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 5ac76db..84883d7 100644 (file)
--- a/src/jalview/gui/AnnotationChooser.java
+++ b/src/jalview/gui/AnnotationChooser.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.gui;
 
 import jalview.datamodel.AlignmentAnnotation;
@@ -36,7 +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;
 
@@ -61,7 +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.
@@ -181,7 +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);
   }
 
   /**
@@ -212,7 +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);
   }
 
   /**
@@ -222,7 +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()
   {
@@ -230,7 +251,7 @@ public class AnnotationChooser extends JPanel
 
     this.ap.updateAnnotation();
     // this.ap.annotationPanel.adjustPanelHeight();
-    this.ap.paintAlignment(true);
+    this.ap.paintAlignment(true, false);
   }
 
   /**
@@ -335,7 +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)