package jalview.analysis;

import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNotSame;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;

import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.MapList;
import jalview.ws.SequenceFetcher;
import jalview.ws.SequenceFetcherFactory;

import java.util.List;

import org.testng.annotations.Test;

public class CrossRefsTest
{

  /**
   * Test for finding 'product' sequences for the case where the selected
   * sequence has a dbref with a mapping to a sequence
   */
  @Test(groups = { "Functional" })
  public void testFindXrefSequences_fromDbRefMap()
  {
    /*
     * two peptide sequences each with a DBRef and SequenceFeature
     */
    SequenceI pep1 = new Sequence("Q9ZTS2", "MALFQRSV");
    pep1.addDBRef(new DBRefEntry("Pfam", "0", "PF00111"));
    pep1.addSequenceFeature(new SequenceFeature("type", "desc", 12, 14, 1f,
            "group"));
    SequenceI pep2 = new Sequence("P30419", "MTRRSQIF");
    pep2.addDBRef(new DBRefEntry("PDB", "0", "3JTK"));
    pep2.addSequenceFeature(new SequenceFeature("type2", "desc2", 13, 15,
            12f, "group2"));
  
    /*
     * nucleotide sequence (to go in the alignment)
     */
    SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
  
    /*
     * add DBRefEntry's to dna1 with mappings from dna to both peptides
     */
    MapList mapList = new MapList(new int[] { 1, 24 }, new int[] { 1, 3 },
            3, 1);
    Mapping map = new Mapping(pep1, mapList);
    DBRefEntry dbRef1 = new DBRefEntry("UNIPROT", "0", "Q9ZTS2", map);
    dna1.addDBRef(dbRef1);
    mapList = new MapList(new int[] { 1, 24 }, new int[] { 1, 3 }, 3, 1);
    map = new Mapping(pep2, mapList);
    DBRefEntry dbRef2 = new DBRefEntry("UNIPROT", "0", "P30419", map);
    dna1.addDBRef(dbRef2);
  
    /*
     * find UNIPROT xrefs for nucleotide sequence - it should pick up 
     * mapped sequences
     */
    AlignmentI al = new Alignment(new SequenceI[] { dna1 });
    AlignmentI xrefs = CrossRefs.findXrefSequences(
            new SequenceI[] { dna1 },
            true, "UNIPROT", al);
    assertEquals(2, xrefs.getHeight());
  
    /*
     * cross-refs alignment holds copies of the mapped sequences
     * including copies of their dbrefs and features
     */
    checkCopySequence(pep1, xrefs.getSequenceAt(0));
    checkCopySequence(pep2, xrefs.getSequenceAt(1));
  }

  /**
   * Test for finding 'product' sequences for the case where only an indirect
   * xref is found - not on the peptide sequence but on a nucleotide sequence in
   * the alignment which which it shares a protein dbref
   */
  @Test(groups = { "Functional" })
  public void testFindXrefSequences_indirectDbrefToNucleotide()
  {
    /*
     * Alignment setup:
     *   - peptide    dbref  UNIPROT|Q9ZTS2
     *   - nucleotide dbref  EMBL|AF039662, UNIPROT|Q9ZTS2
     */
    SequenceI uniprotSeq = new Sequence("Q9ZTS2", "MASVSATMISTS");
    uniprotSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
    SequenceI emblSeq = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
    emblSeq.addDBRef(new DBRefEntry("EMBL", "0", "AF039662"));
    emblSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
  
    /*
     * Find EMBL xrefs for peptide 
     * - it has no EMBL dbref of its own
     * - but nucleotide with matching peptide dbref does, so is returned
     */
    AlignmentI al = new Alignment(new SequenceI[] { emblSeq, uniprotSeq });
    AlignmentI xrefs = CrossRefs.findXrefSequences(
            new SequenceI[] { uniprotSeq }, false, "EMBL", al);
    assertEquals(1, xrefs.getHeight());
    assertSame(emblSeq, xrefs.getSequenceAt(0));
  }

  /**
   * Test for finding 'product' sequences for the case where only an indirect
   * xref is found - not on the nucleotide sequence but on a peptide sequence in
   * the alignment which which it shares a nucleotide dbref
   */
  @Test(groups = { "Functional" })
  public void testFindXrefSequences_indirectDbrefToProtein()
  {
    /*
     * Alignment setup:
     *   - nucleotide dbref  EMBL|AF039662
     *   - peptide    dbrefs EMBL|AF039662, UNIPROT|Q9ZTS2
     */
    SequenceI emblSeq = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
    emblSeq.addDBRef(new DBRefEntry("EMBL", "0", "AF039662"));
    SequenceI uniprotSeq = new Sequence("Q9ZTS2", "MASVSATMISTS");
    uniprotSeq.addDBRef(new DBRefEntry("EMBL", "0", "AF039662"));
    uniprotSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
  
    /*
     * Find UNIPROT xrefs for nucleotide 
     * - it has no UNIPROT dbref of its own
     * - but peptide with matching nucleotide dbref does, so is returned
     */
    AlignmentI al = new Alignment(new SequenceI[] { emblSeq, uniprotSeq });
    AlignmentI xrefs = CrossRefs.findXrefSequences(
            new SequenceI[] { emblSeq }, true, "UNIPROT", al);
    assertEquals(1, xrefs.getHeight());
    assertSame(uniprotSeq, xrefs.getSequenceAt(0));
  }

