JAL-964 JAL-2510 update Feature Settings from Amend Features, warn if

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

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index feb09fc..67bfb79 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -61,6 +61,7 @@ import java.io.InputStreamReader;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.util.Arrays;
+import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
@@ -131,6 +132,11 @@ public class FeatureSettings extends JPanel implements
 
   private static final int MIN_HEIGHT = 400;
 
+  /**
+   * Constructor
+   * 
+   * @param af
+   */
   public FeatureSettings(AlignFrame af)
   {
     this.af = af;
@@ -531,27 +537,15 @@ public class FeatureSettings extends JPanel implements
   {
     boolean visible = fr.checkGroupVisibility(group, true);
 
-    if (groupPanel == null)
-    {
-      groupPanel = new JPanel();
-    }
-
-    boolean alreadyAdded = false;
     for (int g = 0; g < groupPanel.getComponentCount(); g++)
     {
       if (((JCheckBox) groupPanel.getComponent(g)).getText().equals(group))
       {
-        alreadyAdded = true;
         ((JCheckBox) groupPanel.getComponent(g)).setSelected(visible);
-        break;
+        return visible;
       }
     }
 
-    if (alreadyAdded)
-    {
-
-      return visible;
-    }
     final String grp = group;
     final JCheckBox check = new JCheckBox(group, visible);
     check.setFont(new Font("Serif", Font.BOLD, 12));
@@ -590,6 +584,7 @@ public class FeatureSettings extends JPanel implements
     SequenceFeature[] tmpfeatures;
     String group = null, type;
     Vector<String> visibleChecks = new Vector<String>();
+    Set<String> foundGroups = new HashSet<String>();
 
     // Find out which features should be visible depending on which groups
     // are selected / deselected
@@ -608,6 +603,7 @@ public class FeatureSettings extends JPanel implements
       while (index < tmpfeatures.length)
       {
         group = tmpfeatures[index].featureGroup;
+        foundGroups.add(group);
 
         if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
         {
@@ -712,20 +708,35 @@ public class FeatureSettings extends JPanel implements
     table.setModel(new FeatureTableModel(data));
     table.getColumnModel().getColumn(0).setPreferredWidth(200);
 
-    if (groupPanel != null)
-    {
-      groupPanel.setLayout(new GridLayout(
-              fr.getFeatureGroupsSize() / 4 + 1, 4));
-
-      groupPanel.validate();
-      bigPanel.add(groupPanel, BorderLayout.NORTH);
-    }
+    groupPanel.setLayout(new GridLayout(fr.getFeatureGroupsSize() / 4 + 1,
+            4));
+    pruneGroups(foundGroups);
+    groupPanel.validate();
 
     updateFeatureRenderer(data, groupChanged != null);
     resettingTable = false;
   }
 
   /**
+   * Remove from the groups panel any checkboxes for groups that are not in the
+   * foundGroups set. This enables removing a group from the display when the
+   * last feature in that group is deleted.
+   * 
+   * @param foundGroups
+   */
+  protected void pruneGroups(Set<String> foundGroups)
+  {
+    for (int g = 0; g < groupPanel.getComponentCount(); g++)
+    {
+      JCheckBox checkbox = (JCheckBox) groupPanel.getComponent(g);
+      if (!foundGroups.contains(checkbox.getText()))
+      {
+        groupPanel.remove(checkbox);
+      }
+    }
+  }
+
+  /**
    * reorder data based on the featureRenderers global priority list.
    * 
    * @param data
@@ -1065,6 +1076,10 @@ public class FeatureSettings extends JPanel implements
     settingsPane.setLayout(borderLayout2);
     dasSettingsPane.setLayout(borderLayout3);
     bigPanel.setLayout(borderLayout4);
+
+    groupPanel = new JPanel();
+    bigPanel.add(groupPanel, BorderLayout.NORTH);
+
     invert.setFont(JvSwingUtils.getLabelFont());
     invert.setText(MessageManager.getString("label.invert_selection"));
     invert.addActionListener(new ActionListener()