com.wcohen.ss.abbvGapsHmm

Class AbbvGapsHMMEvaluator.EvalParam

java.lang.Object

com.wcohen.ss.abbvGapsHmm.AbbvGapsHMMEvaluator.EvalParam

Direct Known Subclasses:

AbbvGapsHmmBackwardsEvaluator.BackwardEvalParam, AbbvGapsHmmForwardEvaluator.ForwardEvalParam

Enclosing class:

AbbvGapsHMMEvaluator

protected abstract class AbbvGapsHMMEvaluator.EvalParam
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
int	_current
int	_currentStringPos
int	_eval_end
int	_eval_mat_size
int	_eval_start
int	_length
String	_partialWord
boolean	_partialWordIsAtStart

Constructor Summary

Constructors

Constructor and Description
EvalParam(String str)

Method Summary

Modifier and Type	Method and Description
abstract void	advanceEvalRange() Advance within evaluation range
abstract int	getCurrentPartialWordLen()
abstract int	getCurrentPartialWordMatchPosition()
int	getEvalMatrixSize()
int	getEvalStringPos()
int	getRangeEnd()
int	getRangeStart()
abstract void	initEvalRange() Init evaluation range
boolean	isAtRangeEnd()
boolean	isAtRangeStart()
abstract boolean	isCurrentPartialWordMatchPositionAtWordStart()
abstract boolean	isInEvalRange() Is in evaluation range
abstract boolean	isInStringMatchingRange()
abstract int	offset(int offset)
abstract void	setPartialWord(String str, boolean isAtWordStart)
int	val()

Methods inherited from class java.lang.Object

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

Field Detail

_eval_start

public int _eval_start

_eval_end

public int _eval_end

_eval_mat_size

public int _eval_mat_size

_length

public int _length

_current

public int _current

_currentStringPos

public int _currentStringPos

_partialWordIsAtStart

public boolean _partialWordIsAtStart

_partialWord

public String _partialWord

Constructor Detail

EvalParam

public EvalParam(String str)

Method Detail

val

public int val()

initEvalRange

public abstract void initEvalRange()

Init evaluation range

advanceEvalRange

public abstract void advanceEvalRange()

Advance within evaluation range

isInEvalRange

public abstract boolean isInEvalRange()

Is in evaluation range

isAtRangeStart

public boolean isAtRangeStart()

isAtRangeEnd

public boolean isAtRangeEnd()

isInStringMatchingRange

public abstract boolean isInStringMatchingRange()

getEvalStringPos

public int getEvalStringPos()

offset

public abstract int offset(int offset)

getEvalMatrixSize

public int getEvalMatrixSize()

getRangeStart

public int getRangeStart()

getRangeEnd

public int getRangeEnd()

setPartialWord

public abstract void setPartialWord(String str,
                                    boolean isAtWordStart)

getCurrentPartialWordLen

public abstract int getCurrentPartialWordLen()

getCurrentPartialWordMatchPosition

public abstract int getCurrentPartialWordMatchPosition()

isCurrentPartialWordMatchPositionAtWordStart

public abstract boolean isCurrentPartialWordMatchPositionAtWordStart()