X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=0b6f8d8fcc6fc033605ccb70526889940e511958;hb=6fc9aca27f606f6e3a0121597896e1a5dae35c36;hp=49e835de3420d933ef681eb44592c9465041c521;hpb=09003bd97d75ad14cd000fc581d6ec93b7a08bcb;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 49e835d..0b6f8d8 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)
   {
@@ -48,7 +49,8 @@ public class AnnotationColourChooser
       for (int g = 0; g < allGroups.size(); g++)
       {
         sg = (SequenceGroup) allGroups.get(g);
-        oldgroupColours.put(sg, sg.cs);
+        if(sg.cs!=null)
+          oldgroupColours.put(sg, sg.cs);
       }
     }
     this.av = av;
@@ -56,7 +58,7 @@ 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 +71,11 @@ 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 +94,7 @@ 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 +105,10 @@ public class AnnotationColourChooser
     threshold.addItem("Above Threshold");
     threshold.addItem("Below Threshold");
 
+    adjusting = false;
+
+    changeColour();
+
   }
 
   public AnnotationColourChooser()
@@ -181,10 +191,12 @@ 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 +265,7 @@ 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 +290,11 @@ 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 +307,11 @@ public class AnnotationColourChooser
                                         currentAnnotation.graphMin) / 2f,
                                       "Threshold",
                                       Color.black));
+    }
+
+    if(aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+    {
+      adjusting = true;
       float range = currentAnnotation.graphMax * 1000 -
           currentAnnotation.graphMin * 1000;
 
@@ -301,9 +320,9 @@ public class AnnotationColourChooser
       slider.setValue( (int) (currentAnnotation.threshold.value * 1000));
       thresholdValue.setText(currentAnnotation.threshold.value + "");
       slider.setMajorTickSpacing( (int) (range / 10f));
-      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();
   }