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package com.wcohen.ss.abbvGapsHmm;
import java.util.List;
import com.wcohen.ss.abbvGapsHmm.AbbvGapsHMM.Emissions;
import com.wcohen.ss.abbvGapsHmm.AbbvGapsHMM.States;
import com.wcohen.ss.abbvGapsHmm.AbbvGapsHMM.Transitions;
/**
* @author Dana Movshovitz-Attias
*/
public class AbbvGapsHmmForwardEvaluator
extends
AbbvGapsHMMEvaluator {
protected class ForwardEvalParam extends EvalParam{
/**
*
*/
public ForwardEvalParam(String str) {
super(str);
_eval_start = 0;
_eval_end = _length;
}
public void advanceEvalRange(){
_current++;
_currentStringPos = _current-1;
}
public boolean isInEvalRange(){ return _current <= _eval_end; }
public boolean isInStringMatchingRange() { return _currentStringPos >= _eval_start; }
public int offset(int offset) { return _current-offset; }
public boolean isCurrentPartialWordMatchPositionAtWordStart() {
return _current == _eval_start;
}
/* (non-Javadoc)
* @see Structures.AbbvGapsHMMEvaluator.EvalParam#initEvalRange()
*/
@Override
public void initEvalRange() {
_current = _eval_start;
_currentStringPos = _current-1;
}
/* (non-Javadoc)
* @see Structures.AbbvGapsHMMEvaluator.EvalParam#setPartialWord()
*/
@Override
public void setPartialWord(String str, boolean isAtWordStart) {
_length = str.length();
_eval_start = 0;
_eval_end = _length-1;
_partialWordIsAtStart = isAtWordStart;
_partialWord = str;
}
/* (non-Javadoc)
* @see Structures.AbbvGapsHMMEvaluator.EvalParam#getCurrentPartialWordLen()
*/
@Override
public int getCurrentPartialWordLen() {
return _length-_current;
}
/* (non-Javadoc)
* @see Structures.AbbvGapsHMMEvaluator.EvalParam#getCurrentPartialWordMatchPosition()
*/
@Override
public int getCurrentPartialWordMatchPosition() {
return _current;
}
}
protected List<Double> _transitionParams;
protected List<Double> _emissionParams;
public AbbvGapsHmmForwardEvaluator(AbbvGapsHMM abbvGapsHMM) {
super(abbvGapsHMM);
}
public void forwardEvaluate(Acronym acronym, List<Double> transitionParams, List<Double> emissionParams){
_transitionParams = transitionParams;
_emissionParams = emissionParams;
super.evaluate(acronym);
}
protected void updateLegalOutgoingEdges(
int currS, int currL, States currState,
int prevS, int prevL, States prevState,
Transitions transition, Emissions emission
){
_evalMat.add(currS, currL, currState.ordinal(),
_evalMat.at(prevS, prevL, prevState.ordinal())*_emissionParams.get(emission.ordinal())*_transitionParams.get(transition.ordinal()));
}
protected String getCurrentChars(String str, int pos, int length){
int startIndex = Math.max(pos-length+1, 0);
return str.substring(startIndex, pos+1);
}
/* (non-Javadoc)
* @see Structures.AbbvGapsHMMEvaluator#getCurrentWord(java.lang.String, int)
*/
@Override
protected String getCurrentWord(String str, int pos) {
return getEndedWord(str, pos);
}
protected EvalParam getPartialWordParam(String str, int pos) {
EvalParam partialWordPraram = new ForwardEvalParam("");
String partialWordStr = getPartialEndedWord(str, pos);
if(partialWordStr == null)
return null;
partialWordPraram.setPartialWord(partialWordStr, posIsAtWordStart(str, pos-partialWordStr.length()+1));
return partialWordPraram;
}
/**
* If pos is ending a word in str: returns this word.
* Else: returns null;
*/
protected static String getPartialEndedWord(String str, int pos){
assert(pos < str.length() && pos >= 0);
if( posIsAtWord(str, pos) ){
int prevSpace = findLastNonLetterOrDigit(str, pos);
return str.substring(prevSpace+1, pos+1);
}
return null;
}
/**
* If pos is ending a word in str: returns this word.
* Else: returns null;
*/
protected static String getEndedWord(String str, int pos){
assert(pos < str.length() && pos >= 0);
if( posIsAtWordEnd(str, pos) ){
int prevSpace = findLastNonLetterOrDigit(str, pos);
return str.substring(prevSpace+1, pos+1);
}
return null;
}
protected static boolean posIsAtWordEnd(String str, int pos){
assert(pos < str.length() && pos >= 0);
// return pos == 0 || Character.isWhitespace(str.charAt(pos-1));
return Character.isLetterOrDigit(str.charAt(pos)) &&
(pos == str.length()-1 || !Character.isLetterOrDigit(str.charAt(pos+1)));
}
protected static int findLastNonLetterOrDigit(String str, int startPos){
int lastNonWord = -1;
for (int i = startPos-1; i >= 0; i--) {
if(!Character.isLetterOrDigit(str.charAt(i))){
lastNonWord = i;
break;
}
}
return lastNonWord;
}
/* (non-Javadoc)
* @see Structures.AbbvGapsHMMEvaluator#initEvalParams(Structures.Acronym)
*/
@Override
protected void initEvalParams() {
_sParam = new ForwardEvalParam(_acronym._shortForm);
_lParam = new ForwardEvalParam(_acronym._longForm);
_partialWordParam = null;
}
/* (non-Javadoc)
* @see Structures.AbbvGapsHMMEvaluator#initEvalMat()
*/
@Override
protected void initEvalMat() {
_evalMat.set(_sParam.getRangeStart(), _lParam.getRangeStart(), States.S.ordinal(), 1);
}
/* (non-Javadoc)
* @see Structures.AbbvGapsHMMEvaluator#initEvalMat()
*/
@Override
protected void finalizeEvalMat() {
updateState(States.END, _sParam.val(), _lParam.val(), _sParam.offset(1), _lParam.offset(1), Emissions.e_END_end);
}
protected boolean transitionIsLegal(
int currS, int currL, States currState,
int prevS, int prevL, States prevState,
Transitions transition, Emissions emission
){
boolean legal = true;
// First match must be to word start
if(transition.equals(Transitions.t_DL_to_M) || transition.equals(Transitions.t_S_to_M)){
if(! (posIsAtWordStart(_acronym._longForm, _lParam.getEvalStringPos()) || _currPartialWord != null || _currWord != null )){
legal = false;
}
}
return legal && super.transitionIsLegal(currS, currL, currState, prevS, prevL, prevState, transition, emission);
}
}
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