From c6f8a2d558a5344ecd5418e434917ca1e4ae3d97 Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Fri, 18 Jul 2014 11:39:02 +0200
Subject: [PATCH 01/28] [cooja] Added @Override annotations for relevant files

---
 .../cooja/avrmote/AvrMoteMemory.java          | 17 ++++
 .../cooja/mspmote/MspMoteMemory.java          | 17 ++++
 .../contikios/cooja/SectionMoteMemory.java    | 18 ++++
 .../cooja/contikimote/ContikiMote.java        |  8 ++
 .../cooja/contikimote/ContikiMoteType.java    | 19 ++++
 .../cooja/motes/AbstractApplicationMote.java  |  9 +-
 .../cooja/plugins/BufferListener.java         | 98 +++++++++++++++++++
 7 files changed, 185 insertions(+), 1 deletion(-)

diff --git a/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/AvrMoteMemory.java b/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/AvrMoteMemory.java
index 0dbdbb45d..ec356879c 100644
--- a/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/AvrMoteMemory.java
+++ b/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/AvrMoteMemory.java
@@ -60,28 +60,34 @@ public class AvrMoteMemory implements MoteMemory, AddressMemory {
         interpreter.getSimulator().insertWatch(w, address);
     }
     
+    @Override
     public void clearMemory() {
         logger.fatal("not implemented");
     }
 
+    @Override
     public byte[] getMemorySegment(int address, int size) {
         logger.fatal("getMemorySegment is not implemented");
         return null;
     }
 
+    @Override
     public int getTotalSize() {
         return 0;
     }
 
+    @Override
     public void setMemorySegment(int address, byte[] data) {
         logger.fatal("setMemorySegment is not implemented");
     }
 
+    @Override
     public byte[] getByteArray(String varName, int length)
             throws UnknownVariableException {
         return null;
     }
 
+    @Override
     public byte getByteValueOf(String varName) throws UnknownVariableException {
         return (byte) getValueOf(varName, 1);
     }
@@ -131,19 +137,23 @@ public class AvrMoteMemory implements MoteMemory, AddressMemory {
         }
     }
     
+    @Override
     public int getIntValueOf(String varName) throws UnknownVariableException {
         return getValueOf(varName, 2);
     }
 
+    @Override
     public int getIntegerLength() {
         return 2;
     }
 
+    @Override
     public int getVariableAddress(String varName)
             throws UnknownVariableException {
         return 0;
     }
 
+    @Override
     public String[] getVariableNames() {
         ArrayList<String> symbols = new ArrayList<String>();
         for (Iterator i = memoryMap.getIterator(); i.hasNext();) {
@@ -152,32 +162,39 @@ public class AvrMoteMemory implements MoteMemory, AddressMemory {
         return symbols.toArray(new String[0]);
     }
 
+    @Override
     public void setByteArray(String varName, byte[] data)
             throws UnknownVariableException {
     }
 
+    @Override
     public void setByteValueOf(String varName, byte newVal)
             throws UnknownVariableException {
         setValue(varName, newVal, 1);
     }
 
+    @Override
     public void setIntValueOf(String varName, int newVal)
             throws UnknownVariableException {
         setValue(varName, newVal, 2);
     }
 
+    @Override
     public boolean variableExists(String varName) {
         return memoryMap.getLocation(varName) != null;
     }
 
+    @Override
     public boolean addMemoryMonitor(int address, int size, MemoryMonitor mm) {
       logger.warn("Not implemented");
       return false;
     }
 
+    @Override
     public void removeMemoryMonitor(int address, int size, MemoryMonitor mm) {
     }
 
+    @Override
     public int parseInt(byte[] memorySegment) {
       logger.warn("Not implemented");
       return 0;
diff --git a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMoteMemory.java b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMoteMemory.java
index 47d18b9ca..824dd6c08 100644
--- a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMoteMemory.java
+++ b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMoteMemory.java
@@ -58,6 +58,7 @@ public class MspMoteMemory implements MoteMemory, AddressMemory {
     this.cpu = cpu;
   }
 
+  @Override
   public String[] getVariableNames() {
     String[] names = new String[mapEntries.size()];
     for (int i = 0; i < mapEntries.size(); i++) {
@@ -75,19 +76,23 @@ public class MspMoteMemory implements MoteMemory, AddressMemory {
     throw new UnknownVariableException(varName);
   }
 
+  @Override
   public int getVariableAddress(String varName) throws UnknownVariableException {
     MapEntry entry = getMapEntry(varName);
     return entry.getAddress();
   }
 
