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package com.wcohen.ss.abbvGapsHmm;
import com.wcohen.ss.abbvGapsHmm.AbbvGapsHMM.*;
/**
* @author Dana Movshovitz-Attias
*/
public abstract class AbbvGapsHMMEvaluator {
protected AbbvGapsHMM _gapsHMM = null;
public AbbvGapsHMMEvaluator(AbbvGapsHMM abbvGapsHMM){
_gapsHMM = abbvGapsHMM;
}
protected abstract class EvalParam{
public int _eval_start;
public int _eval_end;
public int _eval_mat_size;
public int _length;
public int _current = -1;
public int _currentStringPos = -1;
public boolean _partialWordIsAtStart = false;
public String _partialWord = null;
/**
*
*/
public EvalParam(String str) {
_length = str.length();
_eval_mat_size = _length+2;
}
public int val() { return _current; }
/**
* Init evaluation range
*/
public abstract void initEvalRange();
/**
* Advance within evaluation range
*/
public abstract void advanceEvalRange();
/**
* Is in evaluation range
*/
public abstract boolean isInEvalRange();
public boolean isAtRangeStart() { return _current == _eval_start; }
public boolean isAtRangeEnd() { return _current == _eval_start; }
public abstract boolean isInStringMatchingRange();
public int getEvalStringPos() { return _currentStringPos; }
public abstract int offset(int offset);
public int getEvalMatrixSize() { return _eval_mat_size; }
public int getRangeStart() { return _eval_start; }
public int getRangeEnd() { return _eval_end; }
public abstract void setPartialWord(String str, boolean isAtWordStart);
public abstract int getCurrentPartialWordLen();
public abstract int getCurrentPartialWordMatchPosition();
public abstract boolean isCurrentPartialWordMatchPositionAtWordStart();
};
protected abstract void updateLegalOutgoingEdges(
int currS, int currL, States currState,
int prevS, int prevL, States prevState,
Transitions transition, Emissions emission);
protected abstract void initEvalMat();
protected abstract void finalizeEvalMat();
/**
* Get the current long form word going backwards or forwards (depending on the implementing class).
*/
protected abstract String getCurrentWord(String str, int pos);
/**
* Get characters from the string going backwards or forwards (depending on the implementing class),
* and according to the specifies length.
*/
protected abstract String getCurrentChars(String str, int pos, int length);
protected abstract EvalParam getPartialWordParam(String str, int pos);
protected abstract void initEvalParams();
protected Matrix3D _evalMat;
protected EvalParam _sParam;
protected EvalParam _lParam;
protected EvalParam _partialWordParam = null;
protected Acronym _acronym;
protected String _currWord;
protected String _currPartialWord;
public Matrix3D getEvalMatrix(){
return _evalMat;
}
/**
* This function enumerates the possible transitions and emissions in a hard coded way, in order to save running-time
*/
protected void evaluate(Acronym acronym){
_acronym = acronym;
initEvalParams();
// Number of states
int V = States.values().length;
_evalMat = new Matrix3D(_sParam.getEvalMatrixSize(), _lParam.getEvalMatrixSize(), V);
// Iterate over possible alignments
Integer wordLen = -1;
int lPos, sPos;
initEvalMat();
for(_sParam.initEvalRange(); _sParam.isInEvalRange(); _sParam.advanceEvalRange()) {
for (_lParam.initEvalRange(); _lParam.isInEvalRange(); _lParam.advanceEvalRange()) {
wordLen = null;
// Current position in evaluated strings
lPos = _lParam.getEvalStringPos();
sPos = _sParam.getEvalStringPos();
// Deletions
if(_lParam.isInStringMatchingRange()){
_currWord = getCurrentWord(acronym._longForm, lPos);
if(_currWord != null)
wordLen = _currWord.length();
_partialWordParam = getPartialWordParam(acronym._longForm, lPos);
