test/jalview/analysis/scoremodels/FeatureScoreModelTest.java

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