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

Example 16 with Locus

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

the class LinkageDisequilibriumGenotypeListTest method testHaplotypePairs.

@Test
public void testHaplotypePairs() throws IOException {
    LinkageDisequilibriumGenotypeList genotypeList = new LinkageDisequilibriumGenotypeList("HaplotypePairs", TEST_BC_PAIRS);
    Set<Locus> loci = new HashSet<Locus>();
    loci.add(Locus.HLA_B);
    loci.add(Locus.HLA_C);
    Set<MultiLocusHaplotype> possibleHaplotypes = genotypeList.constructPossibleHaplotypes(loci);
    Set<HaplotypePair> linkedPairs = new HaplotypePairSet(new HaplotypePairComparator());
    for (Haplotype haplotype1 : possibleHaplotypes) {
        for (Haplotype haplotype2 : possibleHaplotypes) {
            if ((!genotypeList.hasHomozygous(Locus.HLA_B) && haplotype1.getAlleles(Locus.HLA_B).containsAll(haplotype2.getAlleles(Locus.HLA_B))) || (!genotypeList.hasHomozygous(Locus.HLA_C) && haplotype1.getAlleles(Locus.HLA_C).containsAll(haplotype2.getAlleles(Locus.HLA_C)))) {
                continue;
            }
            HaplotypePair haplotypePair = new HaplotypePair(haplotype1, haplotype2);
            linkedPairs.add(haplotypePair);
        }
    }
    for (HaplotypePair pair : linkedPairs) {
        Haplotype haplotype1 = pair.getHaplotypes().get(0);
        assertTrue(haplotype1 instanceof MultiLocusHaplotype);
        Haplotype haplotype2 = pair.getHaplotypes().get(1);
        assertTrue(haplotype2 instanceof MultiLocusHaplotype);
        assertTrue((haplotype1.getAlleles(Locus.HLA_B).contains(B0704) && haplotype2.getAlleles(Locus.HLA_B).contains(B4403)) || (haplotype1.getAlleles(Locus.HLA_B).contains(B4403) && haplotype2.getAlleles(Locus.HLA_B).contains(B0704)));
        assertTrue((haplotype1.getAlleles(Locus.HLA_C).contains(C0702) && haplotype2.getAlleles(Locus.HLA_C).contains(C1203)) || (haplotype1.getAlleles(Locus.HLA_C).contains(C1203) && haplotype2.getAlleles(Locus.HLA_C).contains(C0702)));
        assertFalse(haplotype1.getAlleles(Locus.HLA_B).contains(B0704) && haplotype2.getAlleles(Locus.HLA_B).contains(B0704));
        assertFalse(haplotype1.getAlleles(Locus.HLA_B).contains(B4403) && haplotype2.getAlleles(Locus.HLA_B).contains(B4403));
        assertFalse(haplotype1.getAlleles(Locus.HLA_C).contains(C0702) && haplotype2.getAlleles(Locus.HLA_C).contains(C0702));
        assertFalse(haplotype1.getAlleles(Locus.HLA_C).contains(C1203) && haplotype2.getAlleles(Locus.HLA_C).contains(C1203));
    }
}

Example 17 with Locus

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

the class HaplotypePairWriter method formatDetectedLinkages.

public static String formatDetectedLinkages(DetectedLinkageFindings findings) {
    StringBuffer sb = new StringBuffer("Id: " + findings.getGLId() + GLStringConstants.NEWLINE + "GL String: " + findings.getGLString());
    sb.append(GLStringConstants.NEWLINE + GLStringConstants.NEWLINE + "HLA DB Version: " + findings.getHladb() + GLStringConstants.NEWLINE);
    sb.append(GLStringConstants.NEWLINE + "Frequencies:  " + findings.getFrequencies() + GLStringConstants.NEWLINE);
    for (EnumSet<Locus> findingSought : findings.getFindingsSought()) {
        if (findings.hasLinkedPairs(findingSought) && findings.getFirstPair(findingSought) != null) {
            sb.append(GLStringConstants.NEWLINE + "First " + findingSought + " Haplotype pair:" + GLStringConstants.NEWLINE + findings.getFirstPair(findingSought));
        } else {
            sb.append(GLStringConstants.NEWLINE + "WARNING - No " + findingSought + " haplotype pairs detected." + GLStringConstants.NEWLINE);
        }
    }
    for (HaplotypePair pair : findings.getLinkedPairs()) {
        if (findings.getFirstPairs().contains(pair)) {
            continue;
        } else {
            sb.append(GLStringConstants.NEWLINE + "Possible " + pair.getLoci() + " Haplotype Pair:" + GLStringConstants.NEWLINE);
        }
        sb.append(pair);
    }
    sb.append(GLStringConstants.NEWLINE + "***************************************" + GLStringConstants.NEWLINE);
    return sb.toString();
}

Example 18 with Locus

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

the class MultiLocusHaplotype method getHaplotypeString.

@Override
public String getHaplotypeString() {
    StringBuffer sb = new StringBuffer();
    Set<Locus> keySet = getAlleleMap().keySet();
    Set<Locus> loci = new LocusSet(new LocusComparator());
    loci.addAll(keySet);
    if (this.linkage != null) {
        for (Locus locus : loci) {
            // TODO:  Make less clumsy to get rid of brackets?
            if (linkage.getDisequilibriumElement().getHlaElement(locus).size() == 1) {
                sb.append(linkage.getDisequilibriumElement().getHlaElement(locus).get(0));
            } else {
                sb.append(linkage.getDisequilibriumElement().getHlaElement(locus));
            }
            sb.append(GLStringConstants.GENE_PHASE_DELIMITER);
        }
    } else {
        for (Locus locus : loci) {
            sb.append(getAlleles(locus));
            sb.append(GLStringConstants.GENE_DELIMITER);
        }
    }
    return sb.substring(0, sb.length() - 1);
}