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/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package tool;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import tool.util.Concept;
import tool.util.DocumentConcepts;
import tool.util.Util;
/**
*
* @author
*/
public class Evaluation {
private static int totalNames = 0;
private static int tp = 0;
private static int fp = 0;
private static double accuracy = 0.0;
public static void incrementTotal() {
totalNames++;
}
public static void incrementTP() {
tp++;
}
public static void incrementFP() {
fp++;
}
public static void evaluateClassification(Concept concept, DocumentConcepts concepts) throws IOException {
incrementTotal();
if ((!concept.getGoldMeSHorSNOMEDCui().equals("") && concept.getGoldMeSHorSNOMEDCui().equals(concept.getCui())) ||
(!concept.getGoldOMIMCuis().isEmpty() && concept.getGoldOMIMCuis().contains(concept.getCui())))
incrementTP();
else if (concept.getGoldMeSHorSNOMEDCui().contains("|") && concept.getCui().contains("|")) {
List<String> gold = new ArrayList<>(Arrays.asList(concept.getGoldMeSHorSNOMEDCui().split("\\|")));
List<String> predicted = new ArrayList<>(Arrays.asList(concept.getCui().split("\\|")));
gold.removeAll(predicted);
if (gold.isEmpty()) {
incrementTP();
}
else {
incrementFP();
}
}
else if (concept.getAlternateCuis() != null && !concept.getAlternateCuis().isEmpty()) {
if (!concept.getGoldMeSHorSNOMEDCui().equals("") && concept.getAlternateCuis().contains(concept.getGoldMeSHorSNOMEDCui())) {
incrementTP();
concept.setCui(concept.getGoldMeSHorSNOMEDCui());
}
else if (!concept.getGoldOMIMCuis().isEmpty() && Util.containsAny(concept.getAlternateCuis(), concept.getGoldOMIMCuis())) {
incrementTP();
if (concept.getGoldOMIMCuis().size() == 1)
concept.setCui(concept.getGoldOMIMCuis().get(0));
}
else {
incrementFP();
}
}
else {
incrementFP();
}
//write output
FileOutputStream output = new FileOutputStream(Main.output_data_dir+"\\"+concepts.getFilename().replace(".txt", ".concept"), true);
output.write((concepts.getFilename().replace(".txt", "")+"||"+concept.getIndexes()+"||"+concept.getName()+"||"+concept.getCui()+"\n").getBytes());
//logger output
//Logger.writeLogFile((concepts.getFilename()+"\t"+concept.getIndexes()+"\t"+concept.getName()+"\t"+concept.getCui()+"\t"+concept.getGoldCui()));
}
public static void computeAccuracy() {
accuracy = (double)tp/(double)totalNames;
}
public static void printResults() {
System.out.println("*********************");
System.out.println("Total Names: "+totalNames);
System.out.println("True Normalizations: "+tp);
System.out.println("False Normalizations: "+fp);
System.out.println("Accuracy: "+accuracy);
System.out.println("*********************");
}
}
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