X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationRowFilter.java;h=c2bf41bc479187990e12fe51f4b930cc59a21399;hb=7e71cd91595a05c75e8491e3ef3fb09f7913ea55;hp=7bf87216a91e4e60f02710e58eaee0a6169fb511;hpb=4ea44eaccf82b15dafb8dd53f5c71de5e9d0d551;p=jalview.git

diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index 7bf8721..c2bf41b 100644
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -93,13 +93,13 @@ public abstract class AnnotationRowFilter extends JPanel
   /**
    * Constructor
    * 
-   * @param av
-   * @param ap
+   * @param viewport
+   * @param alignPanel
    */
-  public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
+  public AnnotationRowFilter(AlignViewport viewport, final AlignmentPanel alignPanel)
   {
-    this.av = av;
-    this.ap = ap;
+    this.av = viewport;
+    this.ap = alignPanel;
     thresholdValue.addFocusListener(new FocusAdapter()
     {
       @Override
@@ -159,14 +159,14 @@ public abstract class AnnotationRowFilter extends JPanel
     });
   }
 
-  /**
-   * Builds and returns a list of menu items (display text) for choice of
-   * annotation. Also builds maps between annotations, their positions in the
-   * list, and their display labels in the list.
-   * 
-   * @param isSeqAssociated
-   * @return
-   */
+/**
+ * Builds and returns a list of menu items (display text) for choice of
+ * annotation. Also builds maps between annotations, their positions in the
+ * list, and their display labels in the list.
+ * 
+ * @param isSeqAssociated
+ * @return
+ */
   public Vector<String> getAnnotationItems(boolean isSeqAssociated)
   {
     annotationLabels = new HashMap<AlignmentAnnotation, String>();
@@ -363,14 +363,14 @@ public abstract class AnnotationRowFilter extends JPanel
     }
   }
 
-  protected AlignmentAnnotation getCurrentAnnotation()
+  public AlignmentAnnotation getCurrentAnnotation()
   {
     return currentAnnotation;
   }
 
-  protected void setCurrentAnnotation(AlignmentAnnotation currentAnnotation)
+  protected void setCurrentAnnotation(AlignmentAnnotation annotation)
   {
-    this.currentAnnotation = currentAnnotation;
+    this.currentAnnotation = annotation;
   }
 
   protected abstract void valueChanged(boolean updateAllAnnotation);