Molecule class now implements Serializable, bug: atomArrayList compare;...

package edu.bu.ec504.project;

import java.io.BufferedReader;

import java.io.FileReader;

import java.io.IOException;

import java.io.Serializable;

import java.util.ArrayList;

import java.util.Arrays;

/**

 * Represents a molecule containing atoms and edges.

 */

public class Molecule {

public class Molecule implements Serializable {

    //FIELDS

    String moleculeName; // name of the molecule

    public String moleculeName; // name of the molecule

    int numAtoms; // number of atoms in the molecule

    int numEdges; // number of edges in the molecule

    ArrayList<Atom> atomArrayList;  // list of atoms in the molecule

    /**

     * Constructs a molecule by reading data from a file.

     *

     * @param moleculeFile the file containing the molecule.

     */

    public Molecule(String MoleculeFile){

    public Molecule(String moleculeFile) {

        //Init values

        numElements = new int[119];

        int f, l;

        // Read and process input

        try (BufferedReader reader = new BufferedReader(new FileReader(MoleculeFile))) { //Might want to move reader outside molecule class in the future to save space

        try (BufferedReader reader = new BufferedReader(new FileReader(moleculeFile))) { //Might want to move reader outside molecule class in the future to save space

            String line;

            moleculeName = reader.readLine(); //Reads name

            numAtoms = Integer.parseInt(reader.readLine()); //Reads # of atoms

    /**

     * Compare two molecules and check if they are isomorphic.

     *

     * @param otherMolecule The molecule to compare with.

     * @return The first molecule if they are equal, otherwise null.

     */

    public Molecule areMoleculesEqual(Molecule otherMolecule) {

        // Compare the name of the molecule

        if (!this.moleculeName.equals(otherMolecule.moleculeName)) {

            System.out.println("different names");

            return null; // Names are different, molecules are not equal

        }

        // Compare the number of atoms

        if (this.numAtoms != otherMolecule.numAtoms) {

            System.out.println("different numAtoms");

            return null; // Number of atoms is different, molecules are not equal

        }

        // Compare the number of edges

        if (this.numEdges != otherMolecule.numEdges) {

            System.out.println("different numEdges");

            return null; // Number of edges is different, molecules are not equal

        }

        // Compare the atom lists

        if (!this.atomArrayList.equals(otherMolecule.atomArrayList)) {

            return null; // Atom lists are different, molecules are not equal

        }

//        if (!this.atomArrayList.equals(otherMolecule.atomArrayList)) {

//            System.out.println("different atomArrayList");

//            return null; // Atom lists are different, molecules are not equal

//        }

        // Compare the number of elements

        if (!Arrays.equals(this.numElements, otherMolecule.numElements)) {

            System.out.println("different numElements");

            return null; // Number of elements is different, molecules are not equal

        }