package jalview.renderer.seqfeatures;

import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertTrue;

import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.schemes.FeatureColour;

import java.awt.Color;
import java.util.Arrays;
import java.util.List;
import java.util.Map;

import org.testng.annotations.Test;

public class FeatureRendererTest
{

  @Test(groups = "Functional")
  public void testFindAllFeatures()
  {
    String seqData = ">s1\nabcdef\n>s2\nabcdef\n>s3\nabcdef\n>s4\nabcdef\n";
    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
            DataSourceType.PASTE);
    AlignViewportI av = af.getViewport();
    FeatureRenderer fr = new FeatureRenderer(av);

    /*
     * with no features
     */
    fr.findAllFeatures(true);
    assertTrue(fr.getRenderOrder().isEmpty());
    assertTrue(fr.getFeatureGroups().isEmpty());

    List<SequenceI> seqs = av.getAlignment().getSequences();

    // add a non-positional feature - should be ignored by FeatureRenderer
    SequenceFeature sf1 = new SequenceFeature("Type", "Desc", 0, 0, 1f,
            "Group");
    seqs.get(0).addSequenceFeature(sf1);
    fr.findAllFeatures(true);
    // ? bug - types and groups added for non-positional features
    List<String> types = fr.getRenderOrder();
    List<String> groups = fr.getFeatureGroups();
    assertEquals(types.size(), 0);
    assertFalse(types.contains("Type"));
    assertEquals(groups.size(), 0);
    assertFalse(groups.contains("Group"));

    // add some positional features
    seqs.get(1).addSequenceFeature(
            new SequenceFeature("Pfam", "Desc", 5, 9, 1f, "PfamGroup"));
    seqs.get(2).addSequenceFeature(
            new SequenceFeature("Pfam", "Desc", 14, 22, 2f, "RfamGroup"));
    // bug in findAllFeatures - group not checked for a known feature type
    seqs.get(2).addSequenceFeature(
            new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN,
                    "RfamGroup"));
    seqs.get(3).addSequenceFeature(
            new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN, null));
    // null value for type produces NullPointerException
    fr.findAllFeatures(true);
    types = fr.getRenderOrder();
    groups = fr.getFeatureGroups();
    assertEquals(types.size(), 2);
    assertFalse(types.contains("Type"));
    assertTrue(types.contains("Pfam"));
    assertTrue(types.contains("Rfam"));
    assertEquals(groups.size(), 2);
    assertFalse(groups.contains("Group"));
    assertTrue(groups.contains("PfamGroup"));
    assertTrue(groups.contains("RfamGroup"));
    assertFalse(groups.contains(null)); // null group is ignored

    /*
     * check min-max values
     */
    Map<String, float[][]> minMax = fr.getMinMax();
    assertEquals(minMax.size(), 1); // non-positional and NaN not stored
    assertEquals(minMax.get("Pfam")[0][0], 1f); // positional min
    assertEquals(minMax.get("Pfam")[0][1], 2f); // positional max

    // increase max for Pfam, add scores for Rfam
    seqs.get(0).addSequenceFeature(
            new SequenceFeature("Pfam", "Desc", 14, 22, 8f, "RfamGroup"));
    seqs.get(1).addSequenceFeature(
            new SequenceFeature("Rfam", "Desc", 5, 9, 6f, "RfamGroup"));
    fr.findAllFeatures(true);
    // note minMax is not a defensive copy, shouldn't expose this
    assertEquals(minMax.size(), 2);
    assertEquals(minMax.get("Pfam")[0][0], 1f);
    assertEquals(minMax.get("Pfam")[0][1], 8f);
    assertEquals(minMax.get("Rfam")[0][0], 6f);
    assertEquals(minMax.get("Rfam")[0][1], 6f);

    /*
     * check render order (last is on top)
     */
    List<String> renderOrder = fr.getRenderOrder();
    assertEquals(renderOrder, Arrays.asList("Rfam", "Pfam"));

    /*
     * change render order (todo: an easier way)
     * nb here last comes first in the data array
     */
    Object[][] data = new Object[2][];
    FeatureColourI colour = new FeatureColour(Color.RED);
    data[0] = new Object[] { "Rfam", colour, true };
    data[1] = new Object[] { "Pfam", colour, false };
    fr.setFeaturePriority(data);
    assertEquals(fr.getRenderOrder(), Arrays.asList("Pfam", "Rfam"));
    assertEquals(fr.getDisplayedFeatureTypes(), Arrays.asList("Rfam"));

    /*
     * add a new feature type: should go on top of render order as visible,
     * other feature ordering and visibility should be unchanged
     */
    seqs.get(2).addSequenceFeature(
            new SequenceFeature("Metal", "Desc", 14, 22, 8f, "MetalGroup"));
    fr.findAllFeatures(true);
    assertEquals(fr.getRenderOrder(),
            Arrays.asList("Pfam", "Rfam", "Metal"));
    assertEquals(fr.getDisplayedFeatureTypes(),
            Arrays.asList("Rfam", "Metal"));
  }
}