package jalview.datamodel;

import static org.testng.Assert.assertEquals;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import org.testng.annotations.Test;

import jalview.util.MapList;

public class MappedFeaturesTest
{
  @Test(groups = "Functional")
  public void testFindProteinVariants()
  {
    /*
     * scenario: 
     * dna/10-20 aCGTaGctGAa (codons CGT=R, GGA = G)
     * mapping: 3:1 from [11-13,15,18-19] to peptide/1-2 RG 
     */
    SequenceI from = new Sequence("dna/10-20", "aCGTaGctGAa");
    SequenceI to = new Sequence("peptide", "RG");
    MapList map = new MapList(new int[] { 11, 13, 15, 15, 18, 19 },
            new int[]
            { 1, 2 }, 3, 1);
    Mapping mapping = new Mapping(to, map);

    /*
     * variants
     * C>T at dna11, consequence CGT>TGT=C
     * T>C at dna13, consequence CGT>CGC synonymous
     */
    List<SequenceFeature> features = new ArrayList<>();
    SequenceFeature sf1 = new SequenceFeature("sequence_variant", "C,T",
            11, 11, null);
    sf1.setValue("alleles", "C,T");
    features.add(sf1);
    SequenceFeature sf2 = new SequenceFeature("sequence_variant", "T,C", 13,
            13, null);
    sf2.setValue("alleles", "T,C");
    features.add(sf2);

    /*
     * missense variant in first codon
     */
    MappedFeatures mf = new MappedFeatures(mapping, from, 1, 'R',
            features);
    String variant = mf.findProteinVariants(sf1);
    assertEquals(variant, "p.Arg1Cys");

    /*
     * more than one alternative allele
     * C>G consequence is GGT=G
     * peptide variants as a comma-separated list
     */
    sf1.setValue("alleles", "C,T,G");
    variant = mf.findProteinVariants(sf1);
    assertEquals(variant, "p.Arg1Cys,p.Arg1Gly");

    /*
     * synonymous variant in first codon
     * shown in HGVS notation on peptide
     */
    variant = mf.findProteinVariants(sf2);
    assertEquals(variant, "c.13T>C(p.=)");

    /*
     * CSQ:HGVSp value is used if present 
     * _and_ it contains "p." following a colon
     */
    Map<String, String> csq = new HashMap<>();
    csq.put("HGVSp", "hello:world");
    sf2.setValue("CSQ", csq);
    variant = mf.findProteinVariants(sf2);
    assertEquals(variant, "c.13T>C(p.=)");
    csq.put("HGVSp", "p.HelloWorld");
    variant = mf.findProteinVariants(sf2);
    assertEquals(variant, "c.13T>C(p.=)");
    csq.put("HGVSp", "try this:hellop.world");
    variant = mf.findProteinVariants(sf2);
    assertEquals(variant, "hellop.world");

    /*
     * missense and indel variants in second codon
     * - codon is GGA spliced from dna positions 15,18,19
     * - SNP G>T in second position mutates GGA>G to GTA>V
     * - indel variants are not computed or reported
     */
    mf = new MappedFeatures(mapping, from, 2, 'G', features);
    features.clear();
    SequenceFeature sf3 = new SequenceFeature("sequence_variant",
            "G,-,CG,T", 18, 18, null);
    sf3.setValue("alleles", "G,-,CG,T");
    features.add(sf3);
    variant = mf.findProteinVariants(sf3);
    assertEquals(variant, "p.Gly2Val");

    /*
     * G>T in first position gives TGA Stop
     * shown with HGVS notation as 'Ter'
     */
    SequenceFeature sf4 = new SequenceFeature("sequence_variant", "G,T", 15,
            15, null);
    sf4.setValue("alleles", "G,-,CG,T");
    features.add(sf4);
    variant = mf.findProteinVariants(sf4);
    assertEquals(variant, "p.Gly2Ter");

    /*
     * feature must be one of those in MappedFeatures
     */
    SequenceFeature sf9 = new SequenceFeature("sequence_variant", "G,C", 15,
            15, null);
    variant = mf.findProteinVariants(sf9);
    assertEquals(variant, "");
  }

  @Test(groups = "Functional")
  public void testGetMappedPositions()
  {
    // CDS including stop codon taa
    SequenceI cds = new Sequence("cds/10-21", "ATGcgtGGAtaa");
    SequenceI peptide = new Sequence("peptide", "MRG"); // ATG, CGT, GGA
    
    /*
     * emulate 'map from' range based on CDS _including_ stop codon
     */
    MapList map = new MapList(new int[] { 10, 21 }, new int[] { 1, 3 }, 3,
            1);
    Mapping mapping = new Mapping(peptide, map);

    MappedFeatures mf = new MappedFeatures(mapping, cds, 2, 'M', null);
    
    /*
     * scenario: sequence_variant feature on CDS at position 14;
     * find the corresponding position on peptide
     */
    int[] pepPos = mf.getMappedPositions(14,  14);
    assertEquals(pepPos[0], 2);
    assertEquals(pepPos[1], 2);
    
    /*
     * scenario: CDS feature on CDS including stop codon;
     */
    pepPos = mf.getMappedPositions(10, 21);
    assertEquals(pepPos[0], 1);
    assertEquals(pepPos[1], 3);
    
    /*
     * scenario: exon feature on CDS extending beyond start and stop codons
     */
    pepPos = mf.getMappedPositions(2, 222);
    assertEquals(pepPos[0], 1);
    assertEquals(pepPos[1], 3);
    
    /*
     * now with the mapping from protein to CDS
     */
    mapping = new Mapping(cds, map.getInverse());
    mf = new MappedFeatures(mapping, peptide, 15, 't', null);
    int[] cdsPos = mf.getMappedPositions(2,  2);
    assertEquals(cdsPos[0], 13);
    assertEquals(cdsPos[1], 15);
  }
}