charite.christo
Class DNA_Util

java.lang.Object
  charite.christo.DNA_Util

public class DNA_Util
extends java.lang.Object

Field Summary

static byte[]

COMPLEMENT

Method Summary

static int	actg2int(byte[] bb, int from)
static byte	complement(byte b)
static byte[]	complement(byte[] dna, int len)
static byte[]	firstCodonToUpperCase(byte[] nuclSequ)
static byte[]	int2actg(int i, byte[] bb0, boolean uracil)
static byte[]	onlyTranslated(byte[] dna, boolean[] isTranslated)
static byte[]	reverse(byte[] dna, int len)
static byte[]	reverseComplementDestructive(byte[] dna, int to)
static byte[]	translateTriplet2aaCompact(byte[] dna, boolean[] isTranslated) translates the nucleotide sequence this.dna into the amino acid sequence this.residueType depending on the array dnaDeletionsAndInsertions.
static byte	triplet2aa(int trip0, int trip1, int trip2)

Methods inherited from class java.lang.Object

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

Field Detail

COMPLEMENT

public static final byte[] COMPLEMENT

Method Detail

translateTriplet2aaCompact

public static byte[] translateTriplet2aaCompact(byte[] dna,
                                                boolean[] isTranslated)

translates the nucleotide sequence this.dna into the amino acid sequence this.residueType depending on the array dnaDeletionsAndInsertions. With the variable dnaDeletionsAndInsertions one can compensate for sequenceing errors. A positive value in dnaDeletionsAndInsertions indicates a missing nucleotide, a negative value may compansate a nucleotide which shouldn't be there

firstCodonToUpperCase

public static byte[] firstCodonToUpperCase(byte[] nuclSequ)

triplet2aa

public static final byte triplet2aa(int trip0,
                                    int trip1,
                                    int trip2)

complement

public static byte complement(byte b)

complement

public static byte[] complement(byte[] dna,
                                int len)

reverse

public static byte[] reverse(byte[] dna,
                             int len)

reverseComplementDestructive

public static byte[] reverseComplementDestructive(byte[] dna,
                                                  int to)

onlyTranslated

public static byte[] onlyTranslated(byte[] dna,
                                    boolean[] isTranslated)

actg2int

public static int actg2int(byte[] bb,
                           int from)

int2actg

public static byte[] int2actg(int i,
                              byte[] bb0,
                              boolean uracil)