X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;fp=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=fa06d94c2836e0369c6ed507ef6cf9a7494a2ec8;hb=42f65528bd74e645fe66664007669f2d083b8eee;hp=fcd952b0bebe9d898d0048a2cc2f649078c6ff32;hpb=72dbda1ebc7b6fe0ffbb486a3c3fb973a73483e7;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index fcd952b..fa06d94 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -36,10 +36,7 @@ import java.awt.image.*;
 public class FeatureRenderer
 {
     AlignViewport av;
-    SequenceGroup currentSequenceGroup = null;
-    SequenceGroup[] allGroups = null;
     Color resBoxColour;
-    Graphics graphics;
     float transparency = 1.0f;
     FontMetrics fm;
     int charOffset;
@@ -47,7 +44,7 @@ public class FeatureRenderer
 
     // The following vector holds the features which are
     // to be added, in the correct order or rendering
-    Vector featuresDisplayed;
+    Vector featuresDisplayed = null;
 
     /**
      * Creates a new FeatureRenderer object.
@@ -65,17 +62,17 @@ public class FeatureRenderer
      * of the rendered sequence
      */
     BufferedImage bi;
-    public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+    public synchronized Color findFeatureColour(Color initialCol, SequenceI seq, int i)
     {
       if(!av.showSequenceFeatures)
         return initialCol;
 
-      if(bi==null)
-        bi = new BufferedImage(1,1,BufferedImage.TYPE_INT_RGB);
+      if (bi == null)
+        bi = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB);
+
+      bi.setRGB(0,0, initialCol.getRGB());
 
       drawText = false;
-      bi.getGraphics().setColor(initialCol);
-      bi.getGraphics().fillRect(0, 0, 1, 1);
       drawSequence(bi.getGraphics(), seq, i, i, 0, 0, 1, 1);
       drawText = true;
 
@@ -100,6 +97,7 @@ public class FeatureRenderer
                              int start, int end, int x1, int y1, int width, int height)
     {
 
+//System.out.println(start+" "+end+" "+x1+" "+y1);
       if (seq.getDatasetSequence().getSequenceFeatures() == null
           || seq.getDatasetSequence().getSequenceFeatures().size()==0)
         return;
@@ -260,7 +258,7 @@ public class FeatureRenderer
       // The feature table will display high priority
       // features at the top, but theses are the ones
       // we need to render last, so invert the data
-      featuresDisplayed = new Vector();
+      featuresDisplayed.clear();
       for(int i=data.length-1; i>-1; i--)
       {
        String type = data[i][0].toString();