package jalview.analysis.scoremodels;

import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;

import org.testng.AssertJUnit;
import org.testng.annotations.Test;

public class FeatureScoreModelTest
{
  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";

  int[] sf1 = new int[]
  { 74, 74, 73, 73, 23, 23, -1, -1 };

  int[] sf2 = new int[]
  { -1, -1, 74, 75, -1, -1, 76, 77 };

  int[] sf3 = new int[]
  { -1, -1, -1, -1, -1, -1, 76, 77 };

  @Test(groups ={ "Functional" })
  public void testFeatureScoreModel() throws Exception
  {
    AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(alntestFile,
            FormatAdapter.PASTE);
    AlignmentI al = alf.getViewport().getAlignment();
    AssertJUnit.assertEquals(4, al.getHeight());
    AssertJUnit.assertEquals(5, al.getWidth());
    for (int i = 0; i < 4; i++)
    {
      SequenceI ds = al.getSequenceAt(i).getDatasetSequence();
      if (sf1[i * 2] > 0)
      {
        ds.addSequenceFeature(new SequenceFeature("sf1", "sf1", "sf1",
                sf1[i * 2], sf1[i * 2 + 1], "sf1"));
      }
      if (sf2[i * 2] > 0)
      {
        ds.addSequenceFeature(new SequenceFeature("sf2", "sf2", "sf2",
                sf2[i * 2], sf2[i * 2 + 1], "sf2"));
      }
      if (sf3[i * 2] > 0)
      {
        ds.addSequenceFeature(new SequenceFeature("sf3", "sf3", "sf3",
                sf3[i * 2], sf3[i * 2 + 1], "sf3"));
      }
    }
    alf.setShowSeqFeatures(true);
    alf.getFeatureRenderer().setVisible("sf1");
    alf.getFeatureRenderer().setVisible("sf2");
    alf.getFeatureRenderer().setVisible("sf3");
    alf.getFeatureRenderer().findAllFeatures(true);
    AssertJUnit.assertEquals("Number of feature types", 3, alf
            .getFeatureRenderer().getDisplayedFeatureTypes().length);
    AssertJUnit.assertTrue(alf.getCurrentView().areFeaturesDisplayed());
    FeatureScoreModel fsm = new FeatureScoreModel();
    AssertJUnit.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
            .getAlignPanel()));
    alf.selectAllSequenceMenuItem_actionPerformed(null);
    float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
            true));
    AssertJUnit.assertTrue("FER1_MESCR should be identical with RAPSA (2)",
            dm[0][2] == 0f);
    AssertJUnit.assertTrue(
            "FER1_MESCR should be further from SPIOL (1) than it is from RAPSA (2)",
            dm[0][1] > dm[0][2]);

  }
}