From 5aae79c31ad27e418e887151f27819516b725ace Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 21 Jun 2013 15:08:37 +0100
Subject: [PATCH] JAL-1326 JAL-1327 update all graphline thresholds with flag
 for interactive or final adjustment event

---
 src/jalview/gui/AnnotationColourChooser.java |   49 +++++++++++++++++++++++---
 1 file changed, 45 insertions(+), 4 deletions(-)

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 599cf0b..96bf602 100755
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -47,6 +47,10 @@ public class AnnotationColourChooser extends JPanel
   jalview.datamodel.AlignmentAnnotation currentAnnotation;
 
   boolean adjusting = false;
+  /**
+   * enabled if the user is dragging the slider - try to keep updates to a minimun
+   */
+  boolean sliderDragging = false;
 
   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
   {
@@ -76,14 +80,32 @@ public class AnnotationColourChooser extends JPanel
         if (!adjusting)
         {
           thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
-          valueChanged();
+          valueChanged(!sliderDragging);
         }
       }
     });
     slider.addMouseListener(new MouseAdapter()
     {
+      @Override
+      public void mousePressed(MouseEvent e)
+      {
+        sliderDragging=true;
+        super.mousePressed(e);
+      }
+
+      @Override
+      public void mouseDragged(MouseEvent e)
+      {
+        sliderDragging=true;
+        super.mouseDragged(e);
+      }
       public void mouseReleased(MouseEvent evt)
       {
+        if (sliderDragging)
+        {
+          sliderDragging=false;
+          valueChanged(true);
+        }
         ap.paintAlignment(true);
       }
     });
@@ -193,7 +215,6 @@ public class AnnotationColourChooser extends JPanel
     System.arraycopy(anmap, 0, annmap, 0, annmap.length);
     return list;
   }
-
   private void setDefaultMinMax()
   {
     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
@@ -632,18 +653,38 @@ public class AnnotationColourChooser extends JPanel
     }
   }
 
-  public void valueChanged()
+  public void valueChanged(boolean updateAllAnnotation)
   {
     if (currentColours.isSelected()
             && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
     {
       changeColour();
     }
-
     currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
+    propagateSeqAssociatedThreshold(updateAllAnnotation);
     ap.paintAlignment(false);
   }
 
+  private void propagateSeqAssociatedThreshold(boolean allAnnotation)
+  {
+    if (currentAnnotation.sequenceRef == null
+            || currentAnnotation.threshold == null)
+    {
+      return;
+    }
+    // TODO: only update visible annotation thresholds if allAnnotation is false, since we only need to provide a quick visual indicator
+
+    float thr = currentAnnotation.threshold.value;
+    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    {
+      AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
+      if (aa.label.equals(currentAnnotation.label))
+      {
+        aa.threshold.value = thr;
+      }
+    }
+  }
+
   public void currentColours_actionPerformed(ActionEvent e)
   {
     if (currentColours.isSelected())
-- 
1.7.10.2