Character corruption going from BufferedReader to BufferedWriter in java

Question

In Java, I am trying to parse an HTML file that contains complex text such as greek symbols.

I encounter a known problem when text contains a left facing quotation mark. Text such as

mutations to particular “hotspot” regions

becomes

 mutations to particular “hotspot�? regions

I have isolated the problem by writting a simple text copy meathod:

public static int CopyFile()
{
    try
    {
    StringBuffer sb = null;
    String NullSpace = System.getProperty("line.separator");
    Writer output = new BufferedWriter(new FileWriter(outputFile));
    String line;
    BufferedReader input =  new BufferedReader(new FileReader(myFile));
while((line = input.readLine())!=null)
    {
        sb = new StringBuffer();
        //Parsing would happen
        sb.append(line);
        output.write(sb.toString()+NullSpace);
    }
        return 0;
    }
    catch (Exception e)
    {
        return 1;
    }
}

Can anybody offer some advice as how to correct this problem?

★My solution

InputStream in = new FileInputStream(myFile);
        Reader reader = new InputStreamReader(in,"utf-8");
        Reader buffer = new BufferedReader(reader);
        Writer output = new BufferedWriter(new FileWriter(outputFile));
        int r;
        while ((r = reader.read()) != -1)
        {
            if (r<126)
            {
                output.write(r);
            }
            else
            {
                output.write("&#"+Integer.toString(r)+";");
            }
        }
        output.flush();

Answer 1

The file read is not in the same encoding (probably UTF-8) as the file written (probably ISO-8859-1).

Try the following to generate a file with UTF-8 encoding:

BufferedWriter output = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(outputFile),"UTF8"));

Unfortunately, determining the encoding of a file is very difficult. See Java : How to determine the correct charset encoding of a stream