Inital test (from beerduino, https://github.com/ilyevsky/beerduino) to establish protocol buffer communication between java and arduino powered by purejavacomm (https://github.com/nyholku/purejavacomm).

src/main/java/test/Arduino.java

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+package test;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.TooManyListenersException;
+
+import purejavacomm.CommPortIdentifier;
+import purejavacomm.PortInUseException;
+import purejavacomm.SerialPort;
+import purejavacomm.SerialPortEvent;
+import purejavacomm.SerialPortEventListener;
+import purejavacomm.UnsupportedCommOperationException;
+
+import beerduino.Beerduino.Echo;
+ 
+public class Arduino implements SerialPortEventListener {
+    public static final int TIME_OUT = 1000; 
+    public static final String PORT_NAMES[] = {
+        "tty.usbmodem", // Mac OS X
+        "usbdev",       // Linux
+        "tty",          // Linux
+        "serial",       // Linux
+        "COM3",         // Windows
+    };
+
+    protected SerialPort port = null;
+    protected InputStream inputStream = null;
+    protected ArrayList<EchoListener> listenerList = new ArrayList<EchoListener>();
+
+    public void connect() throws UnsupportedCommOperationException, PortInUseException, IOException, TooManyListenersException {
+        CommPortIdentifier portid = null;
+        Enumeration<?> portEnum = CommPortIdentifier.getPortIdentifiers();
+        while (portEnum.hasMoreElements()) {
+            portid = (CommPortIdentifier)portEnum.nextElement();
+            if (portid != null) {              
+                System.out.println("Trying: " + portid.getName());
+                for ( String portName: PORT_NAMES) {
+                    if ( portid.getName().equals(portName) || portid.getName().contains(portName)) {
+                        port = (SerialPort) portid.open("", TIME_OUT);
+                        port.setFlowControlMode(
+                                SerialPort.FLOWCONTROL_XONXOFF_IN + 
+                                SerialPort.FLOWCONTROL_XONXOFF_OUT);
+                        inputStream = port.getInputStream();
+                        System.out.println( "Connected on port: " + portid.getName());
+                        port.addEventListener(this);
+                        port.notifyOnDataAvailable(true);
+                    }
+                }
+            }
+        }
+    }
+ 
+    public void serialEvent(SerialPortEvent event) {
+		try {
+			switch (event.getEventType()) {
+                case SerialPortEvent.DATA_AVAILABLE:
+            		Echo echo = Echo.parseDelimitedFrom(inputStream);
+                    for (EchoListener listener : listenerList) {
+                    	listener.receive(echo);
+                    }
+                    break; 
+                default:
+                    break;
+            }
+		} catch (IOException e) {			
+			e.printStackTrace();
+		}
+
+    }
+
+	public InputStream getInputStream() throws IOException {
+		return port.getInputStream();
+	}
+
+	public OutputStream getOutputStream() throws IOException {
+		return port.getOutputStream();
+	}
+
+	public void addListener(EchoListener listener) {
+        listenerList.add(listener);
+	}
+	
+	public void removeListener(EchoListener listener) {
+		listenerList.remove(listener);
+	}
+
+	public void close() {
+		port.close();		
+	}
+}

src/main/java/test/EchoListener.java

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+package test;
+
+import beerduino.Beerduino.Echo;
+
+public interface EchoListener {
+	public void receive(Echo echo);
+}

src/main/java/test/Test.java

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+package test;
+
+import java.io.OutputStream;
+
+import beerduino.Beerduino.Echo;
+import beerduino.Beerduino.Ping;
+
+public class Test implements EchoListener {
+	public static void main(String[] argv) {
+		try {
+			new Test().start();
+		} catch (Exception e) {
+			e.printStackTrace();
+		}
+	}
+
+	private void start() throws Exception {
+		Arduino arduino = new Arduino();
+		arduino.connect();
+		arduino.addListener(this);
+		OutputStream outputStream = arduino.getOutputStream();
+        int i = 123;
+        while ( i < 10000) {
+            Ping ping = Ping.newBuilder().setId(i++).build();
+            System.out.println("writing!");
+            ping.writeDelimitedTo(outputStream);
+           Thread.sleep(1000);
+        }
+        arduino.close();	
+	}
+
+	public void receive(Echo echo) {
+		System.out.println("> " + echo.getMessage() + " " + echo.getId());
+	}
+}