charite.christo.protein
Class Blosum

java.lang.Object
  charite.christo.protein.Blosum

public class Blosum
extends java.lang.Object

Field Summary

static byte[][]	BL2SEQ_MIDLINE
static byte[][]	BLASTMIDLINE
static byte[][]	BLOSUM62
static byte	BLOSUM62_MAX
static byte	BLOSUM62_MIN

Method Summary

static float	blosumScore(float gapOpen, float gapExt, byte[] s0, byte[] s1, byte[] s2, int colFrom, int colTo)
static float	pairAignScore(float gapOpen, float gapExt, byte[] s0, byte[] s1)
static float	pairAignScore(float gapOpen, float gapExt, byte[] s0, byte[] s1, float addConstant)

Methods inherited from class java.lang.Object

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

Field Detail

BLOSUM62

public static final byte[][] BLOSUM62

BLASTMIDLINE

public static final byte[][] BLASTMIDLINE

BL2SEQ_MIDLINE

public static final byte[][] BL2SEQ_MIDLINE

BLOSUM62_MAX

public static final byte BLOSUM62_MAX

See Also:

Constant Field Values

BLOSUM62_MIN

public static final byte BLOSUM62_MIN

See Also:

Constant Field Values

Method Detail

pairAignScore

public static float pairAignScore(float gapOpen,
                                  float gapExt,
                                  byte[] s0,
                                  byte[] s1)

pairAignScore

public static float pairAignScore(float gapOpen,
                                  float gapExt,
                                  byte[] s0,
                                  byte[] s1,
                                  float addConstant)

blosumScore

public static float blosumScore(float gapOpen,
                                float gapExt,
                                byte[] s0,
                                byte[] s1,
                                byte[] s2,
                                int colFrom,
                                int colTo)