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 26796de..84883d7 100644 (file)
--- a/src/jalview/gui/AnnotationChooser.java
+++ b/src/jalview/gui/AnnotationChooser.java
@@ -82,7 +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.
@@ -202,7 +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);
   }
 
   /**
@@ -233,7 +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);
   }
 
   /**
@@ -251,7 +251,7 @@ public class AnnotationChooser extends JPanel
 
     this.ap.updateAnnotation();
     // this.ap.annotationPanel.adjustPanelHeight();
-    this.ap.paintAlignment(true);
+    this.ap.paintAlignment(true, false);
   }
 
   /**
@@ -356,7 +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)