Writing an file using UTF-8 without BOM encoding

gistfile1.java

import java.io.BufferedInputStream;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;

import org.eclipse.swt.widgets.Display;
import org.eclipse.swt.widgets.Label;
import org.eclipse.swt.widgets.ProgressBar;
import org.eclipse.swt.widgets.Shell;

public class LimpiezaRunnable implements Runnable {

	public Shell shell;
	
	public Display display;
	
	public String fileFilterPath;
	public String fileName;
	public String fileExtension;
	public String filePath;

	public Label labelMensajePrincipal;
	public Label labelMensajeSecundario;

	public LimpiezaCompletaListener listener;
	
	public ProgressBar progressBar;

	public Shell getShell() {
		return shell;
	}

	public void setShell(Shell shell) {
		this.shell = shell;
	}

	public LimpiezaCompletaListener getListener() {
		return listener;
	}

	public void setListener(LimpiezaCompletaListener listener) {
		this.listener = listener;
	}
	
	public String getFileFilterPath() {
		return fileFilterPath;
	}

	public void setFileFilterPath(String fileFilterPath) {
		this.fileFilterPath = fileFilterPath;
	}

	public String getFileName() {
		return fileName;
	}

	public void setFileName(String fileName) {
		this.fileName = fileName;
	}

	public String getFileExtension() {
		return fileExtension;
	}

	public void setFileExtension(String fileExtension) {
		this.fileExtension = fileExtension;
	}

	public String getFilePath() {
		return filePath;
	}

	public void setFilePath(String filePath) {
		this.filePath = filePath;
	}
	
	public Display getDisplay() {
		return display;
	}

	public void setDisplay(Display display) {
		this.display = display;
	}

	public ProgressBar getProgressBar() {
		return progressBar;
	}

	public void run() {

		try {

			BufferedReader br;
			BufferedWriter writer = null;
			BufferedWriter writer2 = null;

			// Leer archivo
			br = new BufferedReader(new InputStreamReader(new FileInputStream(
					filePath), "UTF-8"));
			
			final Integer lines = this.countLines(filePath);
			
			this.display.syncExec(new Runnable() {
	            @Override
	            public void run() {
	            	progressBar.setMaximum(lines);
	            }
	        });

			// Preparar creación de archivo de resultado
			writer = new BufferedWriter(new OutputStreamWriter(
					new FileOutputStream(fileFilterPath + "/" + fileName
							+ "_LIMPIO" + fileExtension), "UTF-8"));
						
			// Preparar creación de archivo de log
			writer2 = new BufferedWriter(new OutputStreamWriter(
					new FileOutputStream(fileFilterPath + "/" + fileName
							+ "_LOG_LIMPIEZA" + fileExtension), "UTF-8"));

			String line = br.readLine();
			
			int i = 0;
			
			boolean sw = false;
					
			if(line.startsWith("\uFEFF")){
				System.out.println(line.charAt(0));
				line = line.substring(1);
			}

			while (line != null) {
				
				String tmpline = line.substring(27,67);
								
				if (tmpline.contains("Ä")) {
					writer2.write("Reemplazado caracteres Ä en la línea " + i);
					writer2.newLine();
				}
				String cleaned_line = tmpline.replace("Ä", "A");

				if (cleaned_line.contains("Å")) {
					writer2.write("Reemplazado caracteres Å en la línea " + i);
					writer2.newLine();
				}
				cleaned_line = cleaned_line.replace("Å", "A");

				if (cleaned_line.contains("É")) {
					writer2.write("Reemplazado caracteres É en la línea " + i);
					writer2.newLine();
				}
				cleaned_line = cleaned_line.replace("É", "E");

				if (cleaned_line.contains("Ö")) {
					writer2.write("Reemplazado caracteres Ö en la línea " + i);
					writer2.newLine();
				}
				cleaned_line = cleaned_line.replace("Ö", "O");

				if (cleaned_line.contains("Ü")) {
					writer2.write("Reemplazado caracteres Ü en la línea " + i);
					writer2.newLine();
				}
				cleaned_line = cleaned_line.replace("Ü", "U");

				if (cleaned_line.contains("Ñ")) {
					writer2.write("Reemplazado caracteres Ñ en la línea " + i);
					writer2.newLine();
				}
				cleaned_line = cleaned_line.replace("Ñ", "N");

