JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / schemes / TCoffeeColourScheme.java

diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index 48c52f1..2be51c2 100644 (file)
--- a/src/jalview/schemes/TCoffeeColourScheme.java
+++ b/src/jalview/schemes/TCoffeeColourScheme.java
@@ -20,7 +20,6 @@
  */
 package jalview.schemes;
 
-import jalview.analysis.SequenceIdMatcher;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
@@ -33,7 +32,6 @@ import java.awt.Color;
 import java.util.ArrayList;
 import java.util.IdentityHashMap;
 import java.util.Map;
-import java.util.TreeMap;
 
 /**
  * Defines the color score for T-Coffee MSA
@@ -47,8 +45,7 @@ import java.util.TreeMap;
 public class TCoffeeColourScheme extends ResidueColourScheme
 {
 
-  static final Color[] colors =
-  { new Color(102, 102, 255), // #6666FF
+  static final Color[] colors = { new Color(102, 102, 255), // #6666FF
       new Color(0, 255, 0), // #00FF00
       new Color(102, 255, 0), // #66FF00
       new Color(204, 255, 0), // #CCFF00
@@ -89,6 +86,10 @@ public class TCoffeeColourScheme extends ResidueColourScheme
     seqMap = new IdentityHashMap<SequenceI, Color[]>();
     AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
             : alignment.getContext();
+    if (alcontext == null)
+    {
+      return;
+    }
     int w = 0;
     for (AlignmentAnnotation al : alcontext
             .findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))