JAL-1713 update from Jalview 2.11.3 develop

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

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index ac04a1f..2c8f47a 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -20,8 +20,6 @@
  */
 package jalview.gui;
 
-import java.util.Locale;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Component;
@@ -54,6 +52,7 @@ import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Set;
 
@@ -63,7 +62,6 @@ import javax.swing.BorderFactory;
 import javax.swing.Icon;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
-import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JLayeredPane;
@@ -217,6 +215,7 @@ public class FeatureSettings extends JPanel
     transparency.setValue(100 - transparencyAsPercent);
     inConstruction = incon;
   }
+
   /**
    * Constructor
    * 
@@ -412,6 +411,7 @@ public class FeatureSettings extends JPanel
     {
       frame = new JInternalFrame();
       frame.setContentPane(this);
+      frame.setFrameIcon(null);
       Rectangle bounds = af.getFeatureSettingsGeometry();
       String title;
       if (af.getAlignPanels().size() > 1 || Desktop.getAlignmentPanels(
@@ -457,8 +457,8 @@ public class FeatureSettings extends JPanel
               });
       frame.setLayer(JLayeredPane.PALETTE_LAYER);
     }
-               inConstruction = false;
-       }
+    inConstruction = false;
+  }
 
   /**
    * Sets the state of buttons to show complement features from viewport
@@ -484,16 +484,17 @@ public class FeatureSettings extends JPanel
     change = null;
   }
 
-       /**
-        * Constructs and shows a popup menu of possible actions on the selected row and
-        * feature type
-        * 
-        * @param rowSelected
-        * @param type
-        * @param typeCol
-        * @param pt
-        */
-       protected void showPopupMenu(final int rowSelected, final String type, final Object typeCol, final Point pt)
+  /**
+   * Constructs and shows a popup menu of possible actions on the selected row
+   * and feature type
+   * 
+   * @param rowSelected
+   * @param type
+   * @param typeCol
+   * @param pt
+   */
+  protected void showPopupMenu(final int rowSelected, final String type,
+          final Object typeCol, final Point pt)
   {
     JPopupMenu men = new JPopupMenu(MessageManager
             .formatMessage("label.settings_for_param", new String[]
@@ -947,14 +948,10 @@ public class FeatureSettings extends JPanel
     chooser.setDialogTitle(
             MessageManager.getString("label.load_feature_colours"));
     chooser.setToolTipText(MessageManager.getString("action.load"));
-    chooser.setResponseHandler(0, new Runnable()
-    {
-      @Override
-      public void run()
-      {
-        File file = chooser.getSelectedFile();
-        load(file);
-      }
+    chooser.setResponseHandler(0, () -> {
+      File file = chooser.getSelectedFile();
+      load(file);
+      return null;
     });
     chooser.showOpenDialog(this);
   }
@@ -1201,8 +1198,8 @@ public class FeatureSettings extends JPanel
   }
 
   /**
-   * close ourselves but leave any existing UI handlers (e.g a CDS/Protein tabbed
-   * feature settings dialog) intact
+   * close ourselves but leave any existing UI handlers (e.g a CDS/Protein
+   * tabbed feature settings dialog) intact
    */
   public void closeOldSettings()
   {
@@ -1318,7 +1315,8 @@ public class FeatureSettings extends JPanel
       }
     });
 
-    final String byScoreLabel = MessageManager.getString("label.seq_sort_by_score");
+    final String byScoreLabel = MessageManager
+            .getString("label.seq_sort_by_score");
     JButton sortByScore = new JButton(byScoreLabel);
     sortByScore.setFont(JvSwingUtils.getLabelFont());
     sortByScore.addActionListener(new ActionListener()
@@ -1332,7 +1330,8 @@ public class FeatureSettings extends JPanel
         }
       }
     });
-    final String byDensityLabel = MessageManager.getString("label.sequence_sort_by_density");
+    final String byDensityLabel = MessageManager
+            .getString("label.sequence_sort_by_density");
     JButton sortByDens = new JButton(byDensityLabel);
     sortByDens.setFont(JvSwingUtils.getLabelFont());
     sortByDens.addActionListener(new ActionListener()
@@ -1363,7 +1362,8 @@ public class FeatureSettings extends JPanel
         }
       }
     });
-    // Cancel for a SplitFrame should just revert changes to the currently displayed
+    // Cancel for a SplitFrame should just revert changes to the currently
+    // displayed
     // settings. May want to do this for either or both - so need a splitview
     // feature settings cancel/OK.
     JButton cancel = new JButton(MessageManager
@@ -1453,11 +1453,12 @@ public class FeatureSettings extends JPanel
             MessageManager.getString("label.transparency_tip"));
 
     boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
-    String text = MessageManager.formatMessage("label.show_linked_features",
-            nucleotide
-                    ? MessageManager.getString("label.protein")
-                            .toLowerCase(Locale.ROOT)
-                    : "CDS");
+    String text = MessageManager
+            .formatMessage("label.show_linked_features",
+                    nucleotide
+                            ? MessageManager.getString("label.protein")
+                                    .toLowerCase(Locale.ROOT)
+                            : "CDS");
     showComplement = new JCheckBox(text);
     showComplement.addActionListener(new ActionListener()
     {
@@ -1541,7 +1542,7 @@ public class FeatureSettings extends JPanel
    * 
    * @param fcol
    * @param withHint
-   *                   if true include 'click to edit' and similar text
+   *          if true include 'click to edit' and similar text
    * @return
    */
   public static String getColorTooltip(FeatureColourI fcol,