package jalview.datamodel.features;

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

import jalview.datamodel.SequenceFeature;

import java.util.List;
import java.util.Set;

import org.testng.annotations.Test;

public class SequenceFeaturesTest
{
  @Test(groups = "Functional")
  public void testGetPositionalFeatures()
  {
    SequenceFeatures store = new SequenceFeatures();
    SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
            Float.NaN, null);
    store.add(sf1);
    // same range, different description
    SequenceFeature sf2 = new SequenceFeature("Metal", "desc2", 10, 20,
            Float.NaN, null);
    store.add(sf2);
    // discontiguous range
    SequenceFeature sf3 = new SequenceFeature("Metal", "desc", 30, 40,
            Float.NaN, null);
    store.add(sf3);
    // overlapping range
    SequenceFeature sf4 = new SequenceFeature("Metal", "desc", 15, 35,
            Float.NaN, null);
    store.add(sf4);
    // enclosing range
    SequenceFeature sf5 = new SequenceFeature("Metal", "desc", 5, 50,
            Float.NaN, null);
    store.add(sf5);
    // non-positional feature
    SequenceFeature sf6 = new SequenceFeature("Metal", "desc", 0, 0,
            Float.NaN, null);
    store.add(sf6);
    // contact feature
    SequenceFeature sf7 = new SequenceFeature("Disulphide bond", "desc",
            18, 45, Float.NaN, null);
    store.add(sf7);
    // different feature type
    SequenceFeature sf8 = new SequenceFeature("Pfam", "desc", 30, 40,
            Float.NaN, null);
    store.add(sf8);
    SequenceFeature sf9 = new SequenceFeature("Pfam", "desc", 15, 35,
            Float.NaN, null);
    store.add(sf9);

    /*
     * get all positional features
     */
    List<SequenceFeature> features = store.getPositionalFeatures();
    assertEquals(features.size(), 8);
    assertTrue(features.contains(sf1));
    assertTrue(features.contains(sf2));
    assertTrue(features.contains(sf3));
    assertTrue(features.contains(sf4));
    assertTrue(features.contains(sf5));
    assertFalse(features.contains(sf6)); // non-positional
    assertTrue(features.contains(sf7));
    assertTrue(features.contains(sf8));
    assertTrue(features.contains(sf9));

    /*
     * get features by type
     */
    assertTrue(store.getPositionalFeatures((String) null).isEmpty());
    assertTrue(store.getPositionalFeatures("Cath").isEmpty());
    assertTrue(store.getPositionalFeatures("METAL").isEmpty());

    features = store.getPositionalFeatures("Metal");
    assertEquals(features.size(), 5);
    assertTrue(features.contains(sf1));
    assertTrue(features.contains(sf2));
    assertTrue(features.contains(sf3));
    assertTrue(features.contains(sf4));
    assertTrue(features.contains(sf5));
    assertFalse(features.contains(sf6));

    features = store.getPositionalFeatures("Disulphide bond");
    assertEquals(features.size(), 1);
    assertTrue(features.contains(sf7));

    features = store.getPositionalFeatures("Pfam");
    assertEquals(features.size(), 2);
    assertTrue(features.contains(sf8));
    assertTrue(features.contains(sf9));
  }

  @Test(groups = "Functional")
  public void testGetContactFeatures()
  {
    SequenceFeatures store = new SequenceFeatures();
    // non-contact
    SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
            Float.NaN, null);
    store.add(sf1);
    // non-positional
    SequenceFeature sf2 = new SequenceFeature("Metal", "desc", 0, 0,
            Float.NaN, null);
    store.add(sf2);
    // contact feature
    SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc",
            18, 45, Float.NaN, null);
    store.add(sf3);
    // repeat for different feature type
    SequenceFeature sf4 = new SequenceFeature("Pfam", "desc", 10, 20,
            Float.NaN, null);
    store.add(sf4);
    SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 0, 0,
            Float.NaN, null);
    store.add(sf5);
    SequenceFeature sf6 = new SequenceFeature("Disulfide bond", "desc", 18,
            45, Float.NaN, null);
    store.add(sf6);
  
    /*
     * get all contact features
     */
    List<SequenceFeature> features = store.getContactFeatures();
    assertEquals(features.size(), 2);
    assertTrue(features.contains(sf3));
    assertTrue(features.contains(sf6));
  
