JAVA MAIL API

If you want to Delete a Message or Mail for Using Java Mail API. Then you using a method call for deleting messages call setFlag() on set the message and set the Flags.Flag.DELETED flag is true.

message.setFlag(Flags.Flag.DELETED, true);

When you close the folder, deleted message will be removed. then be sure the open the folder for read/write access

folder.open(Folder.READ_WRITE);

package R4R;
import java.io.*;
import javax.mail.*;
import javax.mail.internet.*;
public class deletemail{
  public static void main (String args[]) throws Exception {
    String host = args[0];
    String username = args[1];
    String password = args[2];
    // Get session
    Session session = Session.getInstance(
      System.getProperties(), null);
    // Get the store
    Store store = session.getStore("pop3");
    store.connect(host, username, password);
    // Get folder  
    Folder folder = store.getFolder("INBOX");
    folder.open(Folder.READ_WRITE);
    BufferedReader reader = new BufferedReader (
      new InputStreamReader(System.in));
    // Get directory
    Message message[] = folder.getMessages();
    for (int i=0, n=message.length; i<n; i++) {
       System.out.println(i + ": " + message[i].getFrom()[0] 
         + "\t" + message[i].getSubject());
       System.out.println("Do you want to delete message? [YES to delete]");
       String line = reader.readLine();
       // Mark as deleted if appropriate
       if ("YES".equals(line)) {
         message[i].setFlag(Flags.Flag.DELETED, true);
       }
    }
    // Close connection 
    folder.close(true);
    store.close();
  }
}