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

Example 1 with Linkages

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

the class HLAFrequenciesLoader method init.

private void init(Set<File> frequencyFiles, File allelesFile) {
    Set<Linkages> linkages = new HashSet<Linkages>();
    try {
        for (File frequencyFile : frequencyFiles) {
            InputStream is = new FileInputStream(frequencyFile);
            InputStreamReader isr = new InputStreamReader(is);
            BufferedReader reader = new BufferedReader(isr);
            List<DisequilibriumElement> elements = loadStandardReferenceData(reader);
            EnumSet<Locus> loci = Locus.lookup(elements.iterator().next().getLoci());
            linkages.addAll(Linkages.lookup(loci));
            this.disequilibriumElementsMap.put(loci, elements);
        }
        LinkagesLoader.getInstance(linkages);
        if (allelesFile != null) {
            loadIndividualLocusFrequencies(allelesFile);
        }
    } catch (IOException e) {
        LOGGER.severe("Couldn't load disequilibrium element reference file.");
        e.printStackTrace();
        System.exit(-1);
    }
}

Example 2 with Linkages

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

the class NormalizeFrequencyFile method call.

@Override
public Integer call() throws Exception {
    PrintWriter writer = new PrintWriter(outputFile);
    if (SINGLE.equals(frequencies)) {
        List<String> singleLocusFrequencies = HLAFrequenciesLoader.loadIndividualLocusFrequency(new FileInputStream(inputFile));
        for (String allele : singleLocusFrequencies) {
            writer.write(allele + GLStringConstants.NEWLINE);
        }
    } else {
        HashSet<String> linkageNames = new HashSet<String>();
        linkageNames.add(frequencies);
        Set<Linkages> linkagesSet = Linkages.lookup(linkageNames);
        LinkagesLoader.getInstance(linkagesSet);
        List<DisequilibriumElement> disequilibriumElements = HLAFrequenciesLoader.loadNMDPLinkageReferenceData(new FileInputStream(inputFile), LOCUS_POSITION_MAP.get(Linkages.lookup(frequencies).getLoci()));
        for (DisequilibriumElement element : disequilibriumElements) {
            StringBuffer sb = new StringBuffer();
            int locusCounter = 0;
            for (Locus locus : Locus.lookup(element.getLoci())) {
                if (locusCounter > 0) {
                    sb.append(GLStringConstants.GENE_PHASE_DELIMITER);
                }
                sb.append(element.getHlaElement(locus).get(0));
                locusCounter++;
            }
            List<FrequencyByRace> frequencies = ((DisequilibriumElementByRace) element).getFrequenciesByRace();
            for (FrequencyByRace frequency : frequencies) {
                writer.write(frequency.getRace() + GLStringConstants.COMMA + sb + GLStringConstants.COMMA + frequency.getFrequency() + GLStringConstants.COMMA + frequency.getRank() + GLStringConstants.NEWLINE);
            }
        }
    }
    writer.close();
    return 0;
}

Example 3 with Linkages

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

the class DetectedFindingsWriter method reportDetectedFindings.

/**
 * @param linkagesFound
 * @throws IOException
 * @throws SecurityException
 */
public synchronized void reportDetectedFindings(DetectedLinkageFindings findings) {
    XSSFRow row = spreadsheet.createRow(rowId++);
    int cellId = 0;
    XSSFCell cell = row.createCell(cellId++);
    cell.setCellValue(findings.getGLId());
    cell = row.createCell(cellId++);
    cell.setCellValue(findings.getAlleleCount(Locus.HLA_A));
    cell = row.createCell(cellId++);
    cell.setCellValue(findings.getAlleleCount(Locus.HLA_B));
    cell = row.createCell(cellId++);
    cell.setCellValue(findings.getAlleleCount(Locus.HLA_C));
    cell = row.createCell(cellId++);
    cell.setCellValue(findings.getAlleleCount(Locus.HLA_DRB1));
    cell = row.createCell(cellId++);
    cell.setCellValue(findings.getAlleleCount(Locus.HLA_DRB345));
    cell = row.createCell(cellId++);
    cell.setCellValue(findings.getAlleleCount(Locus.HLA_DQB1));
    for (Linkages linkage : LinkagesLoader.getInstance().getLinkages()) {
        cell = row.createCell(cellId++);
        cell.setCellValue(findings.getLinkageCount(linkage.getLoci()));
        cell = row.createCell(cellId++);
        cell.setCellValue(findings.getMinimumDifference(linkage.getLoci()) + "");
    }
    String detectedFindings = formatDetectedFindings(findings);
    printWriter.write(detectedFindings);
}

Example 4 with Linkages

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

the class DetectedFindingsWriter method formatDetectedFindings.

public static String formatDetectedFindings(DetectedLinkageFindings findings) {
    StringBuffer sb = new StringBuffer();
    sb.append(findings.getGLId() + GLStringConstants.COMMA);
    sb.append(findings.getAlleleCount(Locus.HLA_A) + GLStringConstants.COMMA);
    sb.append(findings.getAlleleCount(Locus.HLA_B) + GLStringConstants.COMMA);
    sb.append(findings.getAlleleCount(Locus.HLA_C) + GLStringConstants.COMMA);
    sb.append(findings.getAlleleCount(Locus.HLA_DRB1) + GLStringConstants.COMMA);
    sb.append(findings.getAlleleCount(Locus.HLA_DRB345) + GLStringConstants.COMMA);
    sb.append(findings.getAlleleCount(Locus.HLA_DQB1) + GLStringConstants.COMMA);
    for (Linkages linkage : LinkagesLoader.getInstance().getLinkages()) {
        sb.append(findings.getLinkageCount(linkage.getLoci()) + GLStringConstants.COMMA);
        sb.append(findings.getMinimumDifference(linkage.getLoci()) + GLStringConstants.COMMA);
    }
    sb.append(GLStringConstants.NEWLINE);
    return sb.toString();
}