GridLayout(1, 2));
     bigPanel.add(transPanel, BorderLayout.SOUTH);
 
@@ -1269,7 +1287,16 @@ public class FeatureSettings extends JPanel
     transbuttons.add(sortByScore);
     transbuttons.add(sortByDens);
     transbuttons.add(help);
-    transPanel.add(transparency);
+
+    boolean hasComplement = af.getViewport().getCodingComplement() != null;
+    JPanel transPanelLeft = new JPanel(
+            new GridLayout(hasComplement ? 2 : 1, 1));
+    transPanelLeft.add(transparency);
+    if (hasComplement)
+    {
+      transPanelLeft.add(showComplement);
+    }
+    transPanel.add(transPanelLeft);
     transPanel.add(transbuttons);
 
     JPanel buttonPanel = new JPanel();
@@ -1283,6 +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
   // ///////////////////////////////////////////////////////////////////////
@@ -1341,13 +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