edu.umd.hooka.alignment.aer

Class ReferenceAlignment

java.lang.Object

edu.umd.hooka.Alignment

edu.umd.hooka.alignment.aer.ReferenceAlignment

All Implemented Interfaces:

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

public class ReferenceAlignment
extends Alignment

Nested Class Summary

Nested classes/interfaces inherited from class edu.umd.hooka.Alignment

Alignment.AIterator, Alignment.IntPair, Alignment.M2

Field Summary

Fields inherited from class edu.umd.hooka.Alignment

_elen, _flen, DIAG_NEIGHBORS, LNEIGHBORS, NEIGHBORS

Constructor Summary

Constructors

Constructor and Description
ReferenceAlignment()
ReferenceAlignment(int flen, int elen)

Method Summary

Methods

Modifier and Type	Method and Description
void	addAlignmentPointsPharaoh(String p)
int	countProbableHits(Alignment test)
int	countSureAlignmentPoints()
int	countSureHits(Alignment test)
Alignment	getTranspose()
byte	getType()
static edu.umd.hooka.alignment.aer.ReferenceAlignment.WPTFileReader	getWPT03FileIterator(InputStream is)
boolean	isProbableAligned(int f, int e)
boolean	isSureAligned(int f, int e)
void	probableAlign(int f, int e)
void	readFields(DataInput in)
void	sureAlign(int f, int e)
String	toString()
void	write(DataOutput out)

Methods inherited from class edu.umd.hooka.Alignment

align, aligned, clone, countAlignmentPoints, countNeighbors, doubleRookAligned, equals, fromGiza, getELength, getFLength, intersect, isEAligned, isFAligned, iterator, lneighborAligned, mergeEnglishWords, neighborAligned, rookAligned, splitEnglishWords, splitForeignWords, toStringVisual, unalignE, unalignF, union

Methods inherited from class java.lang.Object

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

Constructor Detail

ReferenceAlignment

public ReferenceAlignment()

ReferenceAlignment

public ReferenceAlignment(int flen,
                  int elen)

Method Detail

getType

public byte getType()

Overrides:

getType in class Alignment

sureAlign

public void sureAlign(int f,
             int e)

probableAlign

public void probableAlign(int f,
                 int e)

isSureAligned

public boolean isSureAligned(int f,
                    int e)

isProbableAligned

public boolean isProbableAligned(int f,
                        int e)

countProbableHits

public int countProbableHits(Alignment test)

countSureHits

public int countSureHits(Alignment test)

countSureAlignmentPoints

public int countSureAlignmentPoints()

getTranspose

public Alignment getTranspose()

Overrides:

getTranspose in class Alignment

addAlignmentPointsPharaoh

public void addAlignmentPointsPharaoh(String p)

toString

public String toString()

Overrides:

toString in class Alignment

readFields

public void readFields(DataInput in)
                throws IOException

Specified by:

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

Overrides:

readFields in class Alignment

Throws:

IOException

write

public void write(DataOutput out)
           throws IOException

Specified by:

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

Overrides:

write in class Alignment

Throws:

IOException

getWPT03FileIterator

public static edu.umd.hooka.alignment.aer.ReferenceAlignment.WPTFileReader getWPT03FileIterator(InputStream is)
                                                                                         throws IOException

Throws:

IOException