    /*
     * get contact features by type
     */
    assertTrue(store.getContactFeatures((String) null).isEmpty());
    assertTrue(store.getContactFeatures("Cath").isEmpty());
    assertTrue(store.getContactFeatures("Pfam").isEmpty());
    assertTrue(store.getContactFeatures("DISULPHIDE BOND").isEmpty());
  
    features = store.getContactFeatures("Disulphide bond");
    assertEquals(features.size(), 1);
    assertTrue(features.contains(sf3));
  
    features = store.getContactFeatures("Disulfide bond");
    assertEquals(features.size(), 1);
    assertTrue(features.contains(sf6));
  }

  @Test(groups = "Functional")
  public void testGetNonPositionalFeatures()
  {
    SequenceFeatures store = new SequenceFeatures();
    // positional
    SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
            Float.NaN, null);
    store.add(sf1);
    // non-positional
    SequenceFeature sf2 = new SequenceFeature("Metal", "desc", 0, 0,
            Float.NaN, null);
    store.add(sf2);
    // contact feature
    SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc",
            18, 45, Float.NaN, null);
    store.add(sf3);
    // repeat for different feature type
    SequenceFeature sf4 = new SequenceFeature("Pfam", "desc", 10, 20,
            Float.NaN, null);
    store.add(sf4);
    SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 0, 0,
            Float.NaN, null);
    store.add(sf5);
    SequenceFeature sf6 = new SequenceFeature("Disulfide bond", "desc", 18,
            45, Float.NaN, null);
    store.add(sf6);
    // one more non-positional, different description
    SequenceFeature sf7 = new SequenceFeature("Pfam", "desc2", 0, 0,
            Float.NaN, null);
    store.add(sf7);
  
    /*
     * get all non-positional features
     */
    List<SequenceFeature> features = store.getNonPositionalFeatures();
    assertEquals(features.size(), 3);
    assertTrue(features.contains(sf2));
    assertTrue(features.contains(sf5));
    assertTrue(features.contains(sf7));
  
    /*
     * get non-positional features by type
     */
    assertTrue(store.getNonPositionalFeatures((String) null).isEmpty());
    assertTrue(store.getNonPositionalFeatures("Cath").isEmpty());
    assertTrue(store.getNonPositionalFeatures("PFAM").isEmpty());
  
    features = store.getNonPositionalFeatures("Metal");
    assertEquals(features.size(), 1);
    assertTrue(features.contains(sf2));
  
    features = store.getNonPositionalFeatures("Pfam");
    assertEquals(features.size(), 2);
    assertTrue(features.contains(sf5));
    assertTrue(features.contains(sf7));
  }

  /**
   * Helper method to add a feature of no particular type
   * 
   * @param sf
   * @param type
   * @param from
   * @param to
   * @return
   */
  SequenceFeature addFeature(SequenceFeatures sf, String type, int from,
          int to)
  {
    SequenceFeature sf1 = new SequenceFeature(type, "", from, to,
            Float.NaN,
            null);
    sf.add(sf1);
    return sf1;
  }

  @Test(groups = "Functional")
  public void testFindFeatures()
  {
    SequenceFeatures sf = new SequenceFeatures();
    SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
    SequenceFeature sf2 = addFeature(sf, "Pfam", 1, 15);
    SequenceFeature sf3 = addFeature(sf, "Pfam", 20, 30);
    SequenceFeature sf4 = addFeature(sf, "Pfam", 40, 100);
    SequenceFeature sf5 = addFeature(sf, "Pfam", 60, 100);
    SequenceFeature sf6 = addFeature(sf, "Pfam", 70, 70);
    SequenceFeature sf7 = addFeature(sf, "Cath", 10, 50);
    SequenceFeature sf8 = addFeature(sf, "Cath", 1, 15);
    SequenceFeature sf9 = addFeature(sf, "Cath", 20, 30);
    SequenceFeature sf10 = addFeature(sf, "Cath", 40, 100);
    SequenceFeature sf11 = addFeature(sf, "Cath", 60, 100);
    SequenceFeature sf12 = addFeature(sf, "Cath", 70, 70);
    // null type is weird but possible:
    SequenceFeature sf13 = addFeature(sf, null, 5, 12);
  
