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EncryptedIdentifiersManager.java
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Sat, Oct 5, 17:29

EncryptedIdentifiersManager.java
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package ch.epfl.lca1.medco;
import ch.epfl.lca1.medco.util.Logger;
import ch.epfl.lca1.medco.util.exceptions.UnlynxException;
import java.util.HashMap;
import java.util.Map;
/**
* Defines and manipulates the identifiers that are meant to be encrypted by Unlynx for the purpose of answering queries.
*
* Convention: 64 bits integers.
*
* Genomic variant:
* 1 bit (2): flag genomic variant (1)
* 5 bits (32): chromosome id
* 28 bits (268'435'456): start position of the mutation (1-based coordinate system)
* 3 bits (8): length in # bases of the reference allele
* 12 bits (4'096): reference allele (6 bases)
* 3 bits (8): length in # bases of the alternative allele (mutated)
* 12 bits (4'096): alternative allele (6 bases)
*
* Clinical:
* 1 bit (2): flag clinical (0)
* 32 bits (4'294'967'296): clinical id (ontology), String.hashCode() of the field name
* 31 bits (2'147'483'648): clinical value
*/
public class EncryptedIdentifiersManager {
private long nextUsableClinicalId;
public EncryptedIdentifiersManager(long nextUsableClinicalId) {
this.nextUsableClinicalId = nextUsableClinicalId;
}
/**
* Size in bits of the identifier.
*/
public static final int ID_BIT_SIZE = 64;
/**
* Breakdown of the size in bits.
*/
public static final int TYPE_FLAG_BIT_SIZE = 1,
CLINICAL_ID_BIT_SIZE = 32,
CLINICAL_VAL_BIT_SIZE = 31,
CHR_BIT_SIZE = 5,
POS_BIT_SIZE = 28,
ALLELES_BASE_LENGTH_BIT_SIZE = 3,
ALLELES_BIT_SIZE = 12;
/**
* Valid values for the chromosome id:
* Number from 1 to 23 inclusive, or
* X, Y, or M
*
* -> Range from 1 to 26 inclusive, 2^5 = 32 ==> 5 bits storage
*/
public static final String CHROMOSOME_ID_REGEX = "^[XYM]|[1-9]|(1[0-9])|(2[0-3])$";
/**
* Mapping to encode non-numeric chromosome ids.
*/
public static final long CHROMOSOME_X_INT_ID = 24,
CHROMOSOME_Y_INT_ID = 25,
CHROMOSOME_M_INT_ID = 26;
/**
* Mapping to encode type of id.
*/
public static final long TYPE_FLAG_CLINICAL = 0b0,
TYPE_FLAG_GENOMIC_VARIANT = 0b1;
/**
* Mapping to encode alleles.
*/
public static final Map<Character, Long> ALLELE_MAPPING = new HashMap<>();
static {
ALLELE_MAPPING.put('A', 0L);
ALLELE_MAPPING.put('T', 1L);
ALLELE_MAPPING.put('G', 2L);
ALLELE_MAPPING.put('C', 3L);
}
/**
* Valid values for the alleles.
* Either nothing ("-") or a certain number of bases ({A, T, G, C}).
* Each [A, T, G, C] base is encoded on 2 bits.
*
* The maximum number of bases supported is 6 -> 12bits
* and an additional 3 bits are used to encode the length.
*
*/
public static final String ALLELES_REGEX = "^([ATCG]{1,6}|-)$";
/**
* Possible range of positions values (position in 1-based coordinate system, minimum is 1).
* Result is encoded into bits so the range is rounded to the nearest power of 2.
* According to https://en.wikipedia.org/wiki/Human_genome#Molecular_organization_and_gene_content,
* the chromosome with the higher number of base is #1 with 248'956'422 bases. 2^28 = 268'435'456.
* ==> 28 bits storage
*/
public static final long POSITION_MIN = 1, POSITION_MAX = 1L << POS_BIT_SIZE;
/**
* Encodes a genomic variant ID to be encrypted, according to the specifications.
