edu.umd.hooka

Class Alignment

java.lang.Object

edu.umd.hooka.Alignment

All Implemented Interfaces:

Cloneable, Iterable<Alignment.IntPair>, org.apache.hadoop.io.Writable

Direct Known Subclasses:

ReferenceAlignment

public class Alignment
extends Object
implements org.apache.hadoop.io.Writable, Iterable<Alignment.IntPair>, Cloneable

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	Alignment.AIterator
class	Alignment.IntPair
protected static class	Alignment.M2

Field Summary

Fields

Modifier and Type	Field and Description
protected short	_elen
protected short	_flen
static int[][]	DIAG_NEIGHBORS
static int[][][]	LNEIGHBORS
static int[][]	NEIGHBORS

Constructor Summary

Constructors

Constructor and Description
Alignment()
Alignment(int flen, int elen)
Alignment(int flen, int elen, String pa)

Method Summary

Methods

Modifier and Type	Method and Description
void	align(int f, int e)
boolean	aligned(int f, int e)
Object	clone()
int	countAlignmentPoints()
int	countNeighbors(int f, int e, int[][] rels)
boolean	doubleRookAligned(int i, int j)
boolean	equals(Object o)
static Alignment	fromGiza(String eline, String fline, boolean transpose)
int	getELength()
int	getFLength()
Alignment	getTranspose()
byte	getType()
static Alignment	intersect(Alignment a1, Alignment a2)
boolean	isEAligned(int e)
boolean	isFAligned(int f)
Iterator<Alignment.IntPair>	iterator()
boolean	lneighborAligned(int i, int j)
Alignment	mergeEnglishWords(int i, int j)
boolean	neighborAligned(int i, int j)
void	readFields(DataInput in)
boolean	rookAligned(int i, int j)
Alignment	splitEnglishWords(int i)
Alignment	splitForeignWords(int j)
String	toString()
String	toStringVisual()
void	unalignE(int e)
void	unalignF(int f)
static Alignment	union(Alignment a1, Alignment a2)
void	write(DataOutput out)

Methods inherited from class java.lang.Object

finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

_elen

protected short _elen

_flen

protected short _flen

DIAG_NEIGHBORS

public static final int[][] DIAG_NEIGHBORS

NEIGHBORS

public static final int[][] NEIGHBORS

LNEIGHBORS

public static final int[][][] LNEIGHBORS

Constructor Detail

Alignment

public Alignment()

Alignment

public Alignment(int flen,
         int elen)

Alignment

public Alignment(int flen,
         int elen,
         String pa)

Method Detail

countAlignmentPoints

public int countAlignmentPoints()

mergeEnglishWords

public Alignment mergeEnglishWords(int i,
                          int j)

splitEnglishWords

public Alignment splitEnglishWords(int i)

splitForeignWords

public Alignment splitForeignWords(int j)

readFields

public void readFields(DataInput in)
                throws IOException

Specified by:

readFields in interface org.apache.hadoop.io.Writable

Throws:

IOException

getType

public byte getType()

clone

public Object clone()

Overrides:

clone in class Object

write

public void write(DataOutput out)
           throws IOException

Specified by:

write in interface org.apache.hadoop.io.Writable

Throws:

IOException

equals

public boolean equals(Object o)

Overrides:

equals in class Object

neighborAligned

public boolean neighborAligned(int i,
                      int j)

lneighborAligned

public boolean lneighborAligned(int i,
                       int j)

iterator

public Iterator<Alignment.IntPair> iterator()

Specified by:

iterator in interface Iterable<Alignment.IntPair>

countNeighbors

public final int countNeighbors(int f,
                 int e,
                 int[][] rels)

rookAligned

public final boolean rookAligned(int i,
                  int j)

doubleRookAligned

public final boolean doubleRookAligned(int i,
                        int j)

getELength

public final int getELength()

getFLength

public final int getFLength()

aligned

public final boolean aligned(int f,
              int e)

align

public final void align(int f,
         int e)

isEAligned

public final boolean isEAligned(int e)

isFAligned

public final boolean isFAligned(int f)

unalignF

public final void unalignF(int f)

unalignE

public final void unalignE(int e)

fromGiza

public static Alignment fromGiza(String eline,
                 String fline,
                 boolean transpose)

getTranspose

public Alignment getTranspose()

toStringVisual

public String toStringVisual()

toString

public String toString()

Overrides:

toString in class Object

intersect

public static Alignment intersect(Alignment a1,
                  Alignment a2)

union

public static Alignment union(Alignment a1,
              Alignment a2)