umcg.genetica.io.trityper.util

Class BaseAnnot

java.lang.Object

umcg.genetica.io.trityper.util.BaseAnnot

public class BaseAnnot
extends Object

Author:

harmjan

Field Summary

Fields

Modifier and Type	Field and Description
static byte	A
static byte	C
static byte	G
static byte	I
static byte	N
static byte	T
static byte	U

Constructor Summary

Constructors

Constructor and Description
BaseAnnot()

Method Summary

Modifier and Type	Method and Description
static byte[]	convertToComplementaryAlleles(byte[] allelesToCompare)
static Boolean	flipalleles(String allelesSNP1, String alleleAssessedSNP1, String allelesSNP2, String alleleAssessedSNP2)
static String	getAllelesDescription(byte[] alleles)
static byte	getComplement(byte x)
static String	getComplement(String x)
static String	getFullComplement(String longstr)
static String	getReverseComplement(String str)
static byte	toByte(String x)
static byte[]	toByteArray(String alleles)
static String	toString(byte x)

Methods inherited from class java.lang.Object

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

Field Detail

A

public static final byte A

See Also:

Constant Field Values

C

public static final byte C

See Also:

Constant Field Values

T

public static final byte T

See Also:

Constant Field Values

G

public static final byte G

See Also:

Constant Field Values

U

public static final byte U

See Also:

Constant Field Values

I

public static final byte I

See Also:

Constant Field Values

N

public static final byte N

See Also:

Constant Field Values

Constructor Detail

BaseAnnot

public BaseAnnot()

Method Detail

convertToComplementaryAlleles

public static byte[] convertToComplementaryAlleles(byte[] allelesToCompare)

flipalleles

public static Boolean flipalleles(String allelesSNP1,
                                  String alleleAssessedSNP1,
                                  String allelesSNP2,
                                  String alleleAssessedSNP2)

toString

public static String toString(byte x)

getComplement

public static byte getComplement(byte x)

getReverseComplement

public static String getReverseComplement(String str)

getFullComplement

public static String getFullComplement(String longstr)

getComplement

public static String getComplement(String x)

toByte

public static byte toByte(String x)

getAllelesDescription

public static String getAllelesDescription(byte[] alleles)

toByteArray

public static byte[] toByteArray(String alleles)