From 59c22b05925dd3b4d148c1ce0e43eea12bc64ba7 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 24 Feb 2006 11:45:36 +0000
Subject: [PATCH] Keeps original threshold value

---
 src/jalview/gui/AnnotationColourChooser.java |   37 +++++++++++++++++++++-----
 1 file changed, 30 insertions(+), 7 deletions(-)

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 49e835d..d49a4b6 100755
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -36,6 +36,7 @@ public class AnnotationColourChooser
   ColourSchemeI oldcs;
   Hashtable oldgroupColours;
   jalview.datamodel.AlignmentAnnotation currentAnnotation;
+  boolean adjusting = false;
 
   public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap)
   {
@@ -56,7 +57,7 @@ public class AnnotationColourChooser
     frame = new JInternalFrame();
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145, false);
+    Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145);
 
     try
     {
@@ -69,8 +70,11 @@ public class AnnotationColourChooser
     {
       public void stateChanged(ChangeEvent evt)
       {
-        thresholdValue.setText( ( (float) slider.getValue() / 1000f) + "");
-        valueChanged();
+        if(!adjusting)
+        {
+          thresholdValue.setText( ( (float) slider.getValue() / 1000f) + "");
+          valueChanged();
+        }
       }
     });
 
@@ -89,6 +93,7 @@ public class AnnotationColourChooser
       maxColour.setBackground(Color.red);
     }
 
+    adjusting = true;
     for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
     {
       if (av.alignment.getAlignmentAnnotation()[i].graph > 0)
@@ -99,6 +104,10 @@ public class AnnotationColourChooser
     threshold.addItem("Above Threshold");
     threshold.addItem("Below Threshold");
 
+    adjusting = false;
+
+    changeColour();
+
   }
 
   public AnnotationColourChooser()
@@ -181,10 +190,12 @@ public class AnnotationColourChooser
         thresholdValue_actionPerformed(e);
       }
     });
+    slider.setPaintLabels(false);
     slider.setPaintTicks(true);
     slider.setBackground(Color.white);
     slider.setEnabled(false);
     slider.setOpaque(false);
+    slider.setPreferredSize(new Dimension(150, 32));
     thresholdValue.setEnabled(false);
     thresholdValue.setColumns(10);
     jPanel3.setBackground(Color.white);
@@ -253,7 +264,7 @@ public class AnnotationColourChooser
   void changeColour()
   {
     // Check if combobox is still adjusting
-    if (threshold.getSelectedIndex() == -1)
+    if (adjusting)
       return;
 
     // We removed the non-graph annotations when filling the combobox
@@ -278,9 +289,11 @@ public class AnnotationColourChooser
     else if (threshold.getSelectedItem().equals("Below Threshold"))
       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 
+    slider.setEnabled(true);
+    thresholdValue.setEnabled(true);
+
     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
     {
-      currentAnnotation.threshold = null;
       slider.setEnabled(false);
       thresholdValue.setEnabled(false);
       thresholdValue.setText("");
@@ -293,6 +306,11 @@ public class AnnotationColourChooser
                                         currentAnnotation.graphMin) / 2f,
                                       "Threshold",
                                       Color.black));
+    }
+
+    if(aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+    {
+      adjusting = true;
       float range = currentAnnotation.graphMax * 1000 -
           currentAnnotation.graphMin * 1000;
 
@@ -304,6 +322,7 @@ public class AnnotationColourChooser
       slider.setMinorTickSpacing( (int) (range / 100f));
       slider.setEnabled(true);
       thresholdValue.setEnabled(true);
+      adjusting = false;
     }
 
     AnnotationColourGradient acg = null;
@@ -396,8 +415,6 @@ public class AnnotationColourChooser
 
   public void annotations_actionPerformed(ActionEvent e)
   {
-    if(currentAnnotation!=null)
-      currentAnnotation.threshold = null;
     changeColour();
   }
 
@@ -419,6 +436,12 @@ public class AnnotationColourChooser
 
   public void valueChanged()
   {
+    if (currentColours.isSelected()
+        && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+    {
+      changeColour();
+    }
+
     currentAnnotation.threshold.value = (float)slider.getValue()/1000f;
     ap.repaint();
   }
-- 
1.7.10.2