if(Character.isLetterOrDigit(acronym._longForm.charAt(lPos))){
// Deleting leading letter
updateState(States.DL, _sParam.val(), _lParam.val(), _sParam.val(), _lParam.offset(1), Emissions.e_DL_alphaNumeric_to_none);
// Deleting inner letter
updateState(States.D, _sParam.val(), _lParam.val(), _sParam.val(), _lParam.offset(1), Emissions.e_D_alphaNumeric_to_none);
}
else{
// Deleting leading space
updateState(States.DL, _sParam.val(), _lParam.val(), _sParam.val(), _lParam.offset(1), Emissions.e_DL_nonAlphaNumeric_to_none);
// Deleting inner space
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.val(), _lParam.offset(1), Emissions.e_M_nonAlphaNumeric_to_none);
}
if(_currWord != null){
// Deleting leading word
updateState(States.DL, _sParam.val(), _lParam.val(), _sParam.val(), _lParam.offset(wordLen), Emissions.e_DL_word_to_none);
// Deleting inner word
updateState(States.D, _sParam.val(), _lParam.val(), _sParam.val(), _lParam.offset(wordLen), Emissions.e_D_word_to_none);
// Allow deletion of common word
if(_gapsHMM.useTDIDF()){
Double wordDF = _gapsHMM.getDF(_currWord);
if(wordDF != null){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.val(), _lParam.offset(wordLen), Emissions.e_M_commonWordDeletion);
}
}
}
}//deletions
// Insertions
if(_sParam.isInStringMatchingRange()){
// Allowing digit deletions in the short form can ONLY work if low scoring alignments are discarded.
// Scores are calculated in AbbreviationAlignment by considering the number of deletions vs. the number
// of matched words (and not single letters). This makes for a "nice" alignment which usually corresponds
// with a good alignment.
if(!Character.isLetter(acronym._shortForm.charAt(sPos))){
// Insertion of non-alphanumeric character in short form
updateState(States.D, _sParam.val(), _lParam.val(), _sParam.offset(1), _lParam.val(), Emissions.e_D_none_to_nonAlphaNumeric);
}
}
// Matches
if(_sParam.isInStringMatchingRange() && _lParam.isInStringMatchingRange()){
if(!Character.isLetter(acronym._shortForm.charAt(sPos)) && charEqualIgnoreCase(acronym._shortForm.charAt(sPos), acronym._longForm.charAt(lPos))){
// letter_to_letter
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(1), _lParam.offset(1), Emissions.e_M_letter_to_letter);
}
String sfChars_2 = getCurrentChars(acronym._shortForm, sPos, 2);
if(_currWord != null){
// AND_to_symbol
if(_currWord.equalsIgnoreCase("and") && andToSymbolMatch(acronym._shortForm.charAt(sPos))){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(1), _lParam.offset(wordLen), Emissions.e_M_AND_to_symbol);
}
// numbers
else if(_currWord.equalsIgnoreCase("one") && acronym._shortForm.charAt(sPos) == '1'){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(1), _lParam.offset(wordLen), Emissions.e_M_one_to_1);
}
else if(_currWord.equalsIgnoreCase("two") && acronym._shortForm.charAt(sPos) == '2'){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(1), _lParam.offset(wordLen), Emissions.e_M_two_to_2);
}
else if(_currWord.equalsIgnoreCase("three") && acronym._shortForm.charAt(sPos) == '3'){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(1), _lParam.offset(wordLen), Emissions.e_M_three_to_3);
}
else if(_currWord.equalsIgnoreCase("four") && acronym._shortForm.charAt(sPos) == '4'){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(1), _lParam.offset(wordLen), Emissions.e_M_four_to_4);
}
else if(_currWord.equalsIgnoreCase("five") && acronym._shortForm.charAt(sPos) == '5'){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(1), _lParam.offset(wordLen), Emissions.e_M_five_to_5);
}
else if(_currWord.equalsIgnoreCase("six") && acronym._shortForm.charAt(sPos) == '6'){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(1), _lParam.offset(wordLen), Emissions.e_M_six_to_6);
