X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationChooser.java;h=d9768152af9164f25ea7585d7c093e6db0f44dcb;hb=7fa567506eea0a202c71e6939b961962f515dcec;hp=35b603255e7a2185e5b2fc064a698273feb78db6;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git

diff --git a/src/jalview/gui/AnnotationChooser.java b/src/jalview/gui/AnnotationChooser.java
index 35b6032..d976815 100644
--- a/src/jalview/gui/AnnotationChooser.java
+++ b/src/jalview/gui/AnnotationChooser.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,11 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceGroup;
-import jalview.util.MessageManager;
-
 import java.awt.BorderLayout;
 import java.awt.Checkbox;
 import java.awt.CheckboxGroup;
@@ -45,6 +40,11 @@ import javax.swing.JInternalFrame;
 import javax.swing.JLayeredPane;
 import javax.swing.JPanel;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceGroup;
+import jalview.util.MessageManager;
+
 /**
  * A panel that allows the user to select which sequence-associated annotation
  * rows to show or hide.
@@ -56,7 +56,8 @@ import javax.swing.JPanel;
 public class AnnotationChooser extends JPanel
 {
 
-  private static final Font CHECKBOX_FONT = new Font("Serif", Font.BOLD, 12);
+  private static final Font CHECKBOX_FONT = new Font("Serif", Font.BOLD,
+          12);
 
   private static final int MY_FRAME_WIDTH = 600;
 
@@ -81,7 +82,7 @@ public class AnnotationChooser extends JPanel
   private boolean applyToUnselectedSequences;
 
   // currently selected 'annotation type' checkboxes
-  private Map<String, String> selectedTypes = new HashMap<String, String>();
+  private Map<String, String> selectedTypes = new HashMap<>();
 
   /**
    * Constructor.
@@ -194,14 +195,7 @@ public class AnnotationChooser extends JPanel
   {
     setAnnotationVisibility(true);
 
-    // copied from AnnotationLabel.actionPerformed (after show/hide row)...
-    // TODO should drive this functionality into AlignmentPanel
     ap.updateAnnotation();
-    // this.ap.annotationPanel.adjustPanelHeight();
-    // this.ap.alabels.setSize(this.ap.alabels.getSize().width,
-    // this.ap.annotationPanel.getSize().height);
-    // this.ap.validate();
-    this.ap.paintAlignment(true);
   }
 
   /**
@@ -228,11 +222,6 @@ public class AnnotationChooser extends JPanel
       }
     }
     ap.updateAnnotation();
-    // // this.ap.annotationPanel.adjustPanelHeight();
-    // this.ap.alabels.setSize(this.ap.alabels.getSize().width,
-    // this.ap.annotationPanel.getSize().height);
-    // this.ap.validate();
-    this.ap.paintAlignment(true);
   }
 
   /**
@@ -242,15 +231,13 @@ public class AnnotationChooser extends JPanel
    * type which are in the application scope (all, selected or unselected
    * sequences).
    * 
-   * @param type
+   * @param dataSourceType
    */
   protected void changeShowHide_actionPerformed()
   {
     setAnnotationVisibility(false);
 
-    this.ap.updateAnnotation();
-    // this.ap.annotationPanel.adjustPanelHeight();
-    this.ap.paintAlignment(true);
+    ap.updateAnnotation();
   }
 
   /**
@@ -355,7 +342,7 @@ public class AnnotationChooser extends JPanel
   public static List<String> getAnnotationTypes(AlignmentI alignment,
           boolean sequenceSpecificOnly)
   {
-    List<String> result = new ArrayList<String>();
+    List<String> result = new ArrayList<>();
     for (AlignmentAnnotation aa : alignment.getAlignmentAnnotation())
     {
       if (!sequenceSpecificOnly || aa.sequenceRef != null)
@@ -615,6 +602,7 @@ public class AnnotationChooser extends JPanel
   private void showFrame()
   {
     frame = new JInternalFrame();
+    frame.setFrameIcon(null);
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     Desktop.addInternalFrame(frame,