com.wcohen.ss.abbvGapsHmm

Class AbbvGapsHMMEvaluator

java.lang.Object

com.wcohen.ss.abbvGapsHmm.AbbvGapsHMMEvaluator

Direct Known Subclasses:

AbbvGapsHmmBackwardsEvaluator, AbbvGapsHmmForwardEvaluator

public abstract class AbbvGapsHMMEvaluator
extends Object

Author:

Dana Movshovitz-Attias

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	AbbvGapsHMMEvaluator.EvalParam

Field Summary

Fields

Modifier and Type	Field and Description
protected Acronym	_acronym
protected String	_currPartialWord
protected String	_currWord
protected Matrix3D	_evalMat
protected AbbvGapsHMM	_gapsHMM
protected AbbvGapsHMMEvaluator.EvalParam	_lParam
protected AbbvGapsHMMEvaluator.EvalParam	_partialWordParam
protected AbbvGapsHMMEvaluator.EvalParam	_sParam

Constructor Summary

Constructors

Constructor and Description
AbbvGapsHMMEvaluator(AbbvGapsHMM abbvGapsHMM)

Method Summary

Modifier and Type	Method and Description
protected boolean	andToSymbolMatch(char c)
protected boolean	charEqualIgnoreCase(char c1, char c2)
protected void	evaluate(Acronym acronym) This function enumerates the possible transitions and emissions in a hard coded way, in order to save running-time
protected abstract void	finalizeEvalMat()
protected abstract String	getCurrentChars(String str, int pos, int length) Get characters from the string going backwards or forwards (depending on the implementing class), and according to the specifies length.
protected abstract String	getCurrentWord(String str, int pos) Get the current long form word going backwards or forwards (depending on the implementing class).
Matrix3D	getEvalMatrix()
protected abstract AbbvGapsHMMEvaluator.EvalParam	getPartialWordParam(String str, int pos)
protected abstract void	initEvalMat()
protected abstract void	initEvalParams()
protected static boolean	posIsAtWord(String str, int pos)
protected static boolean	posIsAtWordStart(String str, int pos)
protected boolean	transitionIsLegal(int currS, int currL, AbbvGapsHMM.States currState, int prevS, int prevL, AbbvGapsHMM.States prevState, AbbvGapsHMM.Transitions transition, AbbvGapsHMM.Emissions emission)
protected abstract void	updateLegalOutgoingEdges(int currS, int currL, AbbvGapsHMM.States currState, int prevS, int prevL, AbbvGapsHMM.States prevState, AbbvGapsHMM.Transitions transition, AbbvGapsHMM.Emissions emission)
protected void	updateOutgoingEdges(int currS, int currL, AbbvGapsHMM.States currState, int prevS, int prevL, AbbvGapsHMM.States prevState, AbbvGapsHMM.Transitions transition, AbbvGapsHMM.Emissions emission)
protected void	updateOutgoingEdgesStateD(int currS, int currL, int prevS, int prevL, AbbvGapsHMM.Emissions emission) Enumerates the possible transitions into state D.
protected void	updateOutgoingEdgesStateDL(int currS, int currL, int prevS, int prevL, AbbvGapsHMM.Emissions emission) Enumerates the possible transitions into state DL.
protected void	updateOutgoingEdgesStateEND(int currS, int currL, int prevS, int prevL, AbbvGapsHMM.Emissions emission) Enumerates the possible transitions into state END.
protected void	updateOutgoingEdgesStateM(int currS, int currL, int prevS, int prevL, AbbvGapsHMM.Emissions emission) Enumerates the possible transitions into state M.
protected void	updateState(AbbvGapsHMM.States s, int currS, int currL, int prevS, int prevL, AbbvGapsHMM.Emissions emission)

