How to retrieve messages which are not flagged as deleted?

I flag a message to be deleted after a treatment :

...
import javax.mail.*;
...
public void delete(Message message) throws MessagingException {
        try {
            message.setFlag(Flags.Flag.DELETED, true);
        } catch (Exception e) {
            e.printStackTrace();
            throw e;
        }
    }
...

Then I want to get messages :

...
import com.sun.mail.pop3.POP3Store;
import java.util.Properties;
...
@Value("${mail.host}")
    private String host;
    @Value("${mail.storeType}")
    private String storeType;
    @Value("${mail.port}")
    private int port;
    @Value("${mail.username}")
    private String username;
    @Value("${mail.password}")
    private String password;
    @Value("${mail.auth}")
    private boolean auth;
    @Value("${mail.ssl.trust}")
    private String sss_trust;
    private POP3Store emailstore = null;
    private boolean start = true;
...
public POP3Store getEmailStore() throws Exception {
        Properties properties = new Properties();
        properties.setProperty("mail.store.protocol", storeType);
        properties.setProperty("mail." + storeType + ".host", host);
        properties.setProperty("mail." + storeType + ".port", String.valueOf(port));
        properties.setProperty("mail." + storeType + ".auth", String.valueOf(auth));
        properties.setProperty("mail." + storeType + ".socketFactory.class", "javax.net.ssl.SSLSocketFactory");
        properties.setProperty("mail." + storeType + ".ssl.trust", sss_trust);
        try {
            Session emailSession = Session.getDefaultInstance(properties);
            POP3Store emailStore = (POP3Store) emailSession.getStore(storeType);
            return emailStore;
        } catch (NoSuchProviderException e) {
            e.printStackTrace();
            throw e;
        }
    }

    Folder emailFolder = emailstore.getFolder("INBOX");
                    emailFolder.open(Folder.READ_ONLY);
                    Message[] messages = emailFolder.getMessages(); // how to get messages that are not flagged as deleted ?
                    if (messages != null) {
                        for (Message message : messages) {
                            try {
                                mailService.createTicket(message);
                                mailService.delete(message);
                            } catch (Exception ex) {
                                throw ex;
                            }
                        }
                    }
                    emailFolder.close(true);

As I commented I want to get messages that are not flagged deleted. How to do that ?

Based on Message class, you can do something like this:

    for (Message message : messages) {
        if (!message.getFlags().contains(Flags.Flag.DELETED)) { // This will hopefully help
            try {
                mailService.createTicket(message);
                mailService.delete(message);
            } catch (Exception ex) {
                throw ex;
            }
        }
    }