Examples with Locus org.dash.valid.Locus used on opensource projects

Example 11 with Locus

use of org.dash.valid.Locus in project ImmunogeneticDataTools by nmdp-bioinformatics.

the class DisequilibriumElementComparatorTest method testBaseComparison.

@Test
public void testBaseComparison() {
    HashMap<Locus, List<String>> hlaElementMap = new HashMap<Locus, List<String>>();
    List<String> val = new ArrayList<String>();
    val.add("HLA-B*52:01");
    hlaElementMap.put(Locus.HLA_B, val);
    val = new ArrayList<String>();
    val.add("HLA-C*04:01");
    hlaElementMap.put(Locus.HLA_C, val);
    BaseDisequilibriumElement element1 = new BaseDisequilibriumElement(hlaElementMap, "1", "Some note");
    hlaElementMap = new HashMap<Locus, List<String>>();
    val = new ArrayList<String>();
    val.add("HLA-B*07:01");
    hlaElementMap.put(Locus.HLA_B, val);
    val = new ArrayList<String>();
    val.add("HLA-C*01:01");
    hlaElementMap.put(Locus.HLA_C, val);
    BaseDisequilibriumElement element2 = new BaseDisequilibriumElement(hlaElementMap, "2", "Another note");
    DisequilibriumElementComparator comparator = new DisequilibriumElementComparator();
    assertTrue(comparator.compare(new DetectedDisequilibriumElement(element1), new DetectedDisequilibriumElement(element2)) > 0);
}

Example 12 with Locus

use of org.dash.valid.Locus in project ImmunogeneticDataTools by nmdp-bioinformatics.

the class LinkageElementsMapTest method test.

@Test
public void test() {
    List<FrequencyByRace> frequenciesByRace = new ArrayList<FrequencyByRace>();
    FrequencyByRace freq = new FrequencyByRace(new Double(.2), "1", "AAFA");
    frequenciesByRace.add(freq);
    HashMap<Locus, List<String>> hlaElementMap = new HashMap<Locus, List<String>>();
    List<String> val = new ArrayList<String>();
    val.add("HLA-B*07:01");
    hlaElementMap.put(Locus.HLA_B, val);
    val = new ArrayList<String>();
    val.add("HLA-C*01:01");
    hlaElementMap.put(Locus.HLA_C, val);
    DisequilibriumElementByRace element1 = new DisequilibriumElementByRace(hlaElementMap, frequenciesByRace);
    frequenciesByRace = new ArrayList<FrequencyByRace>();
    freq = new FrequencyByRace(new Double(.3), "2", "CAU");
    frequenciesByRace.add(freq);
    freq = new FrequencyByRace(new Double(.4), "3", "API");
    frequenciesByRace.add(freq);
    hlaElementMap = new HashMap<Locus, List<String>>();
    val = new ArrayList<String>();
    val.add("HLA-B*52:01");
    hlaElementMap.put(Locus.HLA_B, val);
    val = new ArrayList<String>();
    val.add("HLA-C*04:01");
    hlaElementMap.put(Locus.HLA_C, val);
    DisequilibriumElementByRace element2 = new DisequilibriumElementByRace(hlaElementMap, frequenciesByRace);
    Set<DetectedDisequilibriumElement> set = new LinkageElementsSet(new DisequilibriumElementComparator());
    set.add(new DetectedDisequilibriumElement(element1));
    set.add(new DetectedDisequilibriumElement(element2));
    int idx = 0;
    for (DetectedDisequilibriumElement obj : set) {
        if (idx == 0) {
            assertTrue(obj.getDisequilibriumElement().equals(element2));
        } else {
            assertTrue(obj.getDisequilibriumElement().equals(element1));
        }
        idx++;
    }
}

Example 13 with Locus

use of org.dash.valid.Locus in project ImmunogeneticDataTools by nmdp-bioinformatics.

