code: package eu.fbk.dh.tint.eval.ner;
  
  import edu.stanford.nlp.stats.MultiClassChunkEvalStats;
  import eu.fbk.utils.core.CommandLine;
  import org.slf4j.Logger;
  import org.slf4j.LoggerFactory;
  
  import java.io.BufferedReader;
  import java.io.File;
  import java.io.FileReader;
  import java.util.ArrayList;
  import java.util.List;
  
  /**
   * Created by alessio on 20/07/16.
   */
  
  public class PairEvaluation {
  
      private static final Logger LOGGER = LoggerFactory.getLogger(PairEvaluation.class);
  
      public static void main(String[] args) {
          try {
              final CommandLine cmd = CommandLine
                      .parser()
                      .withName("./evaluate-ner")
                      .withHeader("Calculate NER evaluation")
                      .withOption("t", "guessed", "Input file", "FILE",
                              CommandLine.Type.FILE_EXISTING, true, false, true)
                      .withOption("g", "gold-standard", "Input gold standard file", "FILE",
                              CommandLine.Type.FILE, true, false, true)
                      .withLogger(LoggerFactory.getLogger("eu.fbk")).parse(args);
  
              File guessed = cmd.getOptionValue("guessed", File.class);
              File gold = cmd.getOptionValue("gold-standard", File.class);
  
              List<String> guesses = new ArrayList<>();
              List<String> trueLabels = new ArrayList<>();
  
              BufferedReader tReader = new BufferedReader(new FileReader(guessed));
              BufferedReader gReader = new BufferedReader(new FileReader(gold));
  
              String line;
  
              while ((line = tReader.readLine()) != null) {
                  line = line.trim();
                  if (line.startsWith("#")) {
                      continue;
                  }
                  String[] parts = line.split("\t");
                  if (parts.length < 2) {
                      continue;
                  }
  
                  String ner = parts[parts.length - 1];
                  ner = ner.replaceAll("^[A-Za-z]-", "");
                  if (ner.equals("GPE")) {
                      ner = "LOC";
                  }
  
                  guesses.add(ner);
              }
  
              while ((line = gReader.readLine()) != null) {
                  line = line.trim();
                  String[] parts = line.split("\t");
                  if (parts.length < 2) {
                      continue;
                  }
  
                  String ner = parts[parts.length - 1];
                  trueLabels.add(ner);
              }
  
              if (guesses.size() != trueLabels.size()) {
                  LOGGER.error("Sizes are not identical");
              }
              else {
                  MultiClassChunkEvalStats stats = new MultiClassChunkEvalStats("O");
                  stats.score(guesses, trueLabels);
                  System.out.println(stats.getConllEvalString());
              }
              tReader.close();
              gReader.close();
          } catch (Exception e) {
              CommandLine.fail(e);
          }
      }
  }
  