+  @Override
   public int getIntegerLength() {
     return 2;
   }
 
+  @Override
   public void clearMemory() {
     logger.fatal("clearMemory() not implemented");
   }
 
+  @Override
   public byte[] getMemorySegment(int address, int size) {
     int[] memInts = new int[size];
 
@@ -102,6 +107,7 @@ public class MspMoteMemory implements MoteMemory, AddressMemory {
     return memBytes;
   }
 
+  @Override
   public void setMemorySegment(int address, byte[] data) {
     /* Convert to int array */
     int[] memInts = new int[data.length];
@@ -112,10 +118,12 @@ public class MspMoteMemory implements MoteMemory, AddressMemory {
     System.arraycopy(memInts, 0, cpu.memory, address, data.length);
   }
 
+  @Override
   public int getTotalSize() {
     return cpu.memory.length;
   }
 
+  @Override
   public boolean variableExists(String varName) {
     for (MapEntry entry: mapEntries) {
       if (entry.getName().equals(varName)) {
@@ -128,6 +136,7 @@ public class MspMoteMemory implements MoteMemory, AddressMemory {
 
   /* TODO Check correct variable size in below methods */
 
+  @Override
   public int getIntValueOf(String varName) throws UnknownVariableException {
     MapEntry entry = getMapEntry(varName);
 
@@ -136,6 +145,7 @@ public class MspMoteMemory implements MoteMemory, AddressMemory {
     return parseInt(varData);
   }
 
+  @Override
   public void setIntValueOf(String varName, int newVal) throws UnknownVariableException {
     MapEntry entry = getMapEntry(varName);
     int varAddr = entry.getAddress();
@@ -152,6 +162,7 @@ public class MspMoteMemory implements MoteMemory, AddressMemory {
     setMemorySegment(varAddr, varData);
   }
 
+  @Override
   public byte getByteValueOf(String varName) throws UnknownVariableException {
     MapEntry entry = getMapEntry(varName);
     int varAddr = entry.getAddress();
@@ -161,6 +172,7 @@ public class MspMoteMemory implements MoteMemory, AddressMemory {
     return varData[0];
   }
 
+  @Override
   public void setByteValueOf(String varName, byte newVal) throws UnknownVariableException {
     MapEntry entry = getMapEntry(varName);
     int varAddr = entry.getAddress();
@@ -172,6 +184,7 @@ public class MspMoteMemory implements MoteMemory, AddressMemory {
     setMemorySegment(varAddr, varData);
   }
 
+  @Override
   public byte[] getByteArray(String varName, int length) throws UnknownVariableException {
     MapEntry entry = getMapEntry(varName);
     int varAddr = entry.getAddress();
@@ -179,6 +192,7 @@ public class MspMoteMemory implements MoteMemory, AddressMemory {
     return getMemorySegment(varAddr, length);
   }
 
+  @Override
   public void setByteArray(String varName, byte[] data) throws UnknownVariableException {
     MapEntry entry = getMapEntry(varName);
     int varAddr = entry.getAddress();
@@ -209,6 +223,7 @@ public class MspMoteMemory implements MoteMemory, AddressMemory {
     }
   }
 
+  @Override
   public boolean addMemoryMonitor(int address, int size, MemoryMonitor mm) {
     MemoryCPUMonitor t = new MemoryCPUMonitor(mm, address, size);
     cpuMonitorArray.add(t);
@@ -220,6 +235,7 @@ public class MspMoteMemory implements MoteMemory, AddressMemory {
     return true;
   }
 
+  @Override
   public void removeMemoryMonitor(int address, int size, MemoryMonitor mm) {
     for (MemoryCPUMonitor mcm: cpuMonitorArray) {
       if (mcm.mm != mm || mcm.address != address || mcm.size != size) {
@@ -233,6 +249,7 @@ public class MspMoteMemory implements MoteMemory, AddressMemory {
     }
   }
 
+  @Override
   public int parseInt(byte[] memorySegment) {
     if (memorySegment.length < 2) {
       return -1;
diff --git a/tools/cooja/java/org/contikios/cooja/SectionMoteMemory.java b/tools/cooja/java/org/contikios/cooja/SectionMoteMemory.java
index 267bfac7b..79f32a15b 100644
--- a/tools/cooja/java/org/contikios/cooja/SectionMoteMemory.java
+++ b/tools/cooja/java/org/contikios/cooja/SectionMoteMemory.java
@@ -66,10 +66,12 @@ public class SectionMoteMemory implements MoteMemory, AddressMemory {
     this.offset = offset;
   }
 
+  @Override
   public String[] getVariableNames() {
     return addresses.keySet().toArray(new String[0]);
   }
 
