import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.HashSet;
import java.util.Set;

/**
 * @author alt
 */
public class Task06 {

    public static void main(String[] args) throws IOException, ClassNotFoundException, SQLException {
        String genome1 = readFile("Genome_1.txt");
        String genome2 = readFile("Genome_2.txt");



        Class.forName("org.postgresql.Driver");
        Connection connection = DriverManager.getConnection(
                "jdbc:postgresql://localhost:5433/lesson","postgres", "postgres");

        Statement statement = connection.createStatement();

        insertGenomeToDB(genome1, statement, 3);
        insertGenomeToDB(genome2, statement, 4);

        connection.close();

    }

    private static String readFile(String file) throws IOException {
        BufferedReader reader = new BufferedReader(new FileReader (file));

        String line;
        StringBuilder stringBuilder = new StringBuilder();

        try {
            while ((line = reader.readLine()) != null) {
                stringBuilder.append(line);
            }

            return stringBuilder.toString();
        } finally {
            reader.close();
        }
    }

    private static void insertGenomeToDB(String genome, Statement statement, int fileId) throws SQLException {
        Set<String> toInsertSet = new HashSet<>();
        String toInsert;

        for (int i = 0; i < genome.length() - 4; i++) {
            toInsert = genome.substring(i, i+5);
            toInsertSet.add(toInsert);
        }

        for (String str : toInsertSet) {
            statement.executeUpdate("INSERT INTO public.genom(str, file_id) VALUES ('" + str + "'," + fileId +")");
        }
    }
}