Remove illegal xml characters from UTF-16LE encoded file

I have a java application that parses an xml file that was encoded in utf-16le. The xml has been erroring out while being parsed due to illegal xml characters. My solution is to read in this file into a java string, then removing the xml characters, so it can be parsed successfully. It works 99% but there are some slight differences in the input output from this process, not caused by the illegal characters being removed, but going from the utf-16le encoding to java string utf-16.. i think

BufferedReader reader = null;
    String fileText = ""; //stored as UTF-16
    try {
        reader = new BufferedReader(new InputStreamReader(in, "UTF-16LE"));
        for (String line; (line = reader.readLine()) != null; ) {
            fileText += line;
        }
    } catch (Exception ex) {
        logger.log(Level.WARNING, "Error removing illegal xml characters", ex);
    } finally {
        if (reader != null) {
            reader.close();
        }
    }

//code to remove illegal chars from string here, irrelevant to problem 

        ByteArrayInputStream inStream = new ByteArrayInputStream(fileText.getBytes("UTF-16LE"));
    Document doc = XmlUtil.openDocument(inStream, XML_ROOT_NODE_ELEM);

Do characters get changed/lost when going from UTF-16LE to UTF-16? Is there a way to do this in java and assuring the input is exactly the same as the output?

Solution

Certainly one problem is that readLine throws away the line ending.

You would need to do something like:

       fileText += line + "\r\n";

Otherwise XML attributes, DTD entities, or something else could get glued together where at least a space was required. Also you do not want the text content to be altered when it contains a line break.

Performance (speed and memory) can be improved using a

StringBuilder fileText = new StringBuilder();
... fileText.append(line).append("\n");
... fileText.toString();

Then there might be a problem with the first character of the file, which sometimes redundantly is added: a BOM char.

line = line.replace("\uFEFF", "");