+  @Override
   public int getVariableAddress(String varName) throws UnknownVariableException {
     /* Cooja address space */
     if (!addresses.containsKey(varName)) {
@@ -79,14 +81,17 @@ public class SectionMoteMemory implements MoteMemory, AddressMemory {
     return addresses.get(varName).intValue() + offset;
   }
 
+  @Override
   public int getIntegerLength() {
     return 4;
   }
 
+  @Override
   public void clearMemory() {
     sections.clear();
   }
 
+  @Override
   public byte[] getMemorySegment(int address, int size) {
     /* Cooja address space */
     address -= offset;
@@ -113,6 +118,7 @@ public class SectionMoteMemory implements MoteMemory, AddressMemory {
     setMemorySegment(address+offset, data);
   }
 
+  @Override
   public void setMemorySegment(int address, byte[] data) {
     /* Cooja address space */
     address -= offset;
@@ -193,10 +199,12 @@ public class SectionMoteMemory implements MoteMemory, AddressMemory {
     return sections.get(sectionNr).getData();
   }
 
+  @Override
   public boolean variableExists(String varName) {
     return addresses.containsKey(varName);
   }
 
+  @Override
   public int getIntValueOf(String varName) throws UnknownVariableException {
     int varAddr = getVariableAddress(varName);
     byte[] varData = getMemorySegment(varAddr, 4);
@@ -208,6 +216,7 @@ public class SectionMoteMemory implements MoteMemory, AddressMemory {
     return parseInt(varData);
   }
 
+  @Override
   public void setIntValueOf(String varName, int newVal) throws UnknownVariableException {
     int varAddr = getVariableAddress(varName);
 
@@ -225,6 +234,7 @@ public class SectionMoteMemory implements MoteMemory, AddressMemory {
     setMemorySegment(varAddr, varData);
   }
 
+  @Override
   public byte getByteValueOf(String varName) throws UnknownVariableException {
     int varAddr = getVariableAddress(varName);
     byte[] varData = getMemorySegment(varAddr, 1);
@@ -236,6 +246,7 @@ public class SectionMoteMemory implements MoteMemory, AddressMemory {
     return varData[0];
   }
 
+  @Override
   public void setByteValueOf(String varName, byte newVal) throws UnknownVariableException {
     int varAddr = getVariableAddress(varName);
     byte[] varData = new byte[1];
@@ -245,11 +256,13 @@ public class SectionMoteMemory implements MoteMemory, AddressMemory {
     setMemorySegment(varAddr, varData);
   }
 
+  @Override
   public byte[] getByteArray(String varName, int length) throws UnknownVariableException {
     int varAddr = getVariableAddress(varName);
     return getMemorySegment(varAddr, length);
   }
 
+  @Override
   public void setByteArray(String varName, byte[] data) throws UnknownVariableException {
     int varAddr = getVariableAddress(varName);
     setMemorySegment(varAddr, data);
@@ -347,6 +360,7 @@ public class SectionMoteMemory implements MoteMemory, AddressMemory {
       System.arraycopy(data, 0, this.data, addr - startAddr, data.length);
     }
 
+    @Override
     public MoteMemorySection clone() {
       byte[] dataClone = new byte[data.length];
       System.arraycopy(data, 0, dataClone, 0, data.length);
@@ -356,6 +370,7 @@ public class SectionMoteMemory implements MoteMemory, AddressMemory {
     }
   }
 
+  @Override
   public SectionMoteMemory clone() {
     ArrayList<MoteMemorySection> sectionsClone = new ArrayList<MoteMemorySection>();
     for (MoteMemorySection section : sections) {
@@ -401,12 +416,14 @@ public class SectionMoteMemory implements MoteMemory, AddressMemory {
     }
   }
   
+  @Override
   public boolean addMemoryMonitor(int address, int size, MemoryMonitor mm) {
     PolledMemorySegments t = new PolledMemorySegments(mm, address, size);
     polledMemories.add(t);
     return true;
   }
 
+  @Override
   public void removeMemoryMonitor(int address, int size, MemoryMonitor mm) {
     for (PolledMemorySegments mcm: polledMemories) {
       if (mcm.mm != mm || mcm.address != address || mcm.size != size) {
@@ -417,6 +434,7 @@ public class SectionMoteMemory implements MoteMemory, AddressMemory {
     }
   }
 
+  @Override
   public int parseInt(byte[] memorySegment) {
     int retVal = 0;
     int pos = 0;
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMote.java b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMote.java
index b2c814b7b..0567f3cac 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMote.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMote.java
@@ -83,10 +83,12 @@ public class ContikiMote extends AbstractWakeupMote implements Mote {
     requestImmediateWakeup();
   }
 
