X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fschemes%2FHmmerGlobalBackgroundTest.java;h=1cdee9198da64601086c72eeb2ade159b41223ef;hb=2db272981f2778cc64df63bab6893c8347e120f8;hp=b417482499f79da54912879d2ea77fe6b867ba91;hpb=4a1114e5c20bb42ec0bf9fb2a85b54c85ca6c40e;p=jalview.git

diff --git a/test/jalview/schemes/HmmerGlobalBackgroundTest.java b/test/jalview/schemes/HmmerGlobalBackgroundTest.java
index b417482..1cdee91 100644
--- a/test/jalview/schemes/HmmerGlobalBackgroundTest.java
+++ b/test/jalview/schemes/HmmerGlobalBackgroundTest.java
@@ -2,6 +2,9 @@ package jalview.schemes;
 
 import static org.testng.Assert.assertEquals;
 
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.HMMFile;
 
@@ -19,7 +22,9 @@ public class HmmerGlobalBackgroundTest {
     HMMFile file = new HMMFile("test/jalview/io/test_PKinase_hmm.txt",
             DataSourceType.FILE);
 
-    ColourSchemeI scheme = new HmmerGlobalBackground(file.getHMM());
+    SequenceI hmmSeq = file.getSeqsAsArray()[0];
+    AlignmentI al = new Alignment(new SequenceI[] { hmmSeq });
+    ColourSchemeI scheme = new HmmerGlobalBackground(al);
 
     /*
      * 'A' in column 1, node 2, match emission 2.77204