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

Example 1 with Locus

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

the class LinkageDisequilibriumGenotypeList method parseGLString.

private void parseGLString() {
    HashMap<String, Locus> locusMap = new HashMap<String, Locus>();
    Locus locus = null;
    List<String> genes = GLStringUtilities.parse(glString, GLStringConstants.GENE_DELIMITER);
    for (String gene : genes) {
        String[] splitString = gene.split(GLStringUtilities.ESCAPED_ASTERISK);
        String locusVal = splitString[0];
        List<String> genotypeAmbiguities = GLStringUtilities.parse(gene, GLStringConstants.GENOTYPE_AMBIGUITY_DELIMITER);
        for (String genotypeAmbiguity : genotypeAmbiguities) {
            List<String> geneCopies = GLStringUtilities.parse(genotypeAmbiguity, GLStringConstants.GENE_COPY_DELIMITER);
            for (String geneCopy : geneCopies) {
                List<String> genePhases = GLStringUtilities.parse(geneCopy, GLStringConstants.GENE_PHASE_DELIMITER);
                for (String genePhase : genePhases) {
                    List<String> alleleAmbiguities = GLStringUtilities.parse(genePhase, GLStringConstants.ALLELE_AMBIGUITY_DELIMITER);
                    if (locusMap.containsKey(locusVal)) {
                        locus = locusMap.get(locusVal);
                    } else {
                        locus = Locus.normalizeLocus(Locus.lookup(locusVal));
                        locusMap.put(locusVal, locus);
                    }
                    setAlleles(locus, alleleAmbiguities);
                }
            }
        }
    }
}

Example 2 with Locus

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

the class DetectedLinkageFindings method setLinkedPairs.

public void setLinkedPairs(Set<HaplotypePair> linkedPairs) {
    EnumSet<Locus> loci = null;
    if (linkedPairs.iterator().hasNext() && linkedPairs.iterator().next().isByRace()) {
        HashMap<Set<Locus>, HashMap<String, Double>> raceTotalFreqsMap = new HashMap<Set<Locus>, HashMap<String, Double>>();
        Set<HaplotypePair> noRaceOverlapPairs = new HashSet<HaplotypePair>();
        RelativeFrequencyByRace relativeRaceFreq;
        String race;
        Double totalFreq;
        for (HaplotypePair pair : linkedPairs) {
            loci = Locus.lookup(pair.getLoci());
            if (pair.getPrimaryFrequency() == null) {
                noRaceOverlapPairs.add(pair);
                continue;
            }
            for (Object freqByRace : pair.getFrequencies()) {
                relativeRaceFreq = (RelativeFrequencyByRace) freqByRace;
                race = relativeRaceFreq.getRace();
                raceTotalFreqsMap = calculateTotalFrequency(loci, raceTotalFreqsMap, relativeRaceFreq, race);
            }
        }
        linkedPairs.removeAll(noRaceOverlapPairs);
        HashMap<String, List<Float>> minimumDifferenceMap;
        for (HaplotypePair pair : linkedPairs) {
            loci = Locus.lookup(pair.getLoci());
            setLinkedPairs(loci, true);
            minimumDifferenceMap = minimumDifferenceMapOfMaps.get(loci) != null ? minimumDifferenceMapOfMaps.get(loci) : new HashMap<String, List<Float>>();
            Set<RelativeFrequencyByRace> freqsByRace = new RelativeFrequencyByRaceSet(new RelativeFrequencyByRaceComparator());
            for (Object freqByRace : pair.getFrequencies()) {
                relativeRaceFreq = (RelativeFrequencyByRace) freqByRace;
                totalFreq = raceTotalFreqsMap.get(loci).get(relativeRaceFreq.getRace());
                relativeRaceFreq.setRelativeFrequency(new Float((relativeRaceFreq.getFrequency() * 100) / totalFreq));
                freqsByRace.add(relativeRaceFreq);
                List<Float> relativeFrequencies;
                if (minimumDifferenceMap.containsKey(relativeRaceFreq.getRace())) {
                    relativeFrequencies = minimumDifferenceMap.get(relativeRaceFreq.getRace());
                } else {
                    relativeFrequencies = new ArrayList<Float>();
                }
                relativeFrequencies.add(relativeRaceFreq.getRelativeFrequency());
                minimumDifferenceMap.put(relativeRaceFreq.getRace(), relativeFrequencies);
            }
            minimumDifferenceMapOfMaps.put(loci, minimumDifferenceMap);
            this.linkedPairs.add(pair);
        }
    } else {
        for (HaplotypePair pair : linkedPairs) {
            loci = Locus.lookup(pair.getLoci());
            setLinkedPairs(loci, true);
        }
        this.linkedPairs = linkedPairs;
    }
    Set<EnumSet<Locus>> lociSet = this.linkedPairsMap.keySet();
    for (EnumSet<Locus> lociInSet : lociSet) {
        getFirstPair(lociInSet);
    }
}

Example 3 with Locus

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

the class DetectedDisequilibriumElement method toString.

public String toString() {
    StringBuffer sb = new StringBuffer();
    Set<Locus> loci = new LocusSet(new LocusComparator());
    loci.addAll(getDisequilibriumElement().getLoci());
    for (Locus locus : loci) {
        // sb.append(locus.getShortName() + " Locus: " + getDisequilibriumElement().getHlaElement(locus) + GLStringConstants.NEWLINE);
        if (getDisequilibriumElement().getHlaElement(locus).size() == 1) {
            sb.append(getDisequilibriumElement().getHlaElement(locus).get(0));
        } else {
            sb.append(getDisequilibriumElement().getHlaElement(locus));
        }
        sb.append(GLStringConstants.GENE_PHASE_DELIMITER);
    }
    return sb.substring(0, sb.length() - 1) + GLStringConstants.NEWLINE + ((CoreDisequilibriumElement) getDisequilibriumElement()).getFrequencyInfo();
}

Example 4 with Locus

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

the class DisequilibriumElementComparatorTest method testComparisonByRace.

@Test
public void testComparisonByRace() {
    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);
    DisequilibriumElementComparator comparator = new DisequilibriumElementComparator();
    assertTrue(comparator.compare(new DetectedDisequilibriumElement(element1), new DetectedDisequilibriumElement(element2)) > 0);
}

Example 5 with Locus

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

the class HLAFrequenciesLoader method loadIndividualLocusFrequencies.

private void loadIndividualLocusFrequencies(File allelesFile) throws IOException {
    String row;
    String[] parts;
    HashMap<String, Locus> locusMap = new HashMap<String, Locus>();
    Locus locus;
    List<String> singleLocusFrequencies;
    InputStream inStream = new FileInputStream(allelesFile);
    InputStreamReader isr = new InputStreamReader(inStream);
    BufferedReader reader = new BufferedReader(isr);
    while ((row = reader.readLine()) != null) {
        parts = row.split(GLStringUtilities.ESCAPED_ASTERISK);
        if (locusMap.containsKey(parts[0])) {
            locus = locusMap.get(parts[0]);
        } else {
            locus = Locus.lookup(parts[0]);
            locusMap.put(parts[0], locus);
        }
        if (individualLocusFrequencies.containsKey(locus)) {
            singleLocusFrequencies = individualLocusFrequencies.get(locus);
        } else {
            singleLocusFrequencies = new ArrayList<String>();
        }
        singleLocusFrequencies.add(row);
        individualLocusFrequencies.put(locus, singleLocusFrequencies);
    }
    reader.close();
}