    List<SequenceFeature> overlaps = sf.findFeatures(200, 200, "Pfam");
    assertTrue(overlaps.isEmpty());
  
    overlaps = sf.findFeatures( 1, 9, "Pfam");
    assertEquals(overlaps.size(), 1);
    assertTrue(overlaps.contains(sf2));
  
    overlaps = sf.findFeatures( 5, 18, "Pfam");
    assertEquals(overlaps.size(), 2);
    assertTrue(overlaps.contains(sf1));
    assertTrue(overlaps.contains(sf2));
  
    overlaps = sf.findFeatures(30, 40, "Pfam");
    assertEquals(overlaps.size(), 3);
    assertTrue(overlaps.contains(sf1));
    assertTrue(overlaps.contains(sf3));
    assertTrue(overlaps.contains(sf4));
  
    overlaps = sf.findFeatures( 80, 90, "Pfam");
    assertEquals(overlaps.size(), 2);
    assertTrue(overlaps.contains(sf4));
    assertTrue(overlaps.contains(sf5));
  
    overlaps = sf.findFeatures( 68, 70, "Pfam");
    assertEquals(overlaps.size(), 3);
    assertTrue(overlaps.contains(sf4));
    assertTrue(overlaps.contains(sf5));
    assertTrue(overlaps.contains(sf6));

    overlaps = sf.findFeatures(16, 69, "Cath");
    assertEquals(overlaps.size(), 4);
    assertTrue(overlaps.contains(sf7));
    assertFalse(overlaps.contains(sf8));
    assertTrue(overlaps.contains(sf9));
    assertTrue(overlaps.contains(sf10));
    assertTrue(overlaps.contains(sf11));
    assertFalse(overlaps.contains(sf12));

    assertTrue(sf.findFeatures(0, 1000, "Metal").isEmpty());

    overlaps = sf.findFeatures(7, 7, (String) null);
    assertEquals(overlaps.size(), 1);
    assertTrue(overlaps.contains(sf13));
  }

  @Test(groups = "Functional")
  public void testDelete()
  {
    SequenceFeatures sf = new SequenceFeatures();
    SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
    assertTrue(sf.getPositionalFeatures().contains(sf1));

    assertFalse(sf.delete(null));
    SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 15, 0f, null);
    assertFalse(sf.delete(sf2)); // not added, can't delete it
    assertTrue(sf.delete(sf1));
    assertTrue(sf.getPositionalFeatures().isEmpty());
  }

  @Test(groups = "Functional")
  public void testHasFeatures()
  {
    SequenceFeatures sf = new SequenceFeatures();
    assertFalse(sf.hasFeatures());

    SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
    assertTrue(sf.hasFeatures());

    sf.delete(sf1);
    assertFalse(sf.hasFeatures());
  }

  /**
   * Tests for the method that gets feature groups for positional or
   * non-positional features
   */
  @Test(groups = "Functional")
  public void testGetFeatureGroups()
  {
    SequenceFeatures sf = new SequenceFeatures();
    assertTrue(sf.getFeatureGroups(true).isEmpty());
    assertTrue(sf.getFeatureGroups(false).isEmpty());

    /*
     * add a non-positional feature (begin/end = 0/0)
     */
    SequenceFeature sfx = new SequenceFeature("AType", "Desc", 0, 0, 0f,
            "AGroup");
    sf.add(sfx);
    Set<String> groups = sf.getFeatureGroups(true); // for positional
    assertTrue(groups.isEmpty());
    groups = sf.getFeatureGroups(false); // for non-positional
    assertEquals(groups.size(), 1);
    assertTrue(groups.contains("AGroup"));

    /*
     * add, then delete, more non-positional features of different types
     */
    SequenceFeature sfy = new SequenceFeature("AnotherType", "Desc", 0, 0,
            0f,
            "AnotherGroup");
    sf.add(sfy);
    SequenceFeature sfz = new SequenceFeature("AThirdType", "Desc", 0, 0,
            0f,
            null);
    sf.add(sfz);
    groups = sf.getFeatureGroups(false);
    assertEquals(groups.size(), 3);
    assertTrue(groups.contains("AGroup"));
    assertTrue(groups.contains("AnotherGroup"));
    assertTrue(groups.contains(null)); // null is a possible group
    sf.delete(sfz);
    sf.delete(sfy);
    groups = sf.getFeatureGroups(false);
    assertEquals(groups.size(), 1);
    assertTrue(groups.contains("AGroup"));

    /*
     * add positional features
     */
    SequenceFeature sf1 = new SequenceFeature("Pfam", "Desc", 10, 50, 0f,
            "PfamGroup");
    sf.add(sf1);
    groups = sf.getFeatureGroups(true);
    assertEquals(groups.size(), 1);
    assertTrue(groups.contains("PfamGroup"));
    groups = sf.getFeatureGroups(false); // non-positional unchanged
    assertEquals(groups.size(), 1);
    assertTrue(groups.contains("AGroup"));

