test/jalview/io/AlignmentPropertiesTest.java

   1 package jalview.io;
   2
   3 import static org.testng.Assert.assertEquals;
   4
   5 import jalview.datamodel.Alignment;
   6 import jalview.datamodel.AlignmentI;
   7 import jalview.datamodel.Sequence;
   8 import jalview.datamodel.SequenceI;
   9
  10 import org.testng.annotations.Test;
  11
  12 public class AlignmentPropertiesTest
  13 {
  14   @Test(groups="Functional")
  15   public void testWriteProperties_asHtml()
  16   {
  17     SequenceI seq1 = new Sequence("Seq1", "--ABC-DEFGH-"); // 8 residues
  18     SequenceI seq2 = new Sequence("Seq2", "---BC-DE-KH-"); // 6
  19     SequenceI seq3 = new Sequence("Seq3", "-RABCFDE-KH-"); // 9
  20     AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
  21
  22     AlignmentProperties ap = new AlignmentProperties(al);
  23     StringBuilder sb = ap.writeProperties(true);
  24     String expected = "<table border=\"1\">"
  25             + "<tr><td>Sequences</td><td>3</td></tr>"
  26             + "<tr><td>Alignment width</td><td>12</td></tr>"
  27             + "<tr><td>Minimum Sequence Length</td><td>6</td></tr>"
  28             + "<tr><td>Maximum Sequence Length</td><td>9</td></tr>"
  29             + "<tr><td>Average Length</td><td>7</td></tr>"
  30             + "<tr><td>Minimum (sequence length / width)</td><td>50.0%</td></tr>" // 6/12
  31             + "<tr><td>Maximum (sequence length / width)</td><td>75.0%</td></tr>" // 9/12
  32             + "<tr><td>Residue density</td><td>63.9%</td></tr>" // 23/36
  33             + "<tr><td>Gap density</td><td>36.1%</td></tr>" + "</table>";
  34     assertEquals(sb.toString(), expected);
  35   }
  36 }