test/jalview/util/HMMProbabilityDistributionAnalyserTest.java

   1 package jalview.util;
   2
   3 import static org.testng.Assert.assertEquals;
   4
   5 import jalview.datamodel.Sequence;
   6 import jalview.datamodel.SequenceI;
   7
   8 import java.io.BufferedReader;
   9 import java.io.FileReader;
  10 import java.io.IOException;
  11
  12 import org.testng.annotations.Test;
  13
  14 public class HMMProbabilityDistributionAnalyserTest {
  15
  16   HMMProbabilityDistributionAnalyser analyser = new HMMProbabilityDistributionAnalyser();
  17
  18   @Test
  19   public void testMoveToFile() throws IOException
  20   {
  21
  22     BufferedReader br = new BufferedReader(new FileReader(
  23             "test/utils/test_Fams_for_probability_analysis.txt"));
  24     analyser.moveLocationBy(2, br);
  25
  26     String line = br.readLine();
  27     assertEquals(line, "# STOCKHOLM 1.0");
  28     line = br.readLine();
  29     assertEquals(line, "seq1 ATW");
  30     line = br.readLine();
  31     assertEquals(line, "seq2 ATI");
  32
  33   }
  34
  35   @Test
  36   public void testCountValidResidues()
  37   {
  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]);
  44
  45     int count = analyser.countValidResidues();
  46     assertEquals(count, 17);
  47   }
  48 }