JAL-2773 add new flag to paintAlignment(updateOverview,updateStructures) and first...

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

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 46498ad..9a67499 100755 (executable)
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -63,9 +63,9 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
-public class FeatureSettings extends Panel implements ItemListener,
-        MouseListener, MouseMotionListener, ActionListener,
-        AdjustmentListener, FeatureSettingsControllerI
+public class FeatureSettings extends Panel
+        implements ItemListener, MouseListener, MouseMotionListener,
+        ActionListener, AdjustmentListener, FeatureSettingsControllerI
 {
   FeatureRenderer fr;
 
@@ -135,11 +135,18 @@ public class FeatureSettings extends Panel implements ItemListener,
 
     add(lowerPanel, BorderLayout.SOUTH);
 
-    groupPanel.setLayout(new GridLayout(
-            (fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote - this was
-                                                      // scaled on number of
-                                                      // visible groups. seems
-                                                      // broken
+    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);
@@ -174,14 +181,12 @@ public class FeatureSettings extends Panel implements ItemListener,
   public void paint(Graphics g)
   {
     g.setColor(Color.black);
-    g.drawString(MessageManager
-            .getString("label.no_features_added_to_this_alignment"), 10, 20);
-    g.drawString(MessageManager
-            .getString("label.features_can_be_added_from_searches_1"), 10,
-            40);
-    g.drawString(MessageManager
-            .getString("label.features_can_be_added_from_searches_2"), 10,
-            60);
+    g.drawString(MessageManager.getString(
+            "label.no_features_added_to_this_alignment"), 10, 20);
+    g.drawString(MessageManager.getString(
+            "label.features_can_be_added_from_searches_1"), 10, 40);
+    g.drawString(MessageManager.getString(
+            "label.features_can_be_added_from_searches_2"), 10, 60);
   }
 
   protected void popupSort(final MyCheckbox check,
@@ -189,8 +194,9 @@ public class FeatureSettings extends Panel implements ItemListener,
   {
     final String type = check.type;
     final FeatureColourI typeCol = fr.getFeatureStyle(type);
-    PopupMenu men = new PopupMenu(MessageManager.formatMessage(
-            "label.settings_for_type", new String[] { type }));
+    PopupMenu men = new PopupMenu(MessageManager
+            .formatMessage("label.settings_for_type", new String[]
+            { type }));
     java.awt.MenuItem scr = new MenuItem(
             MessageManager.getString("label.sort_by_score"));
     men.add(scr);
@@ -201,8 +207,9 @@ public class FeatureSettings extends Panel implements ItemListener,
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        me.ap.alignFrame.avc.sortAlignmentByFeatureScore(Arrays
-                .asList(new String[] { type }));
+        me.ap.alignFrame.avc
+                .sortAlignmentByFeatureScore(Arrays.asList(new String[]
+                { type }));
       }
 
     });
@@ -214,8 +221,9 @@ public class FeatureSettings extends Panel implements ItemListener,
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(Arrays
-                .asList(new String[] { type }));
+        me.ap.alignFrame.avc
+                .sortAlignmentByFeatureDensity(Arrays.asList(new String[]
+                { type }));
       }
 
     });
@@ -279,8 +287,8 @@ public class FeatureSettings extends Panel implements ItemListener,
     });
     men.add(selectContaining);
 
-    MenuItem selectNotContaining = new MenuItem(
-            MessageManager.getString("label.select_columns_not_containing"));
+    MenuItem selectNotContaining = new MenuItem(MessageManager
+            .getString("label.select_columns_not_containing"));
     selectNotContaining.addActionListener(new ActionListener()
     {
       @Override
@@ -369,8 +377,8 @@ public class FeatureSettings extends Panel implements ItemListener,
   // Group selection states
   void resetTable(boolean groupsChanged)
   {
-    List<String> displayableTypes = new ArrayList<String>();
-    Set<String> foundGroups = new HashSet<String>();
+    List<String> displayableTypes = new ArrayList<>();
+    Set<String> foundGroups = new HashSet<>();
 
     AlignmentI alignment = av.getAlignment();
 
@@ -383,7 +391,7 @@ public class FeatureSettings extends Panel implements ItemListener,
        * and keep track of which groups are visible
        */
       Set<String> groups = seq.getFeatures().getFeatureGroups(true);
-      Set<String> visibleGroups = new HashSet<String>();
+      Set<String> visibleGroups = new HashSet<>();
       for (String group : groups)
       {
         // if (group == null || fr.checkGroupVisibility(group, true))
@@ -454,8 +462,8 @@ public class FeatureSettings extends Panel implements ItemListener,
       addCheck(groupsChanged, type);
     }
 
-    featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(),
-            1, 10, 5));
+    featurePanel.setLayout(
+            new GridLayout(featurePanel.getComponentCount(), 1, 10, 5));
     featurePanel.validate();
 
     if (scrollPane != null)
@@ -545,7 +553,7 @@ public class FeatureSettings extends Panel implements ItemListener,
       Checkbox check = (Checkbox) featurePanel.getComponent(i);
       check.setState(!check.getState());
     }
-    selectionChanged();
+    selectionChanged(true);
   }
 
   private ItemListener groupItemListener = new ItemListener()
@@ -568,10 +576,10 @@ public class FeatureSettings extends Panel implements ItemListener,
   @Override
   public void itemStateChanged(ItemEvent evt)
   {
-    selectionChanged();
+    selectionChanged(true);
   }
 
-  void selectionChanged()
+  void selectionChanged(boolean updateOverview)
   {
     Component[] comps = featurePanel.getComponents();
     int cSize = comps.length;
@@ -592,7 +600,7 @@ public class FeatureSettings extends Panel implements ItemListener,
 
     fr.setFeaturePriority(data);
 
-    ap.paintAlignment(true);
+    ap.paintAlignment(updateOverview, updateOverview);
   }
 
   MyCheckbox selectedCheck;
@@ -634,8 +642,8 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
     else
     {
-      comp = featurePanel.getComponentAt(evt.getX(), evt.getY()
-              + evt.getComponent().getLocation().y);
+      comp = featurePanel.getComponentAt(evt.getX(),
+              evt.getY() + evt.getComponent().getLocation().y);
     }
 
     if (comp != null && comp instanceof Checkbox)
@@ -672,7 +680,7 @@ public class FeatureSettings extends Panel implements ItemListener,
   {
     featurePanel.removeAll();
     resetTable(false);
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
   }
 
   @Override
@@ -724,7 +732,7 @@ public class FeatureSettings extends Panel implements ItemListener,
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     fr.setTransparency((100 - transparency.getValue()) / 100f);
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
   }
 
   class MyCheckbox extends Checkbox