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Код

package test;

import java.io.StringReader;
import java.io.StringWriter;

import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;

import org.w3c.dom.Document;

import org.xml.sax.InputSource;

public class superTest {
    public static void run() {
        try {
            String input = 
            "<?xml version=\"1.0\" encoding=\"windows-1251\" ?>" + 
            "<root doc_version=\"1.0\" doc_type=\"data\">" + 
            "<OTPR name=\"Новокуйбышевска\"/>" +
            "</root>"; 

            InputSource is = new InputSource();
            is.setEncoding("windows-1251");
            is.setCharacterStream(new StringReader(input));
            
            DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
            DocumentBuilder db = dbf.newDocumentBuilder();
            Document doc = db.parse(is);

            StringWriter writer = new StringWriter(); 
            
            TransformerFactory tFactory = TransformerFactory.newInstance();
            Transformer transformer = tFactory.newTransformer();
            transformer.setOutputProperty("encoding", "windows-1251");

            transformer.transform(new DOMSource(doc.getElementsByTagName("OTPR").item(0)), new StreamResult(writer)); 

            String result = writer.toString();
            
            System.out.println(result);

        } catch (Exception ex) {
        }
    }
    
    public static void main(String[] args) {
        superTest.run();
    }
}