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;
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