+  @Override
   public int getID() {
     return myInterfaceHandler.getMoteID().getMoteID();
   }
 
+  @Override
   public MoteInterfaceHandler getInterfaces() {
     return myInterfaceHandler;
   }
@@ -95,6 +97,7 @@ public class ContikiMote extends AbstractWakeupMote implements Mote {
     myInterfaceHandler = newInterfaces;
   }
 
+  @Override
   public MoteMemory getMemory() {
     return myMemory;
   }
@@ -103,6 +106,7 @@ public class ContikiMote extends AbstractWakeupMote implements Mote {
     myMemory = (SectionMoteMemory) memory;
   }
 
+  @Override
   public MoteType getType() {
     return myType;
   }
@@ -121,6 +125,7 @@ public class ContikiMote extends AbstractWakeupMote implements Mote {
    *
    * @param simTime Current simulation time
    */
+  @Override
   public void execute(long simTime) {
 
     /* Poll mote interfaces */
@@ -154,6 +159,7 @@ public class ContikiMote extends AbstractWakeupMote implements Mote {
    *
    * @return Current simulation config
    */
+  @Override
   public Collection<Element> getConfigXML() {
     ArrayList<Element> config = new ArrayList<Element>();
     Element element;
@@ -173,6 +179,7 @@ public class ContikiMote extends AbstractWakeupMote implements Mote {
     return config;
   }
 
+  @Override
   public boolean setConfigXML(Simulation simulation, Collection<Element> configXML, boolean visAvailable) {
     setSimulation(simulation);
     myMemory = myType.createInitialMemory();
@@ -212,6 +219,7 @@ public class ContikiMote extends AbstractWakeupMote implements Mote {
     return true;
   }
 
+  @Override
   public String toString() {
     return "Contiki " + getID();
   }
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
index 78e05abe9..f3ff8f4c4 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
@@ -123,6 +123,7 @@ public class ContikiMoteType implements MoteType {
     DEFAULT, MANUAL;
     public String manualHeader = "netstack-conf-example.h";
 
+    @Override
     public String toString() {
       if (this == DEFAULT) {
         return "Default (from contiki-conf.h)";
@@ -204,10 +205,12 @@ public class ContikiMoteType implements MoteType {
   public ContikiMoteType() {
   }
 
+  @Override
   public Mote generateMote(Simulation simulation) {
     return new ContikiMote(this, simulation);
   }
 
+  @Override
   public boolean configureAndInit(Container parentContainer, Simulation simulation,
       boolean visAvailable) throws MoteTypeCreationException {
     myConfig = simulation.getCooja().getProjectConfig().clone();
@@ -665,34 +668,42 @@ public class ContikiMoteType implements MoteType {
     }
   }
 
+  @Override
   public String getIdentifier() {
     return identifier;
   }
 
+  @Override
   public void setIdentifier(String identifier) {
     this.identifier = identifier;
   }
 
+  @Override
   public File getContikiSourceFile() {
     return fileSource;
   }
 
+  @Override
   public void setContikiSourceFile(File file) {
     fileSource = file;
   }
 
+  @Override
   public File getContikiFirmwareFile() {
     return fileFirmware;
   }
 
+  @Override
   public void setContikiFirmwareFile(File file) {
     fileFirmware = file;
   }
 
+  @Override
   public String getCompileCommands() {
     return compileCommands;
   }
 
+  @Override
   public void setCompileCommands(String commands) {
     this.compileCommands = commands;
   }
@@ -1037,14 +1048,17 @@ public class ContikiMoteType implements MoteType {
     }
   }
 
+  @Override
   public String getDescription() {
     return description;
   }
 
+  @Override
   public void setDescription(String newDescription) {
     description = newDescription;
   }
 
+  @Override
   public ProjectConfig getConfig() {
     return myConfig;
   }
@@ -1088,6 +1102,7 @@ public class ContikiMoteType implements MoteType {
     this.coreInterfaces = coreInterfaces;
   }
 
+  @Override
   public Class<? extends MoteInterface>[] getMoteInterfaceClasses() {
     if (moteInterfacesClasses == null) {
       return null;
@@ -1097,6 +1112,7 @@ public class ContikiMoteType implements MoteType {
     return arr;
   }
 
