Merge branch 'JAL-972-dasobert-to-jdas' into JAL-972-jdas

[jalview.git] / src / jalview / gui / FeatureRenderer.java

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index db2ce7e..2db75bf 100755 (executable)
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -211,7 +211,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
    * This is used by the Molecule Viewer and Overview to get the accurate
    * colourof the rendered sequence
    */
-  public int findFeatureColour(int initialCol, SequenceI seq, int column)
+  public synchronized int findFeatureColour(int initialCol, SequenceI seq, int column)
   {
     if (!av.showSequenceFeatures)
     {
@@ -685,9 +685,10 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     {
       minmax = new Hashtable();
     }
-    for (int i = 0; i < av.alignment.getHeight(); i++)
+    AlignmentI alignment=av.getAlignment();
+    for (int i = 0; i < alignment.getHeight(); i++)
     {
-      SequenceFeature[] features = av.alignment.getSequenceAt(i)
+      SequenceFeature[] features = alignment.getSequenceAt(i)
               .getDatasetSequence().getSequenceFeatures();
 
       if (features == null)
@@ -1122,7 +1123,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
 
     panel = new JPanel();
     panel.add(new JLabel("Description: ", JLabel.RIGHT));
-    description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    description.setFont(JvSwingUtils.getTextAreaFont());
     description.setLineWrap(true);
     panel.add(new JScrollPane(description));