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).

.gitignore

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+/.gradle
+/.settings
+/.classpath
+/.project
+/bin
+/build

build.gradle

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+apply plugin: 'java'
+apply plugin: 'eclipse'
+apply plugin: 'protobuf'
+
+task wrapper(type: Wrapper) {
+	gradleVersion = '2.2'
+}
+
+buildscript {
+	repositories {
+		mavenCentral()
+	}
+
+	dependencies {
+		classpath 'com.andrewkroh.gradle:gradle-protobuf-plugin:0.4.0'
+	}
+}
+
+repositories {
+	maven {
+		url 'http://www.sparetimelabs.com/maven2/'
+	}
+	mavenCentral()
+}
+
+dependencies {
+	compile 'org.msgpack:msgpack:0.6.11'
+    compile 'com.sparetimelabs:purejavacomm:0.0.22'
+}

gradle/wrapper/gradle-wrapper.properties

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+#Sun Feb 01 14:04:45 GMT 2015
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-2.2-bin.zip

gradlew

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+#!/usr/bin/env bash
+
+##############################################################################
+##
+##  Gradle start up script for UN*X
+##
+##############################################################################
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS=""
+
+APP_NAME="Gradle"
+APP_BASE_NAME=`basename "$0"`
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD="maximum"
+
+warn ( ) {
+    echo "$*"
+}
+
+die ( ) {
+    echo
+    echo "$*"
+    echo
+    exit 1
+}
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+case "`uname`" in
+  CYGWIN* )
+    cygwin=true
+    ;;
+  Darwin* )
+    darwin=true
+    ;;
+  MINGW* )
+    msys=true
+    ;;
+esac
+
+# For Cygwin, ensure paths are in UNIX format before anything is touched.
+if $cygwin ; then
+    [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
+fi
+
+# Attempt to set APP_HOME
+# Resolve links: $0 may be a link
+PRG="$0"
+# Need this for relative symlinks.
+while [ -h "$PRG" ] ; do
+    ls=`ls -ld "$PRG"`
+    link=`expr "$ls" : '.*-> \(.*\)$'`
+    if expr "$link" : '/.*' > /dev/null; then
+        PRG="$link"
+    else
+        PRG=`dirname "$PRG"`"/$link"
+    fi
+done
+SAVED="`pwd`"
+cd "`dirname \"$PRG\"`/" >&-
+APP_HOME="`pwd -P`"
+cd "$SAVED" >&-
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+        # IBM's JDK on AIX uses strange locations for the executables
+        JAVACMD="$JAVA_HOME/jre/sh/java"
+    else
+        JAVACMD="$JAVA_HOME/bin/java"
+    fi
+    if [ ! -x "$JAVACMD" ] ; then
+        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD="java"
+    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if [ "$cygwin" = "false" -a "$darwin" = "false" ] ; then
+    MAX_FD_LIMIT=`ulimit -H -n`
+    if [ $? -eq 0 ] ; then
+        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
+            MAX_FD="$MAX_FD_LIMIT"
+        fi
+        ulimit -n $MAX_FD
+        if [ $? -ne 0 ] ; then
+            warn "Could not set maximum file descriptor limit: $MAX_FD"
+        fi
+    else
+        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
+    fi
+fi
+
+# For Darwin, add options to specify how the application appears in the dock
+if $darwin; then
+    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
+fi
+
+# For Cygwin, switch paths to Windows format before running java
+if $cygwin ; then
+    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
+    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
+
+    # We build the pattern for arguments to be converted via cygpath
+    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
+    SEP=""
+    for dir in $ROOTDIRSRAW ; do
+        ROOTDIRS="$ROOTDIRS$SEP$dir"
+        SEP="|"
+    done
+    OURCYGPATTERN="(^($ROOTDIRS))"
+    # Add a user-defined pattern to the cygpath arguments
+    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
+        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
+    fi
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    i=0
+    for arg in "$@" ; do
+        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
+        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
+
+        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
+            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
+        else
+            eval `echo args$i`="\"$arg\""
+        fi
+        i=$((i+1))
+    done
+    case $i in
+        (0) set -- ;;
+        (1) set -- "$args0" ;;
+        (2) set -- "$args0" "$args1" ;;
+        (3) set -- "$args0" "$args1" "$args2" ;;
+        (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
+        (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
+        (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
+        (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
+        (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
+        (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+    esac
+fi
+
+# Split up the JVM_OPTS And GRADLE_OPTS values into an array, following the shell quoting and substitution rules
+function splitJvmOpts() {
+    JVM_OPTS=("$@")
+}
+eval splitJvmOpts $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS
+JVM_OPTS[${#JVM_OPTS[*]}]="-Dorg.gradle.appname=$APP_BASE_NAME"
+
+exec "$JAVACMD" "${JVM_OPTS[@]}" -classpath "$CLASSPATH" org.gradle.wrapper.GradleWrapperMain "$@"

gradlew.bat

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+@if "%DEBUG%" == "" @echo off
+@rem ##########################################################################
+@rem
+@rem  Gradle startup script for Windows
+@rem
+@rem ##########################################################################
+
+@rem Set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" setlocal
+
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS=
+
+set DIRNAME=%~dp0
+if "%DIRNAME%" == "" set DIRNAME=.
+set APP_BASE_NAME=%~n0
+set APP_HOME=%DIRNAME%
+
+@rem Find java.exe
+if defined JAVA_HOME goto findJavaFromJavaHome
+
+set JAVA_EXE=java.exe
+%JAVA_EXE% -version >NUL 2>&1
+if "%ERRORLEVEL%" == "0" goto init
+
+echo.
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:findJavaFromJavaHome
+set JAVA_HOME=%JAVA_HOME:"=%
+set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+
+if exist "%JAVA_EXE%" goto init
+
+echo.
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:init
+@rem Get command-line arguments, handling Windowz variants
+
+if not "%OS%" == "Windows_NT" goto win9xME_args
+if "%@eval[2+2]" == "4" goto 4NT_args
+
+:win9xME_args
+@rem Slurp the command line arguments.
+set CMD_LINE_ARGS=
+set _SKIP=2
+
+:win9xME_args_slurp
+if "x%~1" == "x" goto execute
+
+set CMD_LINE_ARGS=%*
+goto execute
+
+:4NT_args
+@rem Get arguments from the 4NT Shell from JP Software
+set CMD_LINE_ARGS=%$
+
+:execute
+@rem Setup the command line
+
+set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
+@rem Execute Gradle
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
+
+:end
+@rem End local scope for the variables with windows NT shell
+if "%ERRORLEVEL%"=="0" goto mainEnd
+
+:fail
+rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
+rem the _cmd.exe /c_ return code!
+if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
+exit /b 1
+
+:mainEnd
+if "%OS%"=="Windows_NT" endlocal
+
+:omega

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());
+	}
+}

src/main/proto/beerduino.proto

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+package beerduino;
+
+message Ping {
+	required int32 id = 1;
+}
+
+message Echo {
+	required int32 id = 1;
+	optional string message = 2;
+}