the class LinkageDisequilibriumGenotypeList method decomposeMug.

private void decomposeMug() {
    String locusVal = null;
    Locus locus = null;
    HashMap<String, Locus> locusMap = new HashMap<String, Locus>();
    List<GenotypeList> genotypeLists = mug.getGenotypeLists();
    for (GenotypeList gl : genotypeLists) {
        List<Genotype> genotypes = gl.getGenotypes();
        for (Genotype genotype : genotypes) {
            List<Haplotype> haplotypes = genotype.getHaplotypes();
            for (Haplotype haplotype : haplotypes) {
                List<AlleleList> alleleLists = haplotype.getAlleleLists();
                for (AlleleList alleleList : alleleLists) {
                    List<Allele> alleles = alleleList.getAlleles();
                    List<String> alleleStrings = new ArrayList<String>();
                    for (Allele allele : alleles) {
                        alleleStrings.add(allele.getGlstring());
                        locusVal = allele.getLocus().toString();
                    }
                    if (locusMap.containsKey(locusVal)) {
                        locus = locusMap.get(locusVal);
                    } else {
                        locus = Locus.normalizeLocus(Locus.lookup(locusVal));
                        locusMap.put(locusVal, locus);
                    }
                    setAlleles(locus, alleleStrings);
                }
            }
        }
    }
}

Example 14 with Locus

use of org.dash.valid.Locus in project ImmunogeneticDataTools by nmdp-bioinformatics.

the class LinkageDisequilibriumGenotypeList method getAlleles.

private List<?>[] getAlleles(Locus... loci) {
    List<?>[] allelesByLocus = new List[loci.length];
    int i = 0;
    for (Locus locus : loci) {
        allelesByLocus[i] = getAlleles(locus);
        i++;
    }
    return allelesByLocus;
}

Example 15 with Locus

use of org.dash.valid.Locus in project ImmunogeneticDataTools by nmdp-bioinformatics.

the class LinkageDisequilibriumGenotypeList method constructPossibleHaplotypes.

@SuppressWarnings("unchecked")
public Set<MultiLocusHaplotype> constructPossibleHaplotypes(Set<Locus> loci) {
    HashMap<Locus, SingleLocusHaplotype> singleLocusHaplotypes = new HashMap<Locus, SingleLocusHaplotype>();
    Set<MultiLocusHaplotype> possibleHaplotypes = new HashSet<MultiLocusHaplotype>();
    Locus[] locusArray = loci.toArray(new Locus[loci.size()]);
    List<?>[] allelesByLocus = (List<?>[]) getAlleles(locusArray);
    List<List<Object>> haplotypeCombinations = cartesianProduct(allelesByLocus);
    String[] alleleParts;
    Locus locus;
    HashMap<String, Locus> locusMap = new HashMap<String, Locus>();
    for (List<Object> haplotypeCombo : haplotypeCombinations) {
        boolean drb345Homozygous = false;
        for (Object haplotypePart : haplotypeCombo) {
            List<String> alleles = (List<String>) haplotypePart;
            alleleParts = alleles.iterator().next().split(GLStringUtilities.ESCAPED_ASTERISK);
            if (locusMap.containsKey(alleleParts[0])) {
                locus = locusMap.get(alleleParts[0]);
            } else {
                locus = Locus.normalizeLocus(Locus.lookup(alleleParts[0]));
                locusMap.put(alleleParts[0], locus);
            }
            if (Locus.HLA_DRB345.equals(locus) && hasHomozygous(locus)) {
                drb345Homozygous = true;
            }
            singleLocusHaplotypes.put(locus, new SingleLocusHaplotype(locus, (List<String>) haplotypePart, getHaplotypeIndex(locus, (List<String>) haplotypePart)));
        }
        possibleHaplotypes.add(new MultiLocusHaplotype(singleLocusHaplotypes, drb345Homozygous));
    }
    return possibleHaplotypes;
}