XML File looses its format after reading and writing in Java

I'm writing a program in Java that it's going to read a XML file and do some modification,and then write the file with the same format.

The following is the code block that reads and writes the XML file:

        final Document fileDocument = parseFileAsDocument(file);

        final OutputFormat format = new OutputFormat(fileDocument);

        try {
            final FileWriter out = new FileWriter(file);
            final XMLSerializer serializer = new XMLSerializer(out,format);
            serializer.serialize(fileDocument);
        }
         catch (final IOException e) {
            System.out.println(e.getMessage()).
        }

This is the method used to parse the file:

private Document parseFileAsDocument(final File file) {
    Document inputDocument = null;
    try {
        inputDocument = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(file);
    }//catching some exceptions{}

    return inputDocument;
}

I'm noticing two changes after the file is written: Before I had a node similar to this:

<instance ref='filter'>
 <value></value>
</instance>

After reading and writing, the node looks like this:

<instance ref="filter">
 <value/>

As you can see from above, the 'filter' has been changed to "filter" with double quote. The second change is <value></value> has been changed to <value/>. This change happens across the XML file whenever we have a node similar to <tag></tag> with no value in between. So if we have something like <tag>somevalue</tag>, there is no issue. Any thought please how to get the XML nodes format to be the same after writing? I'd appreciate it!