package jalview.datamodel.xdb.embl;

import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;

import jalview.analysis.SequenceIdMatcher;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
import jalview.util.MapList;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

import org.testng.annotations.Test;

public class EmblEntryTest
{
  @Test(groups = "Functional")
  public void testGetCdsRanges()
  {
    EmblEntry testee = new EmblEntry();

    /*
     * Make a (CDS) Feature with 5 locations
     */
    EmblFeature cds = new EmblFeature();
    cds.setLocation("join(10..20,complement(30..40),50..60,70..80,complement(110..120))");

    int[] exons = testee.getCdsRanges(cds);
    assertEquals("[10, 20, 40, 30, 50, 60, 70, 80, 120, 110]",
            Arrays.toString(exons));
  }

  @Test(groups = "Functional")
  public void testParseCodingFeature()
  {
    // not the whole sequence but enough for this test...
    List<SequenceI> peptides = new ArrayList<SequenceI>();
    SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
    EmblFile ef = EmblTestHelper.getEmblFile();
    assertEquals(1, ef.getEntries().size());
    EmblEntry testee = ef.getEntries().get(0);
    String sourceDb = "EMBL";
    SequenceI dna = testee.makeSequence(sourceDb);

    /*
     * parse three CDS features, with two/one/no Uniprot cross-refs
     */
    for (EmblFeature feature : ef.getEntries().get(0).getFeatures())
    {
      if ("CDS".equals(feature.getName()))
      {
        testee.parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
      }
    }

    /*
     * peptides should now have five entries:
     * EMBL product and two Uniprot accessions for the first CDS / translation
     * EMBL product and one Uniprot accession for the second CDS / "
     * EMBL product only for the third
     */
    assertEquals(6, peptides.size());
    assertEquals("CAA30420.1", peptides.get(0).getName());
    assertEquals("MLCF", peptides.get(0).getSequenceAsString());
    assertEquals("UNIPROT|B0BCM4", peptides.get(1).getName());
    assertEquals("MLCF", peptides.get(1).getSequenceAsString());
    assertEquals("UNIPROT|P0CE20", peptides.get(2).getName());
    assertEquals("MLCF", peptides.get(2).getSequenceAsString());
    assertEquals("CAA30421.1", peptides.get(3).getName());
    assertEquals("MSSS", peptides.get(3).getSequenceAsString());
    assertEquals("UNIPROT|B0BCM3", peptides.get(4).getName());
    assertEquals("MSSS", peptides.get(4).getSequenceAsString());
    assertEquals("CAA12345.6", peptides.get(5).getName());
    assertEquals("MSS", peptides.get(5).getSequenceAsString());

    /*
     * verify dna sequence has dbrefs with CDS mappings to the peptide 'products'
     */
    MapList cds1Map = new MapList(new int[] { 57, 46 }, new int[] { 1, 4 },
            3, 1);
    MapList cds2Map = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 },
            3, 1);
    MapList cds3Map = new MapList(new int[] { 4, 6, 10, 15 }, new int[] {
        1, 3 }, 3, 1);
    DBRefEntry[] dbrefs = dna.getDBRefs();
    assertEquals(4, dbrefs.length);
    DBRefEntry dbRefEntry = dbrefs[0];
    assertEquals("UNIPROT", dbRefEntry.getSource());
    assertEquals("B0BCM4", dbRefEntry.getAccessionId());
    assertSame(peptides.get(1), dbRefEntry.getMap().getTo());
    assertEquals(cds1Map, dbRefEntry.getMap().getMap());

    dbRefEntry = dbrefs[1];
    assertEquals("UNIPROT", dbRefEntry.getSource());
    assertEquals("P0CE20", dbRefEntry.getAccessionId());
    assertSame(peptides.get(2), dbRefEntry.getMap().getTo());
    assertEquals(cds1Map, dbRefEntry.getMap().getMap());

    dbRefEntry = dbrefs[2];
    assertEquals("UNIPROT", dbRefEntry.getSource());
    assertEquals("B0BCM3", dbRefEntry.getAccessionId());
    assertSame(peptides.get(4), dbRefEntry.getMap().getTo());
    assertEquals(cds2Map, dbRefEntry.getMap().getMap());

    dbRefEntry = dbrefs[3];
    assertEquals("EMBLCDSPROTEIN", dbRefEntry.getSource());
    assertEquals("CAA12345.6", dbRefEntry.getAccessionId());
    assertSame(peptides.get(5), dbRefEntry.getMap().getTo());
    assertEquals(cds3Map, dbRefEntry.getMap().getMap());

    /*
     * verify peptides have dbrefs
     * - to EMBL sequence (with inverse 1:3 cds mapping)
     * - to EMBLCDS (with 1:3 mapping)
     * - direct (no mapping) to other protein accessions
     */
    MapList proteinToCdsMap1 = new MapList(new int[] { 1, 4 }, new int[] {
        1, 12 }, 1, 3);
    MapList proteinToCdsMap2 = new MapList(new int[] { 1, 3 }, new int[] {
        1, 9 }, 1, 3);