}
else if(_currWord.equalsIgnoreCase("seven") && acronym._shortForm.charAt(sPos) == '7'){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(1), _lParam.offset(wordLen), Emissions.e_M_seven_to_7);
}
else if(_currWord.equalsIgnoreCase("eight") && acronym._shortForm.charAt(sPos) == '8'){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(1), _lParam.offset(wordLen), Emissions.e_M_eight_to_8);
}
else if(_currWord.equalsIgnoreCase("nine") && acronym._shortForm.charAt(sPos) == '9'){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(1), _lParam.offset(wordLen), Emissions.e_M_nine_to_9);
}
// Double letter chemical elements
else if(_currWord.equalsIgnoreCase("Silver") && sfChars_2.equalsIgnoreCase("Ag")){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(2), _lParam.offset(wordLen), Emissions.e_M_Silver_Ag);
}
else if(_currWord.equalsIgnoreCase("Gold") && sfChars_2.equalsIgnoreCase("Au")){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(2), _lParam.offset(wordLen), Emissions.e_M_Gold_Au);
}
else if(_currWord.equalsIgnoreCase("Copper") && sfChars_2.equalsIgnoreCase("Cu")){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(2), _lParam.offset(wordLen), Emissions.e_M_Copper_Cu);
}
else if(_currWord.equalsIgnoreCase("Iron") && sfChars_2.equalsIgnoreCase("Fe")){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(2), _lParam.offset(wordLen), Emissions.e_M_Iron_Fe);
}
else if(_currWord.equalsIgnoreCase("Mercury") && sfChars_2.equalsIgnoreCase("Hg")){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(2), _lParam.offset(wordLen), Emissions.e_M_Mercury_Hg);
}
else if(_currWord.equalsIgnoreCase("Sodium") && sfChars_2.equalsIgnoreCase("Na")){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(2), _lParam.offset(wordLen), Emissions.e_M_Sodium_Na);
}
else if(_currWord.equalsIgnoreCase("Lead") && sfChars_2.equalsIgnoreCase("Pb")){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(2), _lParam.offset(wordLen), Emissions.e_M_Lead_Pb);
}
else if(_currWord.equalsIgnoreCase("Antimony") && sfChars_2.equalsIgnoreCase("Sb")){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(2), _lParam.offset(wordLen), Emissions.e_M_Antimony_Sb);
}
else if(_currWord.equalsIgnoreCase("Tin") && sfChars_2.equalsIgnoreCase("Sn")){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(2), _lParam.offset(wordLen), Emissions.e_M_Tin_Sn);
}
// Single letter chemical elements
else if(_currWord.equalsIgnoreCase("Potassium") && acronym._shortForm.charAt(sPos) == 'K'){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(1), _lParam.offset(wordLen), Emissions.e_M_Potassium_K);
}
else if(_currWord.equalsIgnoreCase("Tungsten") && acronym._shortForm.charAt(sPos) == 'W'){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(1), _lParam.offset(wordLen), Emissions.e_M_Tungsten_W);
}
}
if(_partialWordParam != null){
// Partial Matches
_currPartialWord = _partialWordParam._partialWord;
for (_partialWordParam.initEvalRange(); _partialWordParam.isInEvalRange(); _partialWordParam.advanceEvalRange()) {
if(charEqualIgnoreCase(acronym._shortForm.charAt(sPos), _currPartialWord.charAt(_partialWordParam.getCurrentPartialWordMatchPosition()))){
if(_partialWordParam.getCurrentPartialWordLen() == 1){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(1), _lParam.offset(1), Emissions.e_M_letter_to_letter);
}
else if(_partialWordParam.isCurrentPartialWordMatchPositionAtWordStart()){
updateState(States.M, _sParam.val(), _lParam.val(), _sParam.offset(1), _lParam.offset(_partialWordParam.getCurrentPartialWordLen()), Emissions.e_M_word_to_firstLetter);
}
else{
