/**
* Writes record with information about particular segment (allele).
*
* <p>
*
* <p>There are two main types of such records (depending on value of {@code isReference} option):
*
* <p>
*
* <ul>
* <p>
* <li><b>Reference records (like IMGT *01 alleles).</b> Such records must have accession number
* of source sequence and array of reference points and must not have mutation list and
* reference allele fields.
* <p>
* <li><b>Allele records (other alleles).</b> Such records must have mutation list and reference
* allele field.
* <p>
* </ul>
*
* <p>
*
* <p>Mutation positions in the mutation list ( {@code mutations} option ) must be converted to
* positions relative to the first defined reference point of the reference allele.
*
* @param type type of the segment (V, D, J or C)
* @param alleleName full name of allele (e.g. TRBV12-2*01)
* @param isReference is it a reference allele
* @param isFunctional {@code true} if this gene is functional; {@code false} if this gene is
* pseudogene
* @param accession accession number of original (source) sequence
* @param referencePoints array of reference points
* @param reference allele name of the reference allele
* @param mutations array of mutations
* @param referenceGeneFeature reference gene feature
* @throws java.io.IOException if an I/O error occurs.
*/
public void writeAllele(
GeneType type,
String alleleName,
boolean isReference,
boolean isFunctional,
String accession,
int[] referencePoints,
String reference,
int[] mutations,
GeneFeature referenceGeneFeature)
throws IOException {
// Validation
if ((accession == null) != (referencePoints == null)
|| (reference == null) != (mutations == null)
|| (reference == null) != (referenceGeneFeature == null))
throw new IllegalArgumentException();
if (isReference && (mutations != null || accession == null))
throw new IllegalArgumentException();
if (mutations == null && accession == null) throw new IllegalArgumentException();
stream.writeByte(ALLELE_TYPE);
stream.writeByte(type.id());
stream.writeUTF(alleleName);
stream.writeByte(
(isReference ? 1 : 0)
| (isFunctional ? 2 : 0)
| (accession != null ? 4 : 0)
| (reference != null ? 8 : 0));
if (accession != null) {
if (GENE_TYPE_INFOS_WC.get(type).size != referencePoints.length)
throw new IllegalArgumentException("Wrong number of reference points.");
stream.writeUTF(accession);
for (int i = 0; i < referencePoints.length; ++i) stream.writeInt(referencePoints[i]);
}
if (reference != null) {
stream.writeUTF(reference);
LociLibraryIOUtils.writeReferenceGeneFeature(stream, referenceGeneFeature);
stream.writeInt(mutations.length);
for (int i = 0; i < mutations.length; ++i) stream.writeInt(mutations[i]);
}
}
public static GeneTypeInfo getGeneTypeInfo(GeneType geneType, boolean withFR4Correction) {
return withFR4Correction ? GENE_TYPE_INFOS_WC.get(geneType) : GENE_TYPE_INFOS.get(geneType);
}
