package app;

import com.google.common.collect.Sets;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.TreeSet;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.semanticweb.elk.owlapi.ElkReasonerFactory;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.reasoner.InferenceType;
import org.semanticweb.owlapi.reasoner.Node;
import org.semanticweb.owlapi.reasoner.NodeSet;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;

/**
*
* @author Soniya
*/
public class Main {

// Corpus file path (please change these file path accordingly)
private final String corpus_file = "/Users/surya/NetBeansProjects/GeomProject/src/app/Assignment3-Corpus.txt";
private final String super_class_path = "/Users/surya/NetBeansProjects/GeomProject/src/app/superclasses.txt";
private final String owl_file_path = "/Users/surya/NetBeansProjects/GeomProject/src/app/go.owl";
private final String information_content =
         "/Users/surya/NetBeansProjects/GeomProject/src/app/ic.txt";

private Map<String, Double> mapIC = new HashMap<>();

/**
* This method reads the corpus file and returns the list of GO terms associated with
* CREB3L1 and RPS11.
* @return list of strings
*/
public List<String> getListGoTerms() {

   String CREB3L1 = "CREB3L1";
   String RPS11 = "RPS11";

   List<String> lstGo = new ArrayList<>();
   // List<String> lstRPS11 = new ArrayList<>();

   BufferedReader br = null;
   try {
         br = new BufferedReader(new FileReader(corpus_file));
         try {
            StringBuilder sb = new StringBuilder();
            String line = br.readLine();

            while (line != null) {

               String[] split = line.split(",");

               if (split != null && split.length > 0) {
                     if (CREB3L1.equals(split[0])) {
                        int index = 0;
                        for (String str : split) {

                           if (index == 0) {
                                 index++;
                                 continue;
                           }
                           lstGo.add(str);

                        }
                     } else if (RPS11.equals(split[0])) {
                        int index = 0;
                        for (String str : split) {

                           if (index == 0) {
                                 index++;
                                 continue;
                           }
                           lstGo.add(str);
                           index++;
                        }
                     }
               }

               line = br.readLine();

            }
            String everything = sb.toString();
         } catch (IOException ex) {
            System.out.println(ex.getMessage());
            Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
         } finally {
            try {
               br.close();
            } catch (IOException ex) {
               System.out.println(ex.getMessage());
               Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
            }
         }
   } catch (FileNotFoundException ex) {
         System.out.println(ex.getMessage());
         Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
   } finally {
         try {
            br.close();
         } catch (IOException ex) {
            System.out.println(ex.getMessage());
            Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
         }
   }
   return lstGo;
}

For this assignment, you are going to create a twist on the classic...