+  @Override
   public void setMoteInterfaceClasses(Class<? extends MoteInterface>[] moteInterfaces) {
     this.moteInterfacesClasses = new ArrayList<Class<? extends MoteInterface>>();
     for (Class<? extends MoteInterface> intf: moteInterfaces) {
@@ -1192,6 +1208,7 @@ public class ContikiMoteType implements MoteType {
    *
    * @return Mote type visualizer
    */
+  @Override
   public JComponent getTypeVisualizer() {
     StringBuilder sb = new StringBuilder();
     // Identifier
@@ -1240,6 +1257,7 @@ public class ContikiMoteType implements MoteType {
     return label;
   }
 
+  @Override
   public Collection<Element> getConfigXML(Simulation simulation) {
     ArrayList<Element> config = new ArrayList<Element>();
     Element element;
@@ -1280,6 +1298,7 @@ public class ContikiMoteType implements MoteType {
     return config;
   }
 
+  @Override
   public boolean setConfigXML(Simulation simulation,
       Collection<Element> configXML, boolean visAvailable)
   throws MoteTypeCreationException {
diff --git a/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java b/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
index ec381e163..7321fc0b7 100644
--- a/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
+++ b/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
@@ -33,7 +33,6 @@ import java.util.Collection;
 import java.util.HashMap;
 import java.util.Observable;
 import java.util.Observer;
-import java.util.Properties;
 
 import org.apache.log4j.Logger;
 import org.jdom.Element;
@@ -67,6 +66,7 @@ public abstract class AbstractApplicationMote extends AbstractWakeupMote impleme
 
   /* Observe our own radio for incoming radio packets */
   private Observer radioDataObserver = new Observer() {
+    @Override
     public void update(Observable obs, Object obj) {
       ApplicationRadio radio = (ApplicationRadio) obs;
       if (radio.getLastEvent() == Radio.RadioEvent.RECEPTION_FINISHED) {
@@ -99,6 +99,7 @@ public abstract class AbstractApplicationMote extends AbstractWakeupMote impleme
     ((ApplicationSerialPort)moteInterfaces.getLog()).triggerLog(msg);
   }
   
+  @Override
   public MoteInterfaceHandler getInterfaces() {
     return moteInterfaces;
   }
@@ -107,6 +108,7 @@ public abstract class AbstractApplicationMote extends AbstractWakeupMote impleme
     moteInterfaces = moteInterfaceHandler;
   }
 
+  @Override
   public MoteMemory getMemory() {
     return memory;
   }
@@ -115,6 +117,7 @@ public abstract class AbstractApplicationMote extends AbstractWakeupMote impleme
     this.memory = (SectionMoteMemory) memory;
   }
 
+  @Override
   public MoteType getType() {
     return moteType;
   }
@@ -123,6 +126,7 @@ public abstract class AbstractApplicationMote extends AbstractWakeupMote impleme
     moteType = type;
   }
 
+  @Override
   public Collection<Element> getConfigXML() {
     ArrayList<Element> config = new ArrayList<Element>();
     Element element;
@@ -141,6 +145,7 @@ public abstract class AbstractApplicationMote extends AbstractWakeupMote impleme
     return config;
   }
 
+  @Override
   public boolean setConfigXML(Simulation simulation,
       Collection<Element> configXML, boolean visAvailable) {
     setSimulation(simulation);
@@ -176,10 +181,12 @@ public abstract class AbstractApplicationMote extends AbstractWakeupMote impleme
     return true;
   }
 
+  @Override
   public int getID() {
     return moteInterfaces.getMoteID().getMoteID();
   }
   
+  @Override
   public String toString() {
     return "AppMote " + getID();
   }
diff --git a/tools/cooja/java/org/contikios/cooja/plugins/BufferListener.java b/tools/cooja/java/org/contikios/cooja/plugins/BufferListener.java
index cf6562d8f..9930184b5 100644
--- a/tools/cooja/java/org/contikios/cooja/plugins/BufferListener.java
+++ b/tools/cooja/java/org/contikios/cooja/plugins/BufferListener.java
@@ -163,6 +163,7 @@ public class BufferListener extends VisPlugin {
 
   private Parser parser = null;
   private Buffer buffer = null;
+  @Override
   public void startPlugin() {
     super.startPlugin();
     if (parser == null) {
@@ -214,6 +215,7 @@ public class BufferListener extends VisPlugin {
   private ArrayList<SegmentMemoryMonitor> memoryMonitors = new ArrayList<SegmentMemoryMonitor>();
 
