Examples with HaplotypePair org.dash.valid.gl.haplo.HaplotypePair used on opensource projects

Example 6 with HaplotypePair

use of org.dash.valid.gl.haplo.HaplotypePair 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();
}