    // dbrefs for first CDS EMBL product CAA30420.1
    dbrefs = peptides.get(0).getDBRefs();
    assertEquals(5, dbrefs.length);
    assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
    assertEquals("CAA30420.1", dbrefs[0].getAccessionId());
    assertEquals(cds1Map.getInverse(), dbrefs[0].getMap().getMap());
    assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
    assertEquals("CAA30420.1", dbrefs[1].getAccessionId());
    assertEquals(proteinToCdsMap1, dbrefs[1].getMap().getMap());
    assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
    assertEquals("CAA30420.1", dbrefs[2].getAccessionId());
    assertNull(dbrefs[2].getMap());
    assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
            dbrefs[3]);
    assertNull(dbrefs[3].getMap());
    assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
            dbrefs[4]);
    assertNull(dbrefs[4].getMap());

    // dbrefs for first CDS first Uniprot xref
    dbrefs = peptides.get(1).getDBRefs();
    assertEquals(2, dbrefs.length);
    assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
            dbrefs[0]);
    assertNull(dbrefs[0].getMap());
    assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
    assertEquals("X07547", dbrefs[1].getAccessionId());
    assertEquals(cds1Map.getInverse(), dbrefs[1].getMap().getMap());

    // dbrefs for first CDS second Uniprot xref
    dbrefs = peptides.get(2).getDBRefs();
    assertEquals(2, dbrefs.length);
    assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
            dbrefs[0]);
    assertNull(dbrefs[0].getMap());
    assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
    assertEquals("X07547", dbrefs[1].getAccessionId());
    assertEquals(cds1Map.getInverse(), dbrefs[1].getMap().getMap());

    // dbrefs for second CDS EMBL product CAA30421.1
    dbrefs = peptides.get(3).getDBRefs();
    assertEquals(4, dbrefs.length);
    assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
    assertEquals("CAA30421.1", dbrefs[0].getAccessionId());
    assertEquals(cds2Map.getInverse(), dbrefs[0].getMap().getMap());
    assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
    assertEquals("CAA30421.1", dbrefs[1].getAccessionId());
    assertEquals(proteinToCdsMap1, dbrefs[1].getMap().getMap());
    assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
    assertEquals("CAA30421.1", dbrefs[2].getAccessionId());
    assertNull(dbrefs[2].getMap());
    assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
            dbrefs[3]);
    assertNull(dbrefs[3].getMap());

    // dbrefs for second CDS second Uniprot xref
    dbrefs = peptides.get(4).getDBRefs();
    assertEquals(2, dbrefs.length);
    assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
            dbrefs[0]);
    assertNull(dbrefs[0].getMap());
    assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
    assertEquals("X07547", dbrefs[1].getAccessionId());
    assertEquals(cds2Map.getInverse(), dbrefs[1].getMap().getMap());

    // dbrefs for third CDS inferred EMBL product CAA12345.6
    dbrefs = peptides.get(5).getDBRefs();
    assertEquals(3, dbrefs.length);
    assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
    assertEquals("CAA12345.6", dbrefs[0].getAccessionId());
    assertEquals(cds3Map.getInverse(), dbrefs[0].getMap().getMap());
    assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
    assertEquals("CAA12345.6", dbrefs[1].getAccessionId());
    assertEquals(proteinToCdsMap2, dbrefs[1].getMap().getMap());
    assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
    assertEquals("CAA12345.6", dbrefs[2].getAccessionId());
    assertNull(dbrefs[2].getMap());
  }

  @Test(groups = "Functional")
  public void testAdjustForProteinLength()
  {
    int[] exons = new int[] { 11, 15, 21, 25, 31, 38 }; // 18 bp

    // exact length match:
    assertSame(exons, EmblEntry.adjustForProteinLength(6, exons));

    // match if we assume exons include stop codon not in protein:
    assertSame(exons, EmblEntry.adjustForProteinLength(5, exons));

    // truncate last exon by 6bp
    int[] truncated = EmblEntry.adjustForProteinLength(4, exons);
    assertEquals("[11, 15, 21, 25, 31, 32]",
            Arrays.toString(truncated));

    // remove last exon and truncate preceding by 1bp
    truncated = EmblEntry.adjustForProteinLength(3, exons);
    assertEquals("[11, 15, 21, 24]", Arrays.toString(truncated));

    // exact removal of exon case:
    exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
    truncated = EmblEntry.adjustForProteinLength(4, exons);
    assertEquals("[11, 15, 21, 27]", Arrays.toString(truncated));

    // what if exons are too short for protein?
    truncated = EmblEntry.adjustForProteinLength(7, exons);
    assertSame(exons, truncated);
  }
}