   private TimeEvent hourTimeEvent = new TimeEvent(0) {
+    @Override
     public void execute(long t) {
       hasHours = true;
       repaintTimeColumn();
@@ -224,11 +226,13 @@ public class BufferListener extends VisPlugin {
   private static final int UPDATE_INTERVAL = 250;
   private UpdateAggregator<BufferAccess> logUpdateAggregator = new UpdateAggregator<BufferAccess>(UPDATE_INTERVAL) {
     private Runnable scroll = new Runnable() {
+      @Override
       public void run() {
         logTable.scrollRectToVisible(
             new Rectangle(0, logTable.getHeight() - 2, 1, logTable.getHeight()));
       }
     };
+    @Override
     protected void handle(List<BufferAccess> ls) {
       boolean isVisible = true;
       if (logTable.getRowCount() > 0) {
@@ -276,18 +280,22 @@ public class BufferListener extends VisPlugin {
 
     model = new AbstractTableModel() {
       private static final long serialVersionUID = 3065150390849332924L;
+      @Override
       public String getColumnName(int col) {
         if (col == COLUMN_TIME && formatTimeString) {
           return "Time";
         }
         return COLUMN_NAMES[col];
       }
+      @Override
       public int getRowCount() {
         return logs.size();
       }
+      @Override
       public int getColumnCount() {
         return COLUMN_NAMES.length;
       }
+      @Override
       public Object getValueAt(int row, int col) {
         BufferAccess log = logs.get(row);
         if (col == COLUMN_TIME) {
@@ -307,6 +315,7 @@ public class BufferListener extends VisPlugin {
 
     logTable = new JTable(model) {
       private static final long serialVersionUID = -930616018336483196L;
+      @Override
       public String getToolTipText(MouseEvent e) {
         java.awt.Point p = e.getPoint();
         int rowIndex = rowAtPoint(p);
@@ -356,6 +365,7 @@ public class BufferListener extends VisPlugin {
           new Color(220, 255, 220),
           new Color(255, 200, 255),
       };
+      @Override
       public Component getTableCellRendererComponent(JTable table,
           Object value, boolean isSelected, boolean hasFocus, int row,
           int column) {
@@ -405,6 +415,7 @@ public class BufferListener extends VisPlugin {
     logTable.setAutoResizeMode(JTable.AUTO_RESIZE_LAST_COLUMN);
     logTable.setFont(new Font("Monospaced", Font.PLAIN, 12));
     logTable.addKeyListener(new KeyAdapter() {
+      @Override
       public void keyPressed(KeyEvent e) {
         if (e.getKeyCode() == KeyEvent.VK_SPACE) {
           showInAllAction.actionPerformed(null);
@@ -419,6 +430,7 @@ public class BufferListener extends VisPlugin {
 
     /* Toggle time format */
     logTable.getTableHeader().addMouseListener(new MouseAdapter() {
+      @Override
       public void mouseClicked(MouseEvent e) {
         int colIndex = logTable.columnAtPoint(e.getPoint());
         int columnIndex = logTable.convertColumnIndexToModel(colIndex);
@@ -432,6 +444,7 @@ public class BufferListener extends VisPlugin {
     });
     logTable.addMouseListener(new MouseAdapter() {
       private Parser lastParser = null;
+      @Override
       public void mousePressed(MouseEvent e) {
         if (e.getButton() != MouseEvent.BUTTON2) {
           return;
@@ -444,6 +457,7 @@ public class BufferListener extends VisPlugin {
           setParser(ByteArrayParser.class);
         }
       }
+      @Override
       public void mouseExited(MouseEvent e) {
         if (lastParser != null) {
           /* Switch back to previous parser */
@@ -451,6 +465,7 @@ public class BufferListener extends VisPlugin {
           lastParser = null;
         }
       }
+      @Override
       public void mouseReleased(MouseEvent e) {
         if (lastParser != null) {
           /* Switch back to previous parser */
@@ -458,6 +473,7 @@ public class BufferListener extends VisPlugin {
           lastParser = null;
         }
       }
+      @Override
       public void mouseClicked(MouseEvent e) {
         int colIndex = logTable.columnAtPoint(e.getPoint());
         int columnIndex = logTable.convertColumnIndexToModel(colIndex);
@@ -482,21 +498,27 @@ public class BufferListener extends VisPlugin {
     /* Popup menu */
     JPopupMenu popupMenu = new JPopupMenu();
     bufferMenu.addMenuListener(new MenuListener() {
+      @Override
       public void menuSelected(MenuEvent e) {
         updateBufferMenu();
       }
+      @Override
       public void menuDeselected(MenuEvent e) {
       }
+      @Override
       public void menuCanceled(MenuEvent e) {
       }
     });
     popupMenu.add(bufferMenu);
     parserMenu.addMenuListener(new MenuListener() {
+      @Override
       public void menuSelected(MenuEvent e) {
         updateParserMenu();
       }
+      @Override
       public void menuDeselected(MenuEvent e) {
       }
+      @Override
       public void menuCanceled(MenuEvent e) {
       }
     });
@@ -521,6 +543,7 @@ public class BufferListener extends VisPlugin {
     colorCheckbox = new JCheckBoxMenuItem("Mote-specific coloring");
     popupMenu.add(colorCheckbox);
     colorCheckbox.addActionListener(new ActionListener() {
+      @Override
       public void actionPerformed(ActionEvent e) {
         backgroundColors = colorCheckbox.isSelected();
         repaint();
@@ -529,6 +552,7 @@ public class BufferListener extends VisPlugin {
     inverseFilterCheckbox = new JCheckBoxMenuItem("Inverse filter");
     popupMenu.add(inverseFilterCheckbox);
     inverseFilterCheckbox.addActionListener(new ActionListener() {
+      @Override
       public void actionPerformed(ActionEvent e) {
         inverseFilter = inverseFilterCheckbox.isSelected();
         if (inverseFilter) {
@@ -543,6 +567,7 @@ public class BufferListener extends VisPlugin {
     hideReadsCheckbox = new JCheckBoxMenuItem("Hide READs", hideReads);
     popupMenu.add(hideReadsCheckbox);
     hideReadsCheckbox.addActionListener(new ActionListener() {
+      @Override
       public void actionPerformed(ActionEvent e) {
         hideReads = hideReadsCheckbox.isSelected();
         setFilter(getFilter());
@@ -553,6 +578,7 @@ public class BufferListener extends VisPlugin {
     withStackTraceCheckbox = new JCheckBoxMenuItem("Capture stack traces", withStackTrace);
     popupMenu.add(withStackTraceCheckbox);
     withStackTraceCheckbox.addActionListener(new ActionListener() {
+      @Override
       public void actionPerformed(ActionEvent e) {
         withStackTrace = withStackTraceCheckbox.isSelected();
         setFilter(getFilter());
@@ -564,6 +590,7 @@ public class BufferListener extends VisPlugin {
 
