com.dnastack.beacon.util

Class QueryUtils

java.lang.Object

com.dnastack.beacon.util.QueryUtils

public class QueryUtils
extends Object

Utils for query manipulation.

Version:

1.0

Author:

Miroslav Cupak (mirocupak@gmail.com)

Constructor Summary

Constructors

Constructor and Description
QueryUtils()

Method Summary

Modifier and Type	Method and Description
static Query	getQuery(String chrom, Long pos, String allele, String ref, String dataset) Obtains a canonical query object.
static String	normalizeAllele(String allele) Generate a canonical allele string.
static Chromosome	normalizeChromosome(String chrom) Generates a canonical chrom ID.
static Long	normalizePosition(Long pos) Converts 0-based position to 1-based position.
static Reference	normalizeReference(String ref) Generate a canonical genome representation (hg*).

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

QueryUtils

public QueryUtils()

Method Detail

normalizeChromosome

public static Chromosome normalizeChromosome(String chrom)

Generates a canonical chrom ID.

Parameters:

chrom - chromosome

Returns:

normalized chromosome value

normalizePosition

public static Long normalizePosition(Long pos)

Converts 0-based position to 1-based position.

Parameters:

pos - 0-based position

Returns:

1-based position

normalizeAllele

public static String normalizeAllele(String allele)

Generate a canonical allele string.

Parameters:

allele - denormalized allele

Returns:

normalized allele

normalizeReference

public static Reference normalizeReference(String ref)

Generate a canonical genome representation (hg*).

Parameters:

ref - denormalized genome

Returns:

normalized genome

getQuery

public static Query getQuery(String chrom,
                             Long pos,
                             String allele,
                             String ref,
                             String dataset)

Obtains a canonical query object.

Parameters:

chrom - chromosome

pos - position

allele - allele

ref - genome

dataset - dataset

Returns:

normalized query