JAL-2623 updated Overview/structure on input of threshold value

[jalview.git] / src / jalview / appletgui / FeatureColourChooser.java

diff --git a/src/jalview/appletgui/FeatureColourChooser.java b/src/jalview/appletgui/FeatureColourChooser.java
index f460389..72fa982 100644 (file)
--- a/src/jalview/appletgui/FeatureColourChooser.java
+++ b/src/jalview/appletgui/FeatureColourChooser.java
@@ -277,6 +277,11 @@ public class FeatureColourChooser extends Panel implements ActionListener,
         float f = new Float(thresholdValue.getText()).floatValue();
         slider.setValue((int) (f * SCALE_FACTOR_1K));
         adjustmentValueChanged(null);
+
+        /*
+         * force repaint of any Overview window or structure
+         */
+        changeColour(true);
       } catch (NumberFormatException ex)
       {
       }
@@ -372,14 +377,14 @@ public class FeatureColourChooser extends Panel implements ActionListener,
       return;
     }
 
-    int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
+    int thresholdOption = AnnotationColourGradient.NO_THRESHOLD;
     if (threshold.getSelectedIndex() == 1)
     {
-      aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
+      thresholdOption = AnnotationColourGradient.ABOVE_THRESHOLD;
     }
     else if (threshold.getSelectedIndex() == 2)
     {
-      aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
+      thresholdOption = AnnotationColourGradient.BELOW_THRESHOLD;
     }
 
     slider.setEnabled(true);
@@ -390,14 +395,14 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     acg.setColourByLabel(colourFromLabel.getState());
     maxColour.setEnabled(!colourFromLabel.getState());
     minColour.setEnabled(!colourFromLabel.getState());
-    if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
+    if (thresholdOption == AnnotationColourGradient.NO_THRESHOLD)
     {
       slider.setEnabled(false);
       thresholdValue.setEnabled(false);
       thresholdValue.setText("");
     }
 
-    if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+    if (thresholdOption != AnnotationColourGradient.NO_THRESHOLD)
     {
       adjusting = true;
       acg.setThreshold(threshline.value);
@@ -411,11 +416,13 @@ public class FeatureColourChooser extends Panel implements ActionListener,
       adjusting = false;
     }
 
-    acg.setAboveThreshold(true);
+    acg.setAboveThreshold(thresholdOption == AnnotationColourGradient.ABOVE_THRESHOLD);
+    acg.setBelowThreshold(thresholdOption == AnnotationColourGradient.BELOW_THRESHOLD);
+
     if (thresholdIsMin.getState()
-            && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+            && thresholdOption != AnnotationColourGradient.NO_THRESHOLD)
     {
-      if (aboveThreshold == AnnotationColourGradient.ABOVE_THRESHOLD)
+      if (thresholdOption == AnnotationColourGradient.ABOVE_THRESHOLD)
       {
         acg = new FeatureColour(acg, threshline.value, max);
       }