     /* Column width adjustment */
     java.awt.EventQueue.invokeLater(new Runnable() {
+      @Override
       public void run() {
         /* Make sure this happens *after* adding history */
         adjuster.setDynamicAdjustment(true);
@@ -573,6 +600,7 @@ public class BufferListener extends VisPlugin {
 
     logUpdateAggregator.start();
     simulation.getEventCentral().addMoteCountListener(logOutputListener = new MoteCountListener() {
+      @Override
       public void moteWasAdded(Mote mote) {
         /* Update title */
         try {
@@ -581,6 +609,7 @@ public class BufferListener extends VisPlugin {
           logger.warn("Could not monitor buffer on: " + mote, e);
         }
       }
+      @Override
       public void moteWasRemoved(Mote mote) {
         /* Update title */
         stopObserving(mote);
@@ -596,12 +625,14 @@ public class BufferListener extends VisPlugin {
     filterPanel.add(filterLabel);
     filterPanel.add(filterTextField);
     filterTextField.addActionListener(new ActionListener() {
+      @Override
       public void actionPerformed(ActionEvent e) {
         String str = filterTextField.getText();
         setFilter(str);
 
         /* Autoscroll */
         SwingUtilities.invokeLater(new Runnable() {
+          @Override
           public void run() {
             int s = logTable.getSelectedRow();
             if (s < 0) {
@@ -673,6 +704,7 @@ public class BufferListener extends VisPlugin {
       lastSegmentAddress = segmentAddress;
     }
 
+    @Override
     final public void memoryChanged(MoteMemory memory,
         org.contikios.cooja.MoteMemory.MemoryEventType type, int address) {
       if (type == MemoryEventType.READ) {
@@ -694,10 +726,12 @@ public class BufferListener extends VisPlugin {
       }
     }
 
+    @Override
     public MemoryMonitorType getType() {
       return MemoryMonitorType.POINTER;
     }
 
+    @Override
     public void dispose() {
       super.dispose();
       segmentMonitor.dispose();
@@ -746,6 +780,7 @@ public class BufferListener extends VisPlugin {
       }
     }
 
+    @Override
     public void memoryChanged(MoteMemory memory, MemoryEventType type, int address) {
       byte[] newData = getAddress()==0?null:mote.getMemory().getMemorySegment(getAddress(), getSize());
       addBufferAccess(bl, mote, oldData, newData, type, this.address);
@@ -793,6 +828,7 @@ public class BufferListener extends VisPlugin {
     }
   }
 
+  @Override
   public void closePlugin() {
     if (hourTimeEvent != null) hourTimeEvent.remove();
 
