com.wcohen.ss.abbvGapsHmm

Class AbbvGapsHmmForwardEvaluator

java.lang.Object

com.wcohen.ss.abbvGapsHmm.AbbvGapsHMMEvaluator

com.wcohen.ss.abbvGapsHmm.AbbvGapsHmmForwardEvaluator

Direct Known Subclasses:

AbbvGapsHmmExpectationEvaluator

public class AbbvGapsHmmForwardEvaluator
extends AbbvGapsHMMEvaluator

Author:

Dana Movshovitz-Attias

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	AbbvGapsHmmForwardEvaluator.ForwardEvalParam

Nested classes/interfaces inherited from class com.wcohen.ss.abbvGapsHmm.AbbvGapsHMMEvaluator

AbbvGapsHMMEvaluator.EvalParam

Field Summary

Fields

Modifier and Type	Field and Description
protected List<Double>	_emissionParams
protected List<Double>	_transitionParams

Fields inherited from class com.wcohen.ss.abbvGapsHmm.AbbvGapsHMMEvaluator

_acronym, _currPartialWord, _currWord, _evalMat, _gapsHMM, _lParam, _partialWordParam, _sParam

Constructor Summary

Constructors

Constructor and Description
AbbvGapsHmmForwardEvaluator(AbbvGapsHMM abbvGapsHMM)

Method Summary

Modifier and Type	Method and Description
protected void	finalizeEvalMat()
protected static int	findLastNonLetterOrDigit(String str, int startPos)
void	forwardEvaluate(Acronym acronym, List<Double> transitionParams, List<Double> emissionParams)
protected 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 String	getCurrentWord(String str, int pos) Get the current long form word going backwards or forwards (depending on the implementing class).
protected static String	getEndedWord(String str, int pos) If pos is ending a word in str: returns this word.
protected static String	getPartialEndedWord(String str, int pos) If pos is ending a word in str: returns this word.
protected AbbvGapsHMMEvaluator.EvalParam	getPartialWordParam(String str, int pos)
protected void	initEvalMat()
protected void	initEvalParams()
protected static boolean	posIsAtWordEnd(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 void	updateLegalOutgoingEdges(int currS, int currL, AbbvGapsHMM.States currState, int prevS, int prevL, AbbvGapsHMM.States prevState, AbbvGapsHMM.Transitions transition, AbbvGapsHMM.Emissions emission)

Methods inherited from class com.wcohen.ss.abbvGapsHmm.AbbvGapsHMMEvaluator

andToSymbolMatch, charEqualIgnoreCase, evaluate, getEvalMatrix, posIsAtWord, posIsAtWordStart, updateOutgoingEdges, updateOutgoingEdgesStateD, updateOutgoingEdgesStateDL, updateOutgoingEdgesStateEND, updateOutgoingEdgesStateM, updateState

Methods inherited from class java.lang.Object

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

Field Detail

_transitionParams

protected List<Double> _transitionParams

_emissionParams

protected List<Double> _emissionParams

Constructor Detail

AbbvGapsHmmForwardEvaluator

public AbbvGapsHmmForwardEvaluator(AbbvGapsHMM abbvGapsHMM)

Method Detail

forwardEvaluate

public void forwardEvaluate(Acronym acronym,
                            List<Double> transitionParams,
                            List<Double> emissionParams)

updateLegalOutgoingEdges

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

Specified by:

updateLegalOutgoingEdges in class AbbvGapsHMMEvaluator

getCurrentChars

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

Description copied from class: AbbvGapsHMMEvaluator

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

Specified by:

getCurrentChars in class AbbvGapsHMMEvaluator

getCurrentWord

protected String getCurrentWord(String str,
                                int pos)

Description copied from class: AbbvGapsHMMEvaluator

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

Specified by:

getCurrentWord in class AbbvGapsHMMEvaluator

getPartialWordParam

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

Specified by:

getPartialWordParam in class AbbvGapsHMMEvaluator

getPartialEndedWord

protected static String getPartialEndedWord(String str,
                                            int pos)

If pos is ending a word in str: returns this word. Else: returns null;

getEndedWord

protected static String getEndedWord(String str,
                                     int pos)

If pos is ending a word in str: returns this word. Else: returns null;

posIsAtWordEnd

protected static boolean posIsAtWordEnd(String str,
                                        int pos)

findLastNonLetterOrDigit

protected static int findLastNonLetterOrDigit(String str,
                                              int startPos)

initEvalParams

protected void initEvalParams()

Specified by:

initEvalParams in class AbbvGapsHMMEvaluator

initEvalMat

protected void initEvalMat()

Specified by:

initEvalMat in class AbbvGapsHMMEvaluator

finalizeEvalMat

protected void finalizeEvalMat()

Specified by:

finalizeEvalMat in class AbbvGapsHMMEvaluator

transitionIsLegal

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

Overrides:

transitionIsLegal in class AbbvGapsHMMEvaluator