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c574d3a | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package tool.sieves;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import tool.util.Concept;
import tool.util.Ling;
import tool.util.Terminology;
import tool.util.Util;
/**
*
* @author
*/
public class PartialMatchNCBISieve {
public static String apply(Concept concept) {
String name = concept.getName();
String[] nameTokens = name.split("\\s+");
return partialMatch(name, nameTokens);
}
private static String partialMatch(String phrase, String[] phraseTokens) {
List<String> partialMatchedPhrases = new ArrayList<>();
Map<Integer, Map<String, Integer>> candidateCuiDataMap = init();
for (String phraseToken : phraseTokens) {
if (Ling.getStopwordsList().contains(phraseToken))
continue;
List<String> candidatePhrases = null;
int map = -1;
if (Sieve.getTrainingDataTerminology().getTokenToNameListMap().containsKey(phraseToken)) {
candidatePhrases = new ArrayList<>(Sieve.getTrainingDataTerminology().getTokenToNameListMap().get(phraseToken));
map = 2;
}
else if (Sieve.getStandardTerminology().getTokenToNameListMap().containsKey(phraseToken)) {
candidatePhrases = new ArrayList<>(Sieve.getStandardTerminology().getTokenToNameListMap().get(phraseToken));
map = 3;
}
if (candidatePhrases == null)
continue;
candidatePhrases.removeAll(partialMatchedPhrases);
candidateCuiDataMap = ncbiPartialMatch(phrase, candidatePhrases, partialMatchedPhrases, map == 2 ? Sieve.getTrainingDataTerminology() : Sieve.getStandardTerminology(), candidateCuiDataMap);
}
return !candidateCuiDataMap.get(1).isEmpty() ? getCui(candidateCuiDataMap.get(1), candidateCuiDataMap.get(2)) : "";
}
private static Map<Integer, Map<String, Integer>> init() {
Map<Integer, Map<String, Integer>> candidateCuiDataMap = new HashMap<>();
candidateCuiDataMap.put(1, new HashMap<String, Integer>());
candidateCuiDataMap.put(2, new HashMap<String, Integer>());
return candidateCuiDataMap;
}
private static Map<Integer, Map<String, Integer>> ncbiPartialMatch(String phrase, List<String> candidatePhrases, List<String> partialMatchedPhrases, Terminology terminology, Map<Integer, Map<String, Integer>> cuiCandidateDataMap) {
Map<String, Integer> cuiCandidateMatchingTokensCountMap = cuiCandidateDataMap.get(1);
Map<String, Integer> cuiCandidateLengthMap = cuiCandidateDataMap.get(2);
for (String candidatePhrase : candidatePhrases) {
partialMatchedPhrases = Util.setList(partialMatchedPhrases, candidatePhrase);
int count = Ling.getMatchingTokensCount(phrase, candidatePhrase);
int length = candidatePhrase.split("\\s+").length;
String cui = terminology.getNameToCuiListMap().get(candidatePhrase).get(0);
if (cuiCandidateMatchingTokensCountMap.containsKey(cui)) {
int oldCount = cuiCandidateMatchingTokensCountMap.get(cui);
if (oldCount < count) {
cuiCandidateMatchingTokensCountMap.put(cui, count);
cuiCandidateLengthMap.put(cui, length);
}
continue;
}
cuiCandidateMatchingTokensCountMap.put(cui, count);
cuiCandidateLengthMap.put(cui, length);
}
cuiCandidateDataMap.put(1, cuiCandidateMatchingTokensCountMap);
cuiCandidateDataMap.put(2, cuiCandidateLengthMap);
return cuiCandidateDataMap;
}
private static String getCui(Map<String, Integer> cuiCandidateMatchedTokensCountMap, Map<String, Integer> cuiCandidateLengthMap) {
String cui = "";
int maxMatchedTokensCount = -1;
Map<Integer, List<String>> matchedTokensCountCuiListMap = new HashMap<>();
for (String candidateCui : cuiCandidateMatchedTokensCountMap.keySet()) {
int matchedTokensCount = cuiCandidateMatchedTokensCountMap.get(candidateCui);
if (matchedTokensCount >= maxMatchedTokensCount) {
maxMatchedTokensCount = matchedTokensCount;
List<String> cuiList = matchedTokensCountCuiListMap.get(matchedTokensCount);
if (cuiList == null)
matchedTokensCountCuiListMap.put(matchedTokensCount, cuiList = new ArrayList<>());
cuiList = Util.setList(cuiList, candidateCui);
}
}
List<String> candidateCuiList = matchedTokensCountCuiListMap.get(maxMatchedTokensCount);
if (candidateCuiList.size() == 1)
return candidateCuiList.get(0);
else {
int minCandidateLength = 1000;
for (String candidateCui : candidateCuiList) {
int length = cuiCandidateLengthMap.get(candidateCui);
if (length < minCandidateLength) {
minCandidateLength = length;
cui = candidateCui;
}
}
}
return cui;
}
}
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