charite.christo.blast
Class BlastHitIntersection

java.lang.Object
  charite.christo.blast.BlastHitIntersection

public class BlastHitIntersection
extends java.lang.Object

Field Summary

boolean[]

SELECTED

Constructor Summary

BlastHitIntersection()

Method Summary

static float	expectValueCutoff(int[] cumulHist, int num)
static int[]	expectValueHistogramm(BlastHitIntersection[] v)
BlastAlignment	getAlignment(int i)
double	getExpect()
int	getMatchEnd()
int	getMatchStart()
int	getQueryEnd(int i)
int	getQueryStart(int i)
byte[]	getSeq(char QorM, int i)
static BlastHitIntersection	intersect(BlastAlignment a0, BlastAlignment a1)
static byte[][]	mergeAlignments(byte[] q0, int Lq0, byte[] m0, int Lm0, byte[] q1, int Lq1, byte[] m1, int Lm1)
static int	model2view(byte[] seq, int fromAa)
static BlastAlignment	union(BlastAlignment a1, BlastAlignment a2)

Methods inherited from class java.lang.Object

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

Field Detail

SELECTED

public final boolean[] SELECTED

Constructor Detail

BlastHitIntersection

public BlastHitIntersection()

Method Detail

getSeq

public byte[] getSeq(char QorM,
                     int i)

getQueryStart

public int getQueryStart(int i)

getQueryEnd

public int getQueryEnd(int i)

getMatchStart

public int getMatchStart()

getMatchEnd

public int getMatchEnd()

getAlignment

public BlastAlignment getAlignment(int i)

getExpect

public double getExpect()

intersect

public static BlastHitIntersection intersect(BlastAlignment a0,
                                             BlastAlignment a1)

expectValueHistogramm

public static int[] expectValueHistogramm(BlastHitIntersection[] v)

expectValueCutoff

public static float expectValueCutoff(int[] cumulHist,
                                      int num)

model2view

public static int model2view(byte[] seq,
                             int fromAa)

mergeAlignments

public static byte[][] mergeAlignments(byte[] q0,
                                       int Lq0,
                                       byte[] m0,
                                       int Lm0,
                                       byte[] q1,
                                       int Lq1,
                                       byte[] m1,
                                       int Lm1)

union

public static BlastAlignment union(BlastAlignment a1,
                                   BlastAlignment a2)