updateState(States.M, _sParam.val(), _lParam.val(),
_sParam.offset(1), _lParam.offset(_partialWordParam.getCurrentPartialWordLen()), Emissions.e_M_partialWord_to_letter);
}
}
}
}
}//matches
}//l
}//s
finalizeEvalMat();
}
protected static boolean posIsAtWordStart(String str, int pos){
assert(pos < str.length() && pos >= 0);
return Character.isLetterOrDigit(str.charAt(pos)) &&
(pos == 0 || !Character.isLetterOrDigit(str.charAt(pos-1)));
}
protected boolean charEqualIgnoreCase(char c1, char c2){
boolean charMatch = Character.toLowerCase(c1) == Character.toLowerCase(c2);
return charMatch;
}
protected boolean andToSymbolMatch(char c){
return c == '&' || c == '/' || c == '-';
}
protected static boolean posIsAtWord(String str, int pos){
assert(pos < str.length() && pos >= 0);
return Character.isLetterOrDigit(str.charAt(pos));
}
protected void updateState(
States s,
int currS, int currL,
int prevS, int prevL,
Emissions emission
){
switch (s) {
case M :
updateOutgoingEdgesStateM(currS, currL, prevS, prevL, emission);
break;
case D :
updateOutgoingEdgesStateD(currS, currL, prevS, prevL, emission);
break;
case DL :
updateOutgoingEdgesStateDL(currS, currL, prevS, prevL, emission);
break;
case END :
updateOutgoingEdgesStateEND(currS, currL, prevS, prevL, emission);
break;
default :
break;
}
}
/**
* Enumerates the possible transitions into state M.
* @param currS
* @param currL
* @param prevS
* @param prevL
*/
protected void updateOutgoingEdgesStateM(
int currS, int currL,
int prevS, int prevL,
Emissions emission
){
updateOutgoingEdges(currS, currL, States.M, prevS, prevL, States.DL, Transitions.t_DL_to_M, emission);
updateOutgoingEdges(currS, currL, States.M, prevS, prevL, States.M, Transitions.t_M_in, emission);
updateOutgoingEdges(currS, currL, States.M, prevS, prevL, States.D, Transitions.t_D_to_M, emission);
updateOutgoingEdges(currS, currL, States.M, prevS, prevL, States.S, Transitions.t_S_to_M, emission);
}
/**
* Enumerates the possible transitions into state D.
*/
protected void updateOutgoingEdgesStateD(
int currS, int currL,
int prevS, int prevL,
Emissions emission
){
updateOutgoingEdges(currS, currL, States.D, prevS, prevL, States.D, Transitions.t_D_in, emission);
updateOutgoingEdges(currS, currL, States.D, prevS, prevL, States.M, Transitions.t_M_to_D, emission);
}
/**
* Enumerates the possible transitions into state DL.
*/
protected void updateOutgoingEdgesStateDL(
int currS, int currL,
int prevS, int prevL,
Emissions emission
){
updateOutgoingEdges(currS, currL, States.DL, prevS, prevL, States.DL, Transitions.t_DL_in, emission);
updateOutgoingEdges(currS, currL, States.DL, prevS, prevL, States.S, Transitions.t_S_to_DL, emission);
}
/**
* Enumerates the possible transitions into state END.
*/
protected void updateOutgoingEdgesStateEND(
int currS, int currL,
int prevS, int prevL,
Emissions emission
){
updateOutgoingEdges(currS, currL, States.END, prevS, prevL, States.D, Transitions.t_D_to_END, emission);
updateOutgoingEdges(currS, currL, States.END, prevS, prevL, States.M, Transitions.t_M_to_END, emission);
}
protected void updateOutgoingEdges(
int currS, int currL, States currState,
int prevS, int prevL, States prevState,
Transitions transition, Emissions emission
){
if(! transitionIsLegal(currS, currL, currState, prevS, prevL, prevState, transition, emission) )
return;
updateLegalOutgoingEdges(currS, currL, currState, prevS, prevL, prevState, transition, emission);
}
protected boolean transitionIsLegal(
int currS, int currL, States currState,
int prevS, int prevL, States prevState,
Transitions transition, Emissions emission
){
return true;
}
}
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