				if (cleaned_line.contains("Á")) {
					writer2.write("Reemplazado caracteres Á en la línea " + i);
					writer2.newLine();
				}
				cleaned_line = cleaned_line.replace("Á", "A");

				if (cleaned_line.contains("Â")) {
					writer2.write("Reemplazado caracteres  en la línea " + i);
					writer2.newLine();
				}
				cleaned_line = cleaned_line.replace("Â", "A");

				if (cleaned_line.contains("À")) {
					writer2.write("Reemplazado caracteres À en la línea " + i);
					writer2.newLine();
				}
				cleaned_line = cleaned_line.replace("À", "A");

				if (cleaned_line.contains("Ã")) {
					writer2.write("Reemplazado caracteres à en la línea " + i);
					writer2.newLine();
				}
				cleaned_line = cleaned_line.replace("Ã", "A");

				if (cleaned_line.contains("Ë")) {
					writer2.write("Reemplazado caracteres Ë en la línea " + i);
					writer2.newLine();
				}
				cleaned_line = cleaned_line.replace("Ë", "E");

				if (cleaned_line.contains("È")) {
					writer2.write("Reemplazado caracteres È en la línea " + i);
					writer2.newLine();
				}
				cleaned_line = cleaned_line.replace("È", "E");

				if (cleaned_line.contains("Ì")) {
					writer2.write("Reemplazado caracteres Ì en la línea " + i);
					writer2.newLine();
				}
				cleaned_line = cleaned_line.replace("Ì", "I");

				if (cleaned_line.contains("Ó")) {
					writer2.write("Reemplazado caracteres Ó en la línea " + i);
					writer2.newLine();
				}
				cleaned_line = cleaned_line.replace("Ó", "O");

				if (cleaned_line.contains("Ò")) {
					writer2.write("Reemplazado caracteres Ò en la línea " + i);
					writer2.newLine();
				}
				cleaned_line = cleaned_line.replace("Ò", "O");

				if (cleaned_line.contains("Ú")) {
					writer2.write("Reemplazado caracteres Ú en la línea " + i);
					writer2.newLine();
				}
				cleaned_line = cleaned_line.replace("Ú", "U");

				if (cleaned_line.contains("Û")) {
					writer2.write("Reemplazado caracteres Û en la línea " + i);
					writer2.newLine();
				}
				cleaned_line = cleaned_line.replace("Û", "U");

				if (cleaned_line.contains("Ù")) {
					writer2.write("Reemplazado caracteres Ù en la línea " + i);
					writer2.newLine();
				}
				cleaned_line = cleaned_line.replace("Ù", "U");

				if (cleaned_line.contains("Ý")) {
					writer2.write("Reemplazado caracteres Ý en la línea " + i);
					writer2.newLine();
				}
				cleaned_line = cleaned_line.replace("Ý", "Y");

				if (cleaned_line.matches("[^a-zA-Z\\d]")) {
					writer2.write("Reemplazado otros caracteres extraños en la línea "
							+ i);
					writer2.newLine();
				}
				cleaned_line = cleaned_line.replaceAll("[^a-zA-Z\\d]", " ");
				
				// 28,67
				cleaned_line = line.substring(0,27) + cleaned_line + line.substring(67,line.length());

				writer.write(cleaned_line);
				
				if(!sw){
					writer.write("\uFEFF");
					sw = true;
				}
				
				writer.newLine();
				
				line = br.readLine();
				i++;
				
				final int x = i;
				
				this.display.syncExec(new Runnable() {
		            @Override
		            public void run() {
		            	progressBar.setSelection(x);
		            }
		        });
			}

			br.close();
			writer.close();
			writer2.close();

			listener.onComplete();

		} catch (Exception e) {
			listener.onError(e);
		}

	}
	
	public Integer countLines(String filename) throws IOException {
	    InputStream is = new BufferedInputStream(new FileInputStream(filename));
	    try {
	        byte[] c = new byte[1024];
	        int count = 0;
	        int readChars = 0;
	        boolean empty = true;
	        while ((readChars = is.read(c)) != -1) {
	            empty = false;
	            for (int i = 0; i < readChars; ++i) {
	                if (c[i] == '\n') {
	                    ++count;
	                }
	            }
	        }
	        return (count == 0 && !empty) ? 1 : count;
	    } finally {
	        is.close();
	    }
	}

	public void setProgressBar(ProgressBar progressBar) {
		this.progressBar = progressBar;
	}

}