3 import static org.testng.Assert.assertEquals;
5 import jalview.datamodel.Sequence;
6 import jalview.datamodel.SequenceI;
8 import java.io.BufferedReader;
9 import java.io.FileReader;
10 import java.io.IOException;
12 import org.testng.annotations.Test;
14 public class HMMProbabilityDistributionAnalyserTest {
16 HMMProbabilityDistributionAnalyser analyser = new HMMProbabilityDistributionAnalyser();
19 public void testMoveToFile() throws IOException
22 BufferedReader br = new BufferedReader(new FileReader(
23 "test/utils/test_Fams_for_probability_analysis.txt"));
24 analyser.moveLocationBy(2, br);
26 String line = br.readLine();
27 assertEquals(line, "# STOCKHOLM 1.0");
29 assertEquals(line, "seq1 ATW");
31 assertEquals(line, "seq2 ATI");
36 public void testCountValidResidues()
38 SequenceI[] sequence = new Sequence[] {
39 new Sequence("seq1", "ATGWWSCF"), new Sequence("seq1", "GGWMMKI"),
40 new Sequence("seq1", "--.ATccc") };
41 analyser.sequences.add(sequence[0]);
42 analyser.sequences.add(sequence[1]);
43 analyser.sequences.add(sequence[2]);
45 int count = analyser.countValidResidues();
46 assertEquals(count, 17);