The open source JTidy project does an excellent job of converting HTML files to the newer XHTML standard. The following code shows how to invoke JTidy programmatically from Java:

/*
In:  C:\Data_Local\xml\docs\test.html
Out: C:\Data_Local\xml\docs\testXHTML.xml
*/

import org.w3c.tidy.Tidy;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import org.w3c.dom.Document;

public class HTML_to_XHTML{
   public static void main(String[] args){
      try{
         FileInputStream FIS=new FileInputStream("C://Data_Local
            //xml//docs//test.html");
         FileOutputStream FOS=new FileOutputStream("C://Data_Local
            //xml//docs//testXHTML.xml");   
         Tidy T=new Tidy();
         Document D=T.parseDOM(FIS,FOS);
         }
      catch (java.io.FileNotFoundException e)
         {System.out.println(e.getMessage());}   
      }
   }
}