Merge remote-tracking branch 'origin/develop' into imp/JAL-2774

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

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 0963b31..3f1d9c7 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -131,6 +131,11 @@ public class FeatureSettings extends JPanel
   private static final int MIN_WIDTH = 400;
 
   private static final int MIN_HEIGHT = 400;
+  
+  /**
+   * when true, constructor is still executing - so ignore UI events
+   */
+  protected volatile boolean inConstruction = true;
 
   /**
    * Constructor
@@ -303,6 +308,7 @@ public class FeatureSettings extends JPanel
               };
             });
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    inConstruction = false;
   }
 
   protected void popupSort(final int selectedRow, final String type,
@@ -485,7 +491,7 @@ public class FeatureSettings extends JPanel
   @Override
   synchronized public void discoverAllFeatureData()
   {
-    Set<String> allGroups = new HashSet<String>();
+    Set<String> allGroups = new HashSet<>();
     AlignmentI alignment = af.getViewport().getAlignment();
 
     for (int i = 0; i < alignment.getHeight(); i++)
@@ -535,13 +541,8 @@ public class FeatureSettings extends JPanel
       public void itemStateChanged(ItemEvent evt)
       {
         fr.setGroupVisibility(check.getText(), check.isSelected());
-        af.alignPanel.getSeqPanel().seqCanvas.repaint();
-        if (af.alignPanel.overviewPanel != null)
-        {
-          af.alignPanel.overviewPanel.updateOverviewImage();
-        }
-
         resetTable(new String[] { grp });
+        af.alignPanel.paintAlignment(true, true);
       }
     });
     groupPanel.add(check);
@@ -557,12 +558,12 @@ public class FeatureSettings extends JPanel
       return;
     }
     resettingTable = true;
-    typeWidth = new Hashtable<String, float[]>();
+    typeWidth = new Hashtable<>();
     // TODO: change avWidth calculation to 'per-sequence' average and use long
     // rather than float
 
-    Set<String> displayableTypes = new HashSet<String>();
-    Set<String> foundGroups = new HashSet<String>();
+    Set<String> displayableTypes = new HashSet<>();
+    Set<String> foundGroups = new HashSet<>();
 
     /*
      * determine which feature types may be visible depending on 
@@ -578,7 +579,7 @@ public class FeatureSettings extends JPanel
        * 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 || checkGroupState(group))
@@ -1058,7 +1059,7 @@ public class FeatureSettings extends JPanel
   {
     if (fr.setFeaturePriority(data, visibleNew))
     {
-      af.alignPanel.paintAlignment(true);
+      af.alignPanel.paintAlignment(true, true);
     }
   }
 
@@ -1237,8 +1238,11 @@ public class FeatureSettings extends JPanel
       @Override
       public void stateChanged(ChangeEvent evt)
       {
-        fr.setTransparency((100 - transparency.getValue()) / 100f);
-        af.alignPanel.paintAlignment(true);
+        if (!inConstruction)
+        {
+          fr.setTransparency((100 - transparency.getValue()) / 100f);
+          af.alignPanel.paintAlignment(true,true);
+        }
       }
     });