test/jalview/analysis/scoremodels/FeatureScoreModelTest.java

   1 package jalview.analysis.scoremodels;
   2
   3 import org.testng.annotations.Test;
   4 import org.testng.AssertJUnit;
   5 import jalview.datamodel.AlignmentI;
   6 import jalview.datamodel.SequenceFeature;
   7 import jalview.datamodel.SequenceI;
   8 import jalview.gui.AlignFrame;
   9 import jalview.io.FileLoader;
  10 import jalview.io.FormatAdapter;
  11
  12 public class FeatureScoreModelTest
  13 {
  14   public static String alntestFile = "FER1_MESCR/72-76 DVYIL\nFER1_SPIOL/71-75 DVYIL\nFER3_RAPSA/21-25 DVYVL\nFER1_MAIZE/73-77 DVYIL\n";
  15
  16   int[] sf1 = new int[]
  17   { 74, 74, 73, 73, 23, 23, -1, -1 };
  18
  19   int[] sf2 = new int[]
  20   { -1, -1, 74, 75, -1, -1, 76, 77 };
  21
  22   int[] sf3 = new int[]
  23   { -1, -1, -1, -1, -1, -1, 76, 77 };
  24
  25   @Test
  26   public void testFeatureScoreModel() throws Exception
  27   {
  28     AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(alntestFile,
  29             FormatAdapter.PASTE);
  30     AlignmentI al = alf.getViewport().getAlignment();
  31     AssertJUnit.assertEquals(4, al.getHeight());
  32     AssertJUnit.assertEquals(5, al.getWidth());
  33     for (int i = 0; i < 4; i++)
  34     {
  35       SequenceI ds = al.getSequenceAt(i).getDatasetSequence();
  36       if (sf1[i * 2] > 0)
  37       {
  38         ds.addSequenceFeature(new SequenceFeature("sf1", "sf1", "sf1",
  39                 sf1[i * 2], sf1[i * 2 + 1], "sf1"));
  40       }
  41       if (sf2[i * 2] > 0)
  42       {
  43         ds.addSequenceFeature(new SequenceFeature("sf2", "sf2", "sf2",
  44                 sf2[i * 2], sf2[i * 2 + 1], "sf2"));
  45       }
  46       if (sf3[i * 2] > 0)
  47       {
  48         ds.addSequenceFeature(new SequenceFeature("sf3", "sf3", "sf3",
  49                 sf3[i * 2], sf3[i * 2 + 1], "sf3"));
  50       }
  51     }
  52     alf.setShowSeqFeatures(true);
  53     alf.getFeatureRenderer().setVisible("sf1");
  54     alf.getFeatureRenderer().setVisible("sf2");
  55     alf.getFeatureRenderer().setVisible("sf3");
  56     alf.getFeatureRenderer().findAllFeatures(true);
  57     AssertJUnit.assertEquals("Number of feature types", 3, alf
  58             .getFeatureRenderer().getDisplayedFeatureTypes().length);
  59     AssertJUnit.assertTrue(alf.getCurrentView().areFeaturesDisplayed());
  60     FeatureScoreModel fsm = new FeatureScoreModel();
  61     AssertJUnit.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
  62             .getAlignPanel()));
  63     alf.selectAllSequenceMenuItem_actionPerformed(null);
  64     float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
  65             true));
  66     AssertJUnit.assertTrue("FER1_MESCR should be identical with RAPSA (2)",
  67             dm[0][2] == 0f);
  68     AssertJUnit.assertTrue(
  69             "FER1_MESCR should be further from SPIOL (1) than it is from RAPSA (2)",
  70             dm[0][1] > dm[0][2]);
  71
  72   }
  73 }