Merge branch 'develop' into bug/JAL-2346annotationChoice

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

diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index bc5bc54..c2bf41b 100644 (file)
--- 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>();
@@ -368,9 +368,9 @@ public abstract class AnnotationRowFilter extends JPanel
     return currentAnnotation;
   }
 
-  protected void setCurrentAnnotation(AlignmentAnnotation currentAnnotation)
+  protected void setCurrentAnnotation(AlignmentAnnotation annotation)
   {
-    this.currentAnnotation = currentAnnotation;
+    this.currentAnnotation = annotation;
   }
 
   protected abstract void valueChanged(boolean updateAllAnnotation);