/**
* @param listOfDepRelsInReducedGraph
* @param listFeatIndsOfCurInp
* @param listFeatCountOfCurInp
*/
private void extractDepPatternFeatures(
ArrayList<String> listOfDepRelsInReducedGraph,
ArrayList<Integer> listFeatIndsOfCurInp,
ArrayList<Integer> listFeatCountOfCurInp) {
ArrayList<Integer> listOfMatchedPatternIndexes = new ArrayList<Integer>();
for (int i = 0; i < PatternsDepRelFromGraph.listOfAllPatterns.size(); i++) {
if (DataStrucUtility.hasListOneAllElementsOfListTwo(
listOfDepRelsInReducedGraph, PatternsDepRelFromGraph.listOfAllPatterns.get(i)))
listOfMatchedPatternIndexes.add(i);
}
for (int i = 0; i < listOfMatchedPatternIndexes.size(); i++) {
// add a feature indicating that what dep pattern it is
String[] feature =
new String[] {
"DepPattern-" + listOfMatchedPatternIndexes.get(i) + "@",
};
GenericFeatVect.addNewFeatureInList(
feature, 1, listFeatIndsOfCurInp, listFeatCountOfCurInp, 1);
}
}
public String preProcessWordWithDashEndingAndUpdateEntBoundaries(
String sentence, ArrayList<int[]> entBoundaryList) {
ArrayList<String> words = DataStrucUtility.arrayToList(sentence.split("\\s+"));
String old = sentence;
sentence = "";
int len = 0;
if (old.contains(" of p42 MAPK were completely blocked by")) old.trim();
for (int wi = 0; wi < words.size(); wi++) {
if (words.get(wi).length() == 1) ; // do nothing
else if (words.get(wi).matches(".*[a-zA-Z].*-")) {
/*
* TODO: have to adjust entity boundaries for following entities and sentence
* [liver-, islet-type glucokinase, glucokinase, actin]
* When liver or islet type glucokinase was transiently expressed in COS-7 cells, the expressed glucokinase was also co-localized with actin filaments in the cytoplasm of these transfected cells.
*/
int lastDashInd = -1;
// remove dash from the ending
// identify the next word having dash
// replace the dash of that word with space
for (int x = wi + 1; x < words.size(); x++) {
if ((lastDashInd = words.get(x).lastIndexOf("-")) > 0
&& lastDashInd != words.get(x).length() - 1) {
// System.out.println(old);
// System.out.println(words.get(wi));
String newPart = words.get(x).substring(lastDashInd + 1);
words.set(wi, words.get(wi).substring(0, words.get(wi).length() - 1));
updateBoundaries(entBoundaryList, 1, len - 1, false);
words.set(x, words.get(x).substring(0, lastDashInd));
words.add(x + 1, newPart);
updateBoundaries(entBoundaryList, 1, len - 1, false);
break;
}
}
}
len += words.get(wi).length();
sentence += " " + words.get(wi);
}
return sentence.trim();
}
public String preProcessWordWithDashEndingByAddingExtraWordAndUpdateEntBoundaries(
String sentence, ArrayList<int[]> entBoundaryList) {
ArrayList<String> words = DataStrucUtility.arrayToList(sentence.split("\\s+"));
sentence = "";
int len = 0;
for (int wi = 0; wi < words.size(); wi++) {
if (words.get(wi).length() == 1) ; // do nothing
else if (words.get(wi).matches(".*[0-9a-zA-Z]-")) {
int lastDashInd = -1;
// identify the next word having dash
// add the end token after the dash with the current word
// we assume, the end token would not contain any entity name
// we further assume, the end token is correct part that is meant to be related with the
// current word
for (int x = wi + 1; x < words.size(); x++) {
if ((lastDashInd = words.get(x).lastIndexOf("-")) > 0
&& lastDashInd != words.get(x).length() - 1) {
// System.out.println(old);
// System.out.println(words.get(wi));
String newPart = words.get(x).substring(lastDashInd + 1);
words.set(wi, words.get(wi) + newPart);
updateBoundaries(entBoundaryList, newPart.length(), len - 1, true);
break;
}
}
}
len += words.get(wi).length();
sentence += " " + words.get(wi);
}
return sentence.trim();
}
/**
* Note: This particular pre-processing didn't improve results in the LLL corpus.
*
* @param bioRelExInpFile
* @param psgParsedFileName
* @throws Exception
*/
public String removeCommentsWithNoEntInParentheses(
String sentence, ArrayList<int[]> entBoundaryList) {
ArrayList<String> words = DataStrucUtility.arrayToList(sentence.split("\\s+"));
int bracS = -1, bracE = -1, tb = 0;
boolean isFoundEnt = false;
// the 1st item in the list is sentence id
for (int i = 0; i < words.size(); i++) {
if (words.get(i).matches(".*\\)[?,.:;!]")) {
words.add(i + 1, String.valueOf(words.get(i).charAt(words.get(i).length() - 1)));
words.set(i, words.get(i).substring(0, words.get(i).length() - 1));
}
if (words.get(i).charAt(0) == '(') {
tb++;
if (tb == 1) {
bracS = i;
isFoundEnt = false;
}
}
if (words.get(i).charAt(words.get(i).length() - 1) == ')') {
tb--;
if (tb == 0) {
bracE = i;
int offset = 0, from = 0;
for (int w = 0; w <= bracE; w++) {
offset += words.get(w).length();
if (w < bracS) from = offset;
}
for (int e = 0; e < entBoundaryList.size(); e++) {
if (entBoundaryList.get(e)[0] >= from && entBoundaryList.get(e)[1] <= offset) {
isFoundEnt = true;
break;
}
}
offset = offset - from;
if (!isFoundEnt) {
updateBoundaries(entBoundaryList, offset, from - 1, false);
for (int k = bracE; k >= bracS; k--) words.remove(k);
i = bracS - 1;
}
}
}
}
sentence = "";
for (int i = 0; i < words.size(); i++) sentence += " " + words.get(i);
return sentence.trim();
}
