X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureColourChooser.java;h=0d479f9a9538d74ee6752bac5d627e205607f923;hb=28d2a0b7dde7f6751d9e063fc2e11da065d284a4;hp=f4603895dc6539265f2aa213c34d2779e9f7697b;hpb=93a90c5084d1e81afd65bf2e3063cde96d6b3b48;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureColourChooser.java b/src/jalview/appletgui/FeatureColourChooser.java
index f460389..0d479f9 100644
--- a/src/jalview/appletgui/FeatureColourChooser.java
+++ b/src/jalview/appletgui/FeatureColourChooser.java
@@ -156,8 +156,8 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     } catch (Exception ex)
     {
     }
-    threshold.select(cs.isAboveThreshold() ? 1 : (cs.isBelowThreshold() ? 2
-            : 0));
+    threshold.select(
+            cs.isAboveThreshold() ? 1 : (cs.isBelowThreshold() ? 2 : 0));
 
     adjusting = false;
     changeColour(true);
@@ -165,9 +165,9 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     slider.addAdjustmentListener(this);
     slider.addMouseListener(this);
     owner = (af != null) ? af : fs.frame;
-    frame = new JVDialog(owner, MessageManager.formatMessage(
-            "label.graduated_color_for_params", new String[] { type }),
-            true, 480, 248);
+    frame = new JVDialog(owner, MessageManager
+            .formatMessage("label.graduated_color_for_params", new String[]
+            { type }), true, 480, 248);
     frame.setMainPanel(this);
     validate();
     frame.setVisible(true);
@@ -196,8 +196,8 @@ public class FeatureColourChooser extends Panel implements ActionListener,
 
   private void jbInit() throws Exception
   {
-    Label minLabel = new Label(MessageManager.getString("label.min")), maxLabel = new Label(
-            MessageManager.getString("label.max"));
+    Label minLabel = new Label(MessageManager.getString("label.min")),
+            maxLabel = new Label(MessageManager.getString("label.max"));
     minLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
     maxLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
     // minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
@@ -243,13 +243,13 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     jPanel3.setBackground(Color.white);
 
     colourFromLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    colourFromLabel.setLabel(MessageManager
-            .getString("label.colour_by_label"));
+    colourFromLabel
+            .setLabel(MessageManager.getString("label.colour_by_label"));
     colourFromLabel.setSize(new Dimension(139, 22));
     // threshold.setBounds(new Rectangle(11, 3, 139, 22));
     thresholdIsMin.setBackground(Color.white);
-    thresholdIsMin.setLabel(MessageManager
-            .getString("label.threshold_minmax"));
+    thresholdIsMin
+            .setLabel(MessageManager.getString("label.threshold_minmax"));
     thresholdIsMin.setSize(new Dimension(135, 23));
     // thresholdIsMin.setBounds(new Rectangle(328, 3, 135, 23));
     jPanel1.add(minLabel);
@@ -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)
       {
       }
@@ -333,9 +338,9 @@ public class FeatureColourChooser extends Panel implements ActionListener,
   {
     if (newCol == null)
     {
-      new UserDefinedColours(this,
-              minColour.getBackground(), owner,
-              MessageManager.getString("label.select_colour_minimum_value"));
+      new UserDefinedColours(this, minColour.getBackground(), owner,
+              MessageManager
+                      .getString("label.select_colour_minimum_value"));
     }
     else
     {
@@ -351,9 +356,9 @@ public class FeatureColourChooser extends Panel implements ActionListener,
   {
     if (newCol == null)
     {
-      new UserDefinedColours(this,
-              maxColour.getBackground(), owner,
-              MessageManager.getString("label.select_colour_maximum_value"));
+      new UserDefinedColours(this, maxColour.getBackground(), owner,
+              MessageManager
+                      .getString("label.select_colour_maximum_value"));
     }
     else
     {
@@ -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 +416,15 @@ 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);
       }