    SequenceFeature sf2 = new SequenceFeature("Cath", "Desc", 10, 50, 0f,
            null);
    sf.add(sf2);
    groups = sf.getFeatureGroups(true);
    assertEquals(groups.size(), 2);
    assertTrue(groups.contains("PfamGroup"));
    assertTrue(groups.contains(null));

    sf.delete(sf1);
    sf.delete(sf2);
    assertTrue(sf.getFeatureGroups(true).isEmpty());

    SequenceFeature sf3 = new SequenceFeature("CDS", "", 10, 50, 0f,
            "Ensembl");
    sf.add(sf3);
    SequenceFeature sf4 = new SequenceFeature("exon", "", 10, 50, 0f,
            "Ensembl");
    sf.add(sf4);
    groups = sf.getFeatureGroups(true);
    assertEquals(groups.size(), 1);
    assertTrue(groups.contains("Ensembl"));

    /*
     * delete last Ensembl group feature from CDS features
     * but still have one in exon features
     */
    sf.delete(sf3);
    groups = sf.getFeatureGroups(true);
    assertEquals(groups.size(), 1);
    assertTrue(groups.contains("Ensembl"));

    /*
     * delete the last non-positional feature
     */
    sf.delete(sfx);
    groups = sf.getFeatureGroups(false);
    assertTrue(groups.isEmpty());
  }

  @Test(groups = "Functional")
  public void testGetFeatureTypesForGroups()
  {
    SequenceFeatures sf = new SequenceFeatures();
    assertTrue(sf.getFeatureTypesForGroups(true, (String) null).isEmpty());
  
    /*
     * add feature with group = "Uniprot", type = "helix"
     */
    String groupUniprot = "Uniprot";
    SequenceFeature sf1 = new SequenceFeature("helix", "Desc", 10, 50, 0f,
            groupUniprot);
    sf.add(sf1);
    Set<String> groups = sf.getFeatureTypesForGroups(true, groupUniprot);
    assertEquals(groups.size(), 1);
    assertTrue(groups.contains("helix"));
    assertTrue(sf.getFeatureTypesForGroups(true, (String) null).isEmpty());
  
    /*
     * add feature with group = "Uniprot", type = "strand"
     */
    SequenceFeature sf2 = new SequenceFeature("strand", "Desc", 10, 50, 0f,
            groupUniprot);
    sf.add(sf2);
    groups = sf.getFeatureTypesForGroups(true, groupUniprot);
    assertEquals(groups.size(), 2);
    assertTrue(groups.contains("helix"));
    assertTrue(groups.contains("strand"));

    /*
     * delete the "strand" Uniprot feature - still have "helix"
     */
    sf.delete(sf2);
    groups = sf.getFeatureTypesForGroups(true, groupUniprot);
    assertEquals(groups.size(), 1);
    assertTrue(groups.contains("helix"));

    /*
     * delete the "helix" Uniprot feature - none left
     */
    sf.delete(sf1);
    assertTrue(sf.getFeatureTypesForGroups(true, groupUniprot).isEmpty());

    /*
     * add some null group features
     */
    SequenceFeature sf3 = new SequenceFeature("strand", "Desc", 10, 50, 0f,
            null);
    sf.add(sf3);
    SequenceFeature sf4 = new SequenceFeature("turn", "Desc", 10, 50, 0f,
            null);
    sf.add(sf4);
    groups = sf.getFeatureTypesForGroups(true, (String) null);
    assertEquals(groups.size(), 2);
    assertTrue(groups.contains("strand"));
    assertTrue(groups.contains("turn"));

    /*
     * add strand/Cath  and turn/Scop and query for one or both groups
     * (find feature types for groups selected in Feature Settings)
     */
    SequenceFeature sf5 = new SequenceFeature("strand", "Desc", 10, 50, 0f,
            "Cath");
    sf.add(sf5);
    SequenceFeature sf6 = new SequenceFeature("turn", "Desc", 10, 50, 0f,
            "Scop");
    sf.add(sf6);
    groups = sf.getFeatureTypesForGroups(true, "Cath");
    assertEquals(groups.size(), 1);
    assertTrue(groups.contains("strand"));
    groups = sf.getFeatureTypesForGroups(true, "Scop");
    assertEquals(groups.size(), 1);
    assertTrue(groups.contains("turn"));
    groups = sf.getFeatureTypesForGroups(true, "Cath", "Scop");
    assertEquals(groups.size(), 2);
    assertTrue(groups.contains("turn"));
    assertTrue(groups.contains("strand"));
    // alternative vararg syntax
    groups = sf.getFeatureTypesForGroups(true, new String[] { "Cath",
        "Scop" });
    assertEquals(groups.size(), 2);
    assertTrue(groups.contains("turn"));
    assertTrue(groups.contains("strand"));
  }
}