* @param chromosomeId the chromosome ID
* @param startPosition the start position of the mutation
* @param refAlleles the reference alleles
* @param altAlleles the alternative alleles
* @return the encoded ID
* @throws UnlynxException if the input is not valid and cannot be encoded
*/
public static long getVariantId(String chromosomeId, long startPosition, String refAlleles, String altAlleles) throws UnlynxException {
// validate input
if (!chromosomeId.matches(CHROMOSOME_ID_REGEX) ||
startPosition < POSITION_MIN || startPosition > POSITION_MAX ||
!refAlleles.matches(ALLELES_REGEX) || !altAlleles.matches(ALLELES_REGEX) ||
TYPE_FLAG_BIT_SIZE + CHR_BIT_SIZE + POS_BIT_SIZE + 2 * (ALLELES_BASE_LENGTH_BIT_SIZE + ALLELES_BIT_SIZE) != ID_BIT_SIZE) {
throw Logger.warn(new UnlynxException("Invalid input: chr=" + chromosomeId +
", pos=" + startPosition + ", ref=" + refAlleles + ", alt=" + altAlleles));
}
// interpret chromosome id (content validated by regex)
long chromosomeIntId;
try {
chromosomeIntId = Long.parseLong(chromosomeId);
} catch (NumberFormatException e) {
switch (chromosomeId) {
case "X":
chromosomeIntId = CHROMOSOME_X_INT_ID;
break;
case "Y":
chromosomeIntId = CHROMOSOME_Y_INT_ID;
break;
case "M":
chromosomeIntId = CHROMOSOME_M_INT_ID;
break;
default:
throw Logger.warn(new UnlynxException("Invalid chr id:" + chromosomeId));
}
}
// alleles
if (refAlleles.equals("-")) {
refAlleles = "";
}
if (altAlleles.equals("-")) {
altAlleles = "";
}
long refAllelesBaseLength = refAlleles.length();
long altAllelesBaseLength = altAlleles.length();
// generate the variant
long id = 0L;
id = pushBitsFromRight(id, TYPE_FLAG_BIT_SIZE, TYPE_FLAG_GENOMIC_VARIANT);
id = pushBitsFromRight(id, CHR_BIT_SIZE, chromosomeIntId);
id = pushBitsFromRight(id, POS_BIT_SIZE, startPosition);
id = pushBitsFromRight(id, ALLELES_BASE_LENGTH_BIT_SIZE, refAllelesBaseLength);
id = pushBitsFromRight(id, ALLELES_BIT_SIZE, encodeAlleles(refAlleles));
id = pushBitsFromRight(id, ALLELES_BASE_LENGTH_BIT_SIZE, altAllelesBaseLength);
id = pushBitsFromRight(id, ALLELES_BIT_SIZE, encodeAlleles(altAlleles));
return id;
}
/**
* Encode a string containing alleles.
*
* @param alleles a string containing alleles
* @return the encoded alleles.
*/
protected static long encodeAlleles(String alleles) {
long encodedAlleles = 0b0;
for (int i = 0 ; i < alleles.length() ; i++) {
if (!ALLELE_MAPPING.containsKey(alleles.charAt(i))) {
throw Logger.warn(new IllegalArgumentException("Invalid allele."));
}
encodedAlleles = pushBitsFromRight(
encodedAlleles,
2,
ALLELE_MAPPING.get(alleles.charAt(i)));
}
// padding
encodedAlleles = pushBitsFromRight(
encodedAlleles,
ALLELES_BIT_SIZE - alleles.length() * 2,
0L);
return encodedAlleles;
}
/**
* Takes the nbBits rightmost bits of bitsToPush, and push them to the right of origBits.
*
* @param origBits the value to push bits into
* @param nbBits the number of bits to push
* @param bitsToPush the value to take the bits from
*
* @return the concatenation of origBits and bitsToPush
*/
protected static long pushBitsFromRight(long origBits, int nbBits, long bitsToPush) {
long newBits = origBits << nbBits;
// generate mask
long mask = getMask(nbBits);
// get final value
newBits |= (mask & bitsToPush);
return newBits;
}
protected static long getMask(int nbBits) {
long mask = 0b0;
for (int i = 0 ; i < nbBits ; i++) {
mask <<= 1;
mask |= 0b1;
}
return mask;
}
/**
* Returns and updates (by incrementing) the next usable clinical id.
*
* @return the next usable clinical id
* @throws UnlynxException if an overflow happens and the flag bit is not set correctly
*/
public long getNextUsableClinicalId() throws UnlynxException {
if ((nextUsableClinicalId & (1L << 63)) != 0) {
throw Logger.error(new UnlynxException("Clinical id overflow detected"));
}
return this.nextUsableClinicalId++;
}
}

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