From d03971168d7f0192862cf5b57602ecf3e341b457 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 10 Feb 2006 16:05:27 +0000
Subject: [PATCH] Update overview if features updated

---
 src/jalview/gui/FeatureRenderer.java |    2 +-
 src/jalview/gui/FeatureSettings.java |   32 ++++++++++++++++++--------------
 src/jalview/gui/OverviewPanel.java   |    6 +++---
 3 files changed, 22 insertions(+), 18 deletions(-)

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 03080bd..3f332b5 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -62,7 +62,7 @@ public class FeatureRenderer
      * of the rendered sequence
      */
     BufferedImage bi;
-    public synchronized Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+    public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
     {
       if(!av.showSequenceFeatures)
         return initialCol;
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 7dae703..bbaaa5a 100755
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -136,22 +136,23 @@ public class FeatureSettings extends JPanel
     Enumeration e;
     SequenceFeature sf;
 
-    for(int i=0; i< av.alignment.getHeight(); i++)
-    {
-       features = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
-       if(features==null)
-         continue;
+  for (int i = 0; i < av.alignment.getHeight(); i++)
+  {
+    features = av.alignment.getSequenceAt(i).getDatasetSequence().
+        getSequenceFeatures();
+    if (features == null)
+      continue;
 
-       e = features.elements();
-       while(e.hasMoreElements())
-       {
-         sf = (SequenceFeature)e.nextElement();
-         if(!allFeatures.contains(sf.getType()))
-         {
-           allFeatures.addElement(sf.getType());
-         }
-       }
+    e = features.elements();
+    while (e.hasMoreElements())
+    {
+      sf = (SequenceFeature) e.nextElement();
+      if (!allFeatures.contains(sf.getType()))
+      {
+        allFeatures.addElement(sf.getType());
+      }
     }
+
     if(allFeatures.size()<1)
      {
        try{
@@ -333,6 +334,9 @@ public class FeatureSettings extends JPanel
   {
     fr.setFeaturePriority( data );
     ap.repaint();
+
+    if(ap.overviewPanel!=null)
+      ap.overviewPanel.updateOverviewImage();
   }
 
   int selectedRow =-1;
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index a35966d..e20084c 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -67,7 +67,6 @@ public class OverviewPanel extends JPanel implements Runnable
         sr.renderGaps( false );
         fr = new FeatureRenderer(av);
         fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;
-        fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;
 
         // scale the initial size of overviewpanel to shape of alignment
         float initialScale = (float) av.alignment.getWidth() / (float) av.alignment.getHeight();
@@ -287,8 +286,9 @@ public class OverviewPanel extends JPanel implements Runnable
                 av.alignment.getSequenceAt(lastrow), lastcol);
 
              if(av.showSequenceFeatures)
-                  color = fr.findFeatureColour(color,  av.alignment.getSequenceAt(lastrow),
-                                                       lastcol);
+                 color = fr.findFeatureColour(color,  av.alignment.getSequenceAt(lastrow),
+                                             lastcol);
+
             }
 
             miniMe.setRGB(col,row,color.getRGB());
-- 
1.7.10.2