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

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

diff --git a/src/jalview/gui/AnnotationChooser.java b/src/jalview/gui/AnnotationChooser.java
index 35b6032..84883d7 100644 (file)
--- 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.
  * 
@@ -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.
@@ -201,7 +202,7 @@ public class AnnotationChooser extends JPanel
     // this.ap.alabels.setSize(this.ap.alabels.getSize().width,
     // this.ap.annotationPanel.getSize().height);
     // this.ap.validate();
-    this.ap.paintAlignment(true);
+    this.ap.paintAlignment(true, false);
   }
 
   /**
@@ -232,7 +233,7 @@ public class AnnotationChooser extends JPanel
     // this.ap.alabels.setSize(this.ap.alabels.getSize().width,
     // this.ap.annotationPanel.getSize().height);
     // this.ap.validate();
-    this.ap.paintAlignment(true);
+    this.ap.paintAlignment(true, false);
   }
 
   /**
@@ -242,7 +243,7 @@ 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()
   {
@@ -250,7 +251,7 @@ public class AnnotationChooser extends JPanel
 
     this.ap.updateAnnotation();
     // this.ap.annotationPanel.adjustPanelHeight();
-    this.ap.paintAlignment(true);
+    this.ap.paintAlignment(true, false);
   }
 
   /**
@@ -355,7 +356,7 @@ 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)