Merge branch 'develop' into features/JAL-892varnaToProject

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

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 8ce3e62..2b79256 100755 (executable)
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -20,21 +20,51 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-import java.util.List;
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.AlignmentSorter;
-import jalview.commands.OrderCommand;
-import jalview.datamodel.*;
+import jalview.api.FeatureSettingsControllerI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.GraduatedColor;
 import jalview.util.MessageManager;
 
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Checkbox;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.GridLayout;
+import java.awt.Image;
+import java.awt.Label;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.PopupMenu;
+import java.awt.ScrollPane;
+import java.awt.Scrollbar;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.InputEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
 public class FeatureSettings extends Panel implements ItemListener,
         MouseListener, MouseMotionListener, ActionListener,
-        AdjustmentListener
+        AdjustmentListener, FeatureSettingsControllerI
 {
   FeatureRenderer fr;
 
@@ -84,7 +114,7 @@ public class FeatureSettings extends Panel implements ItemListener,
       fr.findAllFeatures(true); // was default - now true to make all visible
     }
 
-    setTableData();
+    discoverAllFeatureData();
 
     this.setLayout(new BorderLayout());
     scrollPane = new ScrollPane();
@@ -249,7 +279,8 @@ public class FeatureSettings extends Panel implements ItemListener,
     men.show(this.featurePanel, x, y);
   }
 
-  public void setTableData()
+  @Override
+  public void discoverAllFeatureData()
   {
     if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
     {
@@ -276,7 +307,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
     // TODO: JAL-964 - smoothly incorporate new group entries if panel already
     // displayed and new groups present
-    for (String group:(List<String>)fr.getFeatureGroups())
+    for (String group:fr.getFeatureGroups())
     {
       boolean vis = fr.checkGroupVisibility(group, false);
       Checkbox check = new MyCheckbox(group, vis,
@@ -648,7 +679,7 @@ public class FeatureSettings extends Panel implements ItemListener,
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-    fr.setTransparency((float) (100 - transparency.getValue()) / 100f);
+    fr.setTransparency((100 - transparency.getValue()) / 100f);
     ap.seqPanel.seqCanvas.repaint();
 
   }