clean dependencies, change outer database structure to HashMap, add print...

import java.io.Serializable;

import edu.bu.ec504.project.Molecule;

import java.io.FileInputStream;

import java.io.FileOutputStream;

import java.io.IOException;

import java.io.ObjectInputStream;

import java.io.ObjectOutputStream;

import java.util.ArrayList;

package edu.bu.ec504.project;

import java.util.HashMap;

/**

 * A class represents the molecule database

 */

public class MoleculeDatabase implements Serializable {

public class MoleculeDatabase {

    public ArrayList<ArrayList<Molecule>> db;   // Molecule database

    public HashMap<Integer, ArrayList<Molecule>> db;   // Molecule database

    /**

     * Constructs a database

     */

    public MoleculeDatabase() {

        this.db = new ArrayList<>();

        this.db = new HashMap<>();

    }

    public void printDb() {

        for (Integer atomCount : this.db.keySet()) {

            System.out.println(atomCount);

            ArrayList<Molecule> moleculesWithSameNumAtoms = this.db.get(atomCount);

            for (Molecule molecule : moleculesWithSameNumAtoms) {

                System.out.println(molecule.moleculeName);

            }

        }

    }

    /**

     * Add a new molecule into the database

     */

    public void addMolecule(Molecule molecule) {

      return null; // for now

        int numAtoms = molecule.getNumAtoms();

        if (this.db.containsKey(numAtoms)) {

            this.db.get(numAtoms).add(molecule);

        } else {

            ArrayList<Molecule> moleculesWithSameNumAtoms = new ArrayList<>();

            moleculesWithSameNumAtoms.add(molecule);

            this.db.put(numAtoms, moleculesWithSameNumAtoms);

        }

    }

    /**

    public Molecule findMolecule(Molecule molecule) {

        // Retrieve the partitioned array list based on the number of atoms

        int numAtoms = molecule.getNumAtoms();

        if (!db.containsKey(numAtoms)) {

//      System.out.println("no ArrayList with correct # of atoms");

            return null;

        }

        ArrayList<Molecule> moleculesWithSameNumAtoms = db.get(numAtoms);

        // Iterate through the array list of molecules with the same number of atoms

        for (Molecule dbMolecule : moleculesWithSameNumAtoms) {

            System.out.println(dbMolecule.moleculeName + " vs " + molecule.moleculeName);

            Molecule result = dbMolecule.areMoleculesEqual(molecule);

            if (result != null) {

                return result; // Return the isomorphic molecule

            }

        }

        System.out.println("No isomorphic molecule found in database.");

        return null; // Return null if molecule not found

    }

    /**

     * Save database to file system

     */

    public void save(String filename) {

      try {

    public void save(String filename) throws IOException {

        FileOutputStream fileOutStream = new FileOutputStream(filename);

        ObjectOutputStream objOutStream = new ObjectOutputStream(fileOutStream);

        objOutStream.writeObject(this.molecules);

        objOutStream.writeObject(this.db);

        objOutStream.close();

        fileOutStream.close();

        System.out.println("Database saved successfully.");

    }

      catch (IOException e) {

        System.err.println("Error saving database: " + e.getMessage());

      }

    }

    /**

     * Load database from file system

     */

    public void load(String filename) {

      try {

    public void load(String filename) throws IOException {

        FileInputStream fileInStream = new FileInputStream(filename);

        ObjectInputStream objInStream = new ObjectInputStream(fileInStream);

        this.molecules = (ArrayList<Molecule>) objInStream.readObject();

        objInStream.close();

        fileInStream.close();

        try {

            this.db = (HashMap<Integer, ArrayList<Molecule>>) objInStream.readObject();

            System.out.println("Database loaded successfully.");

        } catch (IOException | ClassNotFoundException e) {

            System.out.println("Error loading database: " + e.getMessage());

        }

      catch (IOException | ClassNotFoundException e) {

        System.err.println("Error loading database: " + e.getMessage());

      }

        objInStream.close();

        fileInStream.close();

    }

}