X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationRowFilter.java;h=8b2486fd652b5b14ffc9fa45d793e59abd4104e1;hb=bd894ca9f2aae448653d7431ab8a170e1105e85c;hp=1035a6c72e6f44ded96ec678e74eed295a240967;hpb=ad69997e7967bae13b30470ca6d1ab74e0bb3046;p=jalview.git

diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index 1035a6c..8b2486f 100644
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -98,7 +98,8 @@ public abstract class AnnotationRowFilter extends JPanel
    * @param viewport
    * @param alignPanel
    */
-  public AnnotationRowFilter(AlignViewport viewport, final AlignmentPanel alignPanel)
+  public AnnotationRowFilter(AlignViewport viewport,
+          final AlignmentPanel alignPanel)
   {
     this.av = viewport;
     this.ap = alignPanel;
@@ -129,8 +130,13 @@ public abstract class AnnotationRowFilter extends JPanel
     });
   }
 
+  /**
+   * update the text field from the threshold slider. preserves state of
+   * 'adjusting' so safe to call in init.
+   */
   protected void setThresholdValueText()
   {
+    boolean oldadj = adjusting;
     adjusting = true;
     if (percentThreshold.isSelected())
     {
@@ -141,8 +147,9 @@ public abstract class AnnotationRowFilter extends JPanel
     {
       thresholdValue.setText((slider.getValue() / 1000f) + "");
     }
-    adjusting = false;
+    adjusting = oldadj;
   }
+
   protected void addSliderMouseListeners()
   {
 
@@ -175,23 +182,25 @@ 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>();
 
     Vector<String> list = new Vector<String>();
     int index = 1;
-    int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
+    int[] anmap = new int[av.getAlignment()
+            .getAlignmentAnnotation().length];
     seqAssociated.setEnabled(false);
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    for (int i = 0; i < av.getAlignment()
+            .getAlignmentAnnotation().length; i++)
     {
       AlignmentAnnotation annotation = av.getAlignment()
               .getAlignmentAnnotation()[i];
@@ -291,11 +300,10 @@ public abstract class AnnotationRowFilter extends JPanel
     try
     {
       float f = Float.parseFloat(thresholdValue.getText());
-      if (percentThreshold.isEnabled())
+      if (percentThreshold.isSelected())
       {
-        slider.setValue(slider.getMinimum()
-                + ((int) ((f / 100f) * (slider.getMaximum() - slider
-                        .getMinimum()))));
+        slider.setValue(slider.getMinimum() + ((int) ((f / 100f)
+                * (slider.getMaximum() - slider.getMinimum()))));
       }
       else
       {
@@ -374,9 +382,11 @@ public abstract class AnnotationRowFilter extends JPanel
     }
 
     float thr = annotation.threshold.value;
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    for (int i = 0; i < av.getAlignment()
+            .getAlignmentAnnotation().length; i++)
     {
-      AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
+      AlignmentAnnotation aa = av.getAlignment()
+              .getAlignmentAnnotation()[i];
       if (aa.label.equals(annotation.label)
               && (annotation.getCalcId() == null ? aa.getCalcId() == null
                       : annotation.getCalcId().equals(aa.getCalcId())))
@@ -446,8 +456,8 @@ public abstract class AnnotationRowFilter extends JPanel
         selectedAnnotationChanged();
       }
     });
-    annotations.setToolTipText(MessageManager
-            .getString("info.select_annotation_row"));
+    annotations.setToolTipText(
+            MessageManager.getString("info.select_annotation_row"));
 
     threshold.addActionListener(new ActionListener()
     {
@@ -469,7 +479,8 @@ public abstract class AnnotationRowFilter extends JPanel
       }
     });
 
-    percentThreshold.setText(MessageManager.getString("label.as_percentage"));
+    percentThreshold
+            .setText(MessageManager.getString("label.as_percentage"));
     percentThreshold.addActionListener(new ActionListener()
     {
       @Override