Merge branch 'develop' into documentation/JAL-2418_release2102

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

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 1b9fbf9..9d2f601 100755 (executable)
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -58,8 +58,10 @@ import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.util.Arrays;
 import java.util.Enumeration;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 import java.util.Vector;
 
 public class FeatureSettings extends Panel implements ItemListener,
@@ -106,6 +108,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     {
       fr.findAllFeatures(true); // was default - now true to make all visible
     }
+    groupPanel = new Panel();
 
     discoverAllFeatureData();
 
@@ -133,17 +136,15 @@ public class FeatureSettings extends Panel implements ItemListener,
 
     add(lowerPanel, BorderLayout.SOUTH);
 
-    if (groupPanel != null)
-    {
-      groupPanel.setLayout(new GridLayout(
-              (fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote - this was
-                                                        // scaled on number of
-                                                        // visible groups. seems
-                                                        // broken
-      groupPanel.validate();
+    groupPanel.setLayout(new GridLayout(
+            (fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote - this was
+                                                      // scaled on number of
+                                                      // visible groups. seems
+                                                      // broken
+    groupPanel.validate();
+
+    add(groupPanel, BorderLayout.NORTH);
 
-      add(groupPanel, BorderLayout.NORTH);
-    }
     frame = new Frame();
     frame.add(this);
     final FeatureSettings me = this;
@@ -326,44 +327,43 @@ public class FeatureSettings extends Panel implements ItemListener,
     if (fr.getAllFeatureColours() != null
             && fr.getAllFeatureColours().size() > 0)
     {
-      rebuildGroups();
+      // rebuildGroups();
 
     }
     resetTable(false);
   }
 
   /**
-   * rebuilds the group panel
+   * Answers the visibility of the given group, and adds a checkbox for it if
+   * there is not one already
    */
-  public void rebuildGroups()
+  public boolean checkGroupState(String group)
   {
-    boolean rdrw = false;
-    if (groupPanel == null)
-    {
-      groupPanel = new Panel();
-    }
-    else
-    {
-      rdrw = true;
-      groupPanel.removeAll();
-    }
-    // TODO: JAL-964 - smoothly incorporate new group entries if panel already
-    // displayed and new groups present
-    for (String group : fr.getFeatureGroups())
-    {
-      boolean vis = fr.checkGroupVisibility(group, false);
-      Checkbox check = new MyCheckbox(group, vis, false);
-      check.addMouseListener(this);
-      check.setFont(new Font("Serif", Font.BOLD, 12));
-      check.addItemListener(groupItemListener);
-      // note - visibility seems to correlate with displayed. ???wtf ??
-      check.setVisible(vis);
-      groupPanel.add(check);
-    }
-    if (rdrw)
+    boolean visible = fr.checkGroupVisibility(group, true);
+
+    /*
+     * is there already a checkbox for this group?
+     */
+    for (int g = 0; g < groupPanel.getComponentCount(); g++)
     {
-      groupPanel.validate();
+      if (((Checkbox) groupPanel.getComponent(g)).getLabel().equals(group))
+      {
+        ((Checkbox) groupPanel.getComponent(g)).setState(visible);
+        return visible;
+      }
     }
+
+    /*
+     * add a new checkbox
+     */
+    Checkbox check = new MyCheckbox(group, visible, false);
+    check.addMouseListener(this);
+    check.setFont(new Font("Serif", Font.BOLD, 12));
+    check.addItemListener(groupItemListener);
+    groupPanel.add(check);
+
+    groupPanel.validate();
+    return visible;
   }
 
   // This routine adds and removes checkboxes depending on
@@ -373,7 +373,9 @@ public class FeatureSettings extends Panel implements ItemListener,
     SequenceFeature[] tmpfeatures;
     String group = null, type;
     Vector<String> visibleChecks = new Vector<String>();
+    Set<String> foundGroups = new HashSet<String>();
     AlignmentI alignment = av.getAlignment();
+
     for (int i = 0; i < alignment.getHeight(); i++)
     {
       if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
@@ -386,8 +388,9 @@ public class FeatureSettings extends Panel implements ItemListener,
       while (index < tmpfeatures.length)
       {
         group = tmpfeatures[index].featureGroup;
+        foundGroups.add(group);
 
-        if (group == null || fr.checkGroupVisibility(group, true))
+        if (group == null || checkGroupState(group))
         {
           type = tmpfeatures[index].getType();
           if (!visibleChecks.contains(type))
@@ -399,6 +402,11 @@ public class FeatureSettings extends Panel implements ItemListener,
       }
     }
 
+    /*
+     * remove any checkboxes for groups not present
+     */
+    pruneGroups(foundGroups);
+
     Component[] comps;
     int cSize = featurePanel.getComponentCount();
     MyCheckbox check;
@@ -458,6 +466,25 @@ public class FeatureSettings extends Panel implements ItemListener,
   }
 
   /**
+   * 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++)
+    {
+      Checkbox checkbox = (Checkbox) groupPanel.getComponent(g);
+      if (!foundGroups.contains(checkbox.getLabel()))
+      {
+        groupPanel.remove(checkbox);
+      }
+    }
+  }
+
+  /**
    * update the checklist of feature types with the given type
    * 
    * @param groupsChanged