Methods inherited from class java.lang.Object

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

Field Detail

_gapsHMM

protected AbbvGapsHMM _gapsHMM

_evalMat

protected Matrix3D _evalMat

_sParam

protected AbbvGapsHMMEvaluator.EvalParam _sParam

_lParam

protected AbbvGapsHMMEvaluator.EvalParam _lParam

_partialWordParam

protected AbbvGapsHMMEvaluator.EvalParam _partialWordParam

_acronym

protected Acronym _acronym

_currWord

protected String _currWord

_currPartialWord

protected String _currPartialWord

Constructor Detail

AbbvGapsHMMEvaluator

public AbbvGapsHMMEvaluator(AbbvGapsHMM abbvGapsHMM)

Method Detail

updateLegalOutgoingEdges

protected abstract void updateLegalOutgoingEdges(int currS,
                                                 int currL,
                                                 AbbvGapsHMM.States currState,
                                                 int prevS,
                                                 int prevL,
                                                 AbbvGapsHMM.States prevState,
                                                 AbbvGapsHMM.Transitions transition,
                                                 AbbvGapsHMM.Emissions emission)

initEvalMat

protected abstract void initEvalMat()

finalizeEvalMat

protected abstract void finalizeEvalMat()

getCurrentWord

protected abstract String getCurrentWord(String str,
                                         int pos)

Get the current long form word going backwards or forwards (depending on the implementing class).

getCurrentChars

protected abstract String getCurrentChars(String str,
                                          int pos,
                                          int length)

Get characters from the string going backwards or forwards (depending on the implementing class), and according to the specifies length.

getPartialWordParam

protected abstract AbbvGapsHMMEvaluator.EvalParam getPartialWordParam(String str,
                                                                      int pos)

initEvalParams

protected abstract void initEvalParams()

getEvalMatrix

public Matrix3D getEvalMatrix()

evaluate

protected void evaluate(Acronym acronym)

This function enumerates the possible transitions and emissions in a hard coded way, in order to save running-time

posIsAtWordStart

protected static boolean posIsAtWordStart(String str,
                                          int pos)

charEqualIgnoreCase

protected boolean charEqualIgnoreCase(char c1,
                                      char c2)

andToSymbolMatch

protected boolean andToSymbolMatch(char c)

posIsAtWord

protected static boolean posIsAtWord(String str,
                                     int pos)

updateState

protected void updateState(AbbvGapsHMM.States s,
                           int currS,
                           int currL,
                           int prevS,
                           int prevL,
                           AbbvGapsHMM.Emissions emission)

updateOutgoingEdgesStateM

protected void updateOutgoingEdgesStateM(int currS,
                                         int currL,
                                         int prevS,
                                         int prevL,
                                         AbbvGapsHMM.Emissions emission)

Enumerates the possible transitions into state M.

Parameters:

currS -

currL -

prevS -

prevL -

updateOutgoingEdgesStateD

protected void updateOutgoingEdgesStateD(int currS,
                                         int currL,
                                         int prevS,
                                         int prevL,
                                         AbbvGapsHMM.Emissions emission)

Enumerates the possible transitions into state D.

updateOutgoingEdgesStateDL

protected void updateOutgoingEdgesStateDL(int currS,
                                          int currL,
                                          int prevS,
                                          int prevL,
                                          AbbvGapsHMM.Emissions emission)

Enumerates the possible transitions into state DL.

updateOutgoingEdgesStateEND

protected void updateOutgoingEdgesStateEND(int currS,
                                           int currL,
                                           int prevS,
                                           int prevL,
                                           AbbvGapsHMM.Emissions emission)

Enumerates the possible transitions into state END.

updateOutgoingEdges

protected void updateOutgoingEdges(int currS,
                                   int currL,
                                   AbbvGapsHMM.States currState,
                                   int prevS,
                                   int prevL,
                                   AbbvGapsHMM.States prevState,
                                   AbbvGapsHMM.Transitions transition,
                                   AbbvGapsHMM.Emissions emission)

transitionIsLegal

protected boolean transitionIsLegal(int currS,
                                    int currL,
                                    AbbvGapsHMM.States currState,
                                    int prevS,
                                    int prevL,
                                    AbbvGapsHMM.States prevState,
                                    AbbvGapsHMM.Transitions transition,
                                    AbbvGapsHMM.Emissions emission)