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JAL-3070 JAL-3066 provide standard concrete instances for instantaneous analysis...
[jalview.git]
/
test
/
jalview
/
schemes
/
HmmerGlobalBackgroundTest.java
diff --git
a/test/jalview/schemes/HmmerGlobalBackgroundTest.java
b/test/jalview/schemes/HmmerGlobalBackgroundTest.java
index
b417482
..
1cdee91
100644
(file)
--- 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 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;
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);
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
/*
* 'A' in column 1, node 2, match emission 2.77204