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