update settings for new groups (always displayed) and new feature types (containing...

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 6c5990a..7e817af 100755 (executable)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -132,7 +132,7 @@ public class FeatureSettings
       {
         if (!fs.resettingTable && !fs.handlingUpdate) {
           fs.handlingUpdate=true;
-          fs.resetTable(new String[] {}); // groups may be added
+          fs.resetTable(null); // groups may be added with new seuqence feature types only
           fs.handlingUpdate=false;
         }
       }
@@ -198,57 +198,10 @@ public class FeatureSettings
           if (!allGroups.contains(group))
           {
             allGroups.addElement(group);
-
-            boolean visible;
-            if (fr.featureGroups.containsKey(group))
-            {
-              visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
-            } else {
-              visible=true; //initGroups || fr.av.featuresDisplayed.containsKey(tmpfeatures[index].getType());
-            }
-
-            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;
-                break;
-              }
-            }
-
-            if (alreadyAdded)
+            if (checkGroupState(group))
             {
-              
-              continue;
+              // continue; // skip this group's feature - we've done it already ? 
             }
-
-            fr.featureGroups.put(group, new Boolean(visible));
-            final String grp = group;
-            final JCheckBox check = new JCheckBox(group, visible);
-            check.setFont(new Font("Serif", Font.BOLD, 12));
-            check.addItemListener(new ItemListener()
-            {
-              public void itemStateChanged(ItemEvent evt)
-              {
-                fr.featureGroups.put(check.getText(),
-                                     new Boolean(check.isSelected()));
-                af.alignPanel.seqPanel.seqCanvas.repaint();
-                if (af.alignPanel.overviewPanel != null)
-                {
-                  af.alignPanel.overviewPanel.updateOverviewImage();
-                }
-
-                resetTable(new String[] { grp } );
-              }
-            });
-            groupPanel.add(check);
           }
         }
 
@@ -264,12 +217,70 @@ public class FeatureSettings
 
     validate();
   }
+  /**
+   * 
+   * @param group
+   * @return true if group has been seen before and is already added to set.
+   */
+  private boolean checkGroupState(String group) {
+    boolean visible;
+    if (fr.featureGroups.containsKey(group))
+    {
+      visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
+        } else {
+        visible=true; // new group is always made visible 
+      }
+
+      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;
+        }
+      }
+
+      if (alreadyAdded)
+      {
+        
+        return true;
+      }
+
+      fr.featureGroups.put(group, new Boolean(visible));
+      final String grp = group;
+      final JCheckBox check = new JCheckBox(group, visible);
+      check.setFont(new Font("Serif", Font.BOLD, 12));
+      check.addItemListener(new ItemListener()
+      {
+        public void itemStateChanged(ItemEvent evt)
+        {
+          fr.featureGroups.put(check.getText(),
+                               new Boolean(check.isSelected()));
+          af.alignPanel.seqPanel.seqCanvas.repaint();
+          if (af.alignPanel.overviewPanel != null)
+          {
+            af.alignPanel.overviewPanel.updateOverviewImage();
+          }
+
+          resetTable(new String[] { grp } );
+        }
+      });
+      groupPanel.add(check);
+      return false;
+  }
   boolean resettingTable=false;
   void resetTable(String[] groupChanged)
   {
     resettingTable=true;
     typeWidth=new Hashtable();
-    Vector groupchanged = new Vector();
     // TODO: change avWidth calculation to 'per-sequence' average and use long rather than float
     float[] avWidth=null;
     SequenceFeature[] tmpfeatures;
@@ -303,6 +314,7 @@ public class FeatureSettings
         if (group == null || fr.featureGroups.get(group) == null ||
             ( (Boolean) fr.featureGroups.get(group)).booleanValue())
         {
+          checkGroupState(group);
           type = tmpfeatures[index].getType();
           if (!visibleChecks.contains(type))
           {