JAL-3013 resolve symlink to hmmer binaries folder

[jalview.git] / test / jalview / schemes / HmmerLocalBackgroundTest.java

diff --git a/test/jalview/schemes/HmmerLocalBackgroundTest.java b/test/jalview/schemes/HmmerLocalBackgroundTest.java
index 991adb5..5f2bb8f 100644 (file)
--- a/test/jalview/schemes/HmmerLocalBackgroundTest.java
+++ b/test/jalview/schemes/HmmerLocalBackgroundTest.java
@@ -33,9 +33,11 @@ public class HmmerLocalBackgroundTest {
      */
     SequenceI seq1 = new Sequence("seq1", "AAMMMKKKVV");
     SequenceI seq2 = new Sequence("seq2", "aAM-QKRSSSL");
-    AnnotatedCollectionI ac = new Alignment(new SequenceI[] { seq1, seq2 });
-    ColourSchemeI scheme = new HmmerLocalBackground(ac,
-            file.getHMM());
+    SequenceI hmmSeq = file.getSeqsAsArray()[0];
+    AnnotatedCollectionI ac = new Alignment(
+            new SequenceI[]
+            { hmmSeq, seq1, seq2 });
+    ColourSchemeI scheme = new HmmerLocalBackground(ac);
 
     /*
      * 'A' in column 1, node 2, match emission 2.77204