charite.christo.blast
Class BlastAlignment

java.lang.Object
  charite.christo.blast.BlastAlignment

public class BlastAlignment
extends java.lang.Object

Field Summary

static BlastAlignment[]

NONE

Constructor Summary

BlastAlignment()

Method Summary

double	getBits()
BlastHit	getBlastHit()
java.lang.String	getDatabase()
double	getExpect()
java.lang.String	getID()
int	getIdentity()
int	getMatchEnd()
byte[]	getMatchSeq()
int	getMatchSeqHashCode()
int	getMatchStart()
byte[]	getMatchUngapped()
int	getNumber()
int	getPositives()
int	getQueryEnd()
byte[]	getQuerySeq()
int	getQueryStart()
int	getScore()
boolean	isNovel()
static void	midline(byte[] q, int qFrom, int qTo, byte[] m, int mFrom, int mTo, BA sb)
void	setBits(double d)
void	setBlastHit(BlastHit b)
void	setExpect(double d)
void	setIdentity(int i)
void	setIsNew(boolean b)
void	setMatchSeq(byte[] s, int from, int to)
void	setMatchStartEnd(int s, int e)
void	setNumber(int i)
void	setPositives(int i)
void	setQuerySeq(byte[] s, int from, int to)
void	setQueryStartEnd(int s, int e)
void	setScore(int i)
void	toText(long options, BA sb, int outputWidth)

Methods inherited from class java.lang.Object

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

Field Detail

NONE

public static final BlastAlignment[] NONE

Constructor Detail

BlastAlignment

public BlastAlignment()

Method Detail

setMatchSeq

public void setMatchSeq(byte[] s,
                        int from,
                        int to)

setQuerySeq

public void setQuerySeq(byte[] s,
                        int from,
                        int to)

setQueryStartEnd

public void setQueryStartEnd(int s,
                             int e)

setMatchStartEnd

public void setMatchStartEnd(int s,
                             int e)

setIdentity

public void setIdentity(int i)

setPositives

public void setPositives(int i)

setScore

public void setScore(int i)

setNumber

public void setNumber(int i)

setExpect

public void setExpect(double d)

setBits

public void setBits(double d)

getMatchSeq

public byte[] getMatchSeq()

getMatchSeqHashCode

public int getMatchSeqHashCode()

getQuerySeq

public byte[] getQuerySeq()

getMatchUngapped

public byte[] getMatchUngapped()

getQueryStart

public int getQueryStart()

getQueryEnd

public int getQueryEnd()

getMatchStart

public int getMatchStart()

getMatchEnd

public int getMatchEnd()

getIdentity

public int getIdentity()

getPositives

public int getPositives()

getScore

public int getScore()

getNumber

public int getNumber()

getExpect

public double getExpect()

getBits

public double getBits()

getDatabase

public java.lang.String getDatabase()

getID

public java.lang.String getID()

getBlastHit

public BlastHit getBlastHit()

setBlastHit

public void setBlastHit(BlastHit b)

setIsNew

public void setIsNew(boolean b)

isNovel

public boolean isNovel()

toText

public final void toText(long options,
                         BA sb,
                         int outputWidth)

midline

public static void midline(byte[] q,
                           int qFrom,
                           int qTo,
                           byte[] m,
                           int mFrom,
                           int mTo,
                           BA sb)