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

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

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 0963b31..c5454ab 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -485,7 +485,7 @@ 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++)
@@ -557,12 +557,12 @@ 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 +578,7 @@ 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 +1058,7 @@ public class FeatureSettings extends JPanel
   {
     if (fr.setFeaturePriority(data, visibleNew))
     {
-      af.alignPanel.paintAlignment(true);
+      af.alignPanel.paintAlignment(true, true);
     }
   }
 
@@ -1238,7 +1238,7 @@ public class FeatureSettings extends JPanel
       public void stateChanged(ChangeEvent evt)
       {
         fr.setTransparency((100 - transparency.getValue()) / 100f);
-        af.alignPanel.paintAlignment(true);
+        af.alignPanel.paintAlignment(true, true);
       }
     });