  /**
   * Test for finding 'product' sequences for the case where the selected
   * sequence has no dbref to the desired source, and there are no indirect
   * references via another sequence in the alignment
   */
  @Test(groups = { "Functional" })
  public void testFindXrefSequences_noDbrefs()
  {
    /*
     * two nucleotide sequences, one with UNIPROT dbref
     */
    SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
    dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
    SequenceI dna2 = new Sequence("AJ307031", "AAACCCTTT");
  
    /*
     * find UNIPROT xrefs for peptide sequence - it has no direct
     * dbrefs, and the other sequence (which has a UNIPROT dbref) is not 
     * equatable to it, so no results found
     */
    AlignmentI al = new Alignment(new SequenceI[] { dna1, dna2 });
    AlignmentI xrefs = CrossRefs.findXrefSequences(
            new SequenceI[] { dna2 },
            true, "UNIPROT", al);
    assertNull(xrefs);
  }

  /**
   * Test for finding 'product' sequences for the case where the selected
   * sequence has a dbref with no mapping, triggering a fetch from database
   */
  @Test(groups = { "Functional" })
  public void testFindXrefSequences_withFetch()
  {
    SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
    dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
    dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "P30419"));
    dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314"));
    final SequenceI pep1 = new Sequence("Q9ZTS2", "MYQLIRSSW");
    final SequenceI pep2 = new Sequence("P00314", "MRKLLAASG");
  
    SequenceFetcher mockFetcher = new SequenceFetcher()
    {
  
      @Override
      public boolean isFetchable(String source)
      {
        return true;
      }
  
      @Override
      public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)
      {
        return new SequenceI[] { pep1, pep2 };
      }
    };
    SequenceFetcherFactory.setSequenceFetcher(mockFetcher);
  
    /*
     * find UNIPROT xrefs for nucleotide sequence
     */
    AlignmentI al = new Alignment(new SequenceI[] { dna1 });
    AlignmentI xrefs = CrossRefs.findXrefSequences(
            new SequenceI[] { dna1 },
            true, "UNIPROT", al);
    assertEquals(2, xrefs.getHeight());
    assertSame(pep1, xrefs.getSequenceAt(0));
    assertSame(pep2, xrefs.getSequenceAt(1));
  }

  /**
   * Helper method to assert seq1 looks like a copy of seq2
   * 
   * @param seq1
   * @param seq2
   */
  private void checkCopySequence(SequenceI seq1, SequenceI seq2)
  {
    assertNotSame(seq1, seq2);
    assertEquals(seq1.getName(), seq2.getName());
    assertEquals(seq1.getStart(), seq2.getStart());
    assertEquals(seq1.getEnd(), seq2.getEnd());
    assertEquals(seq1.getSequenceAsString(), seq2.getSequenceAsString());
  
    /*
     * compare dbrefs
     */
    assertArrayEquals(seq1.getDBRefs(), seq2.getDBRefs());
    // check one to verify a copy, not the same object
    if (seq1.getDBRefs().length > 0)
    {
      assertNotSame(seq1.getDBRefs()[0], seq2.getDBRefs()[0]);
    }
  
    /*
     * compare features
     */
    assertArrayEquals(seq1.getSequenceFeatures(),
            seq2.getSequenceFeatures());
    if (seq1.getSequenceFeatures().length > 0)
    {
      assertNotSame(seq1.getSequenceFeatures()[0],
              seq2.getSequenceFeatures()[0]);
    }
  }

  /**
   * Test for finding 'product' sequences for the case where the selected
   * sequence has two dbrefs with no mapping, triggering a fetch from database.
   * 
   * @see http://issues.jalview.org/browse/JAL-2029
   */
  @Test(groups = { "Functional" })
  public void testFindXrefSequences_withFetchMultipleRefs()
  {
    /*
     * EMBL|X07547 has a 
     */
    SequenceI dna1 = new Sequence("X07547", "GGGGCAGCACAAGAAC");
    dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "B0BCM4"));
    dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "P0CE20"));
    final SequenceI pep1 = new Sequence("B0BCM4", "MGKGIL");
    final SequenceI pep2 = new Sequence("P0CE20", "MGKGIL");
  
    SequenceFetcher mockFetcher = new SequenceFetcher()
    {
      int call = 0;

      @Override
      public boolean isFetchable(String source)
      {
        return true;
      }
      @Override
      public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)
      {
        // pending Mockito with its thenReturn(pep1).thenReturn(pep2) syntax!
        return new SequenceI[] { call++ == 0 ? pep1 : pep2 };
      }
    };
    SequenceFetcherFactory.setSequenceFetcher(mockFetcher);
  
    /*
     * find UNIPROT xrefs for nucleotide sequence
     */
    AlignmentI al = new Alignment(new SequenceI[] { dna1 });
    AlignmentI xrefs = CrossRefs.findXrefSequences(
            new SequenceI[] { dna1 },
            true, "UNIPROT", al);
    assertEquals(2, xrefs.getHeight());
    assertSame(pep1, xrefs.getSequenceAt(0));
    assertSame(pep2, xrefs.getSequenceAt(1));
  }

}