@@ -805,6 +841,7 @@ public class BufferListener extends VisPlugin {
     }
   }
 
+  @Override
   public Collection<Element> getConfigXML() {
     ArrayList<Element> config = new ArrayList<Element>();
     Element element;
@@ -845,12 +882,14 @@ public class BufferListener extends VisPlugin {
     return config;
   }
 
+  @Override
   public boolean setConfigXML(Collection<Element> configXML, boolean visAvailable) {
     for (Element element : configXML) {
       String name = element.getName();
       if ("filter".equals(name)) {
         final String str = element.getText();
         EventQueue.invokeLater(new Runnable() {
+          @Override
           public void run() {
             setFilter(str);
           }
@@ -914,6 +953,7 @@ public class BufferListener extends VisPlugin {
         regexp = null;
       }
       RowFilter<Object, Object> wrapped = new RowFilter<Object, Object>() {
+        @Override
         public boolean include(RowFilter.Entry<? extends Object, ? extends Object> entry) {
           if (hideReads) {
             int row = (Integer) entry.getIdentifier();
@@ -945,6 +985,7 @@ public class BufferListener extends VisPlugin {
 
   public void trySelectTime(final long time) {
     java.awt.EventQueue.invokeLater(new Runnable() {
+      @Override
       public void run() {
         for (int i=0; i < logs.size(); i++) {
           if (logs.get(i).time < time) {
@@ -1054,6 +1095,7 @@ public class BufferListener extends VisPlugin {
   private Action saveAction = new AbstractAction("Save to file") {
     private static final long serialVersionUID = -4140706275748686944L;
 
+    @Override
     public void actionPerformed(ActionEvent e) {
       JFileChooser fc = new JFileChooser();
       File suggest = new File(Cooja.getExternalToolsSetting("BUFFER_LISTENER_SAVEFILE", "BufferAccessLogger.txt"));
@@ -1116,6 +1158,7 @@ public class BufferListener extends VisPlugin {
 
   private Action bufferListenerAction = new AbstractAction("in Buffer Listener") {
     private static final long serialVersionUID = -6358463434933029699L;
+    @Override
     public void actionPerformed(ActionEvent e) {
       int view = logTable.getSelectedRow();
       if (view < 0) {
@@ -1139,6 +1182,7 @@ public class BufferListener extends VisPlugin {
 
   private Action timeLineAction = new AbstractAction("in Timeline") {
     private static final long serialVersionUID = -6358463434933029699L;
+    @Override
     public void actionPerformed(ActionEvent e) {
       int view = logTable.getSelectedRow();
       if (view < 0) {
@@ -1162,6 +1206,7 @@ public class BufferListener extends VisPlugin {
 
   private Action radioLoggerAction = new AbstractAction("in Radio Logger") {
     private static final long serialVersionUID = -3041714249257346688L;
+    @Override
     public void actionPerformed(ActionEvent e) {
       int view = logTable.getSelectedRow();
       if (view < 0) {
@@ -1189,6 +1234,7 @@ public class BufferListener extends VisPlugin {
       putValue(ACCELERATOR_KEY, KeyStroke.getKeyStroke(KeyEvent.VK_SPACE, 0, true));
     }
 
+    @Override
     public void actionPerformed(ActionEvent e) {
       timeLineAction.actionPerformed(null);
       radioLoggerAction.actionPerformed(null);
@@ -1197,6 +1243,7 @@ public class BufferListener extends VisPlugin {
 
   private Action clearAction = new AbstractAction("Clear") {
     private static final long serialVersionUID = -2115620313183440224L;
+    @Override
     public void actionPerformed(ActionEvent e) {
       int size = logs.size();
       if (size > 0) {
@@ -1208,6 +1255,7 @@ public class BufferListener extends VisPlugin {
 
   private Action copyAction = new AbstractAction("Selected") {
     private static final long serialVersionUID = -8433490108577001803L;
+    @Override
     public void actionPerformed(ActionEvent e) {
       Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
 
@@ -1240,6 +1288,7 @@ public class BufferListener extends VisPlugin {
   private Action copyAllAction = new AbstractAction("All") {
     private static final long serialVersionUID = -5038884975254178373L;
 
+    @Override
     public void actionPerformed(ActionEvent e) {
       Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
 
@@ -1269,6 +1318,7 @@ public class BufferListener extends VisPlugin {
 
   private final ActionListener parserSelectedListener = new ActionListener() {
     @SuppressWarnings("unchecked")
+    @Override
     public void actionPerformed(ActionEvent e) {
       Class<? extends Parser> bpClass =
         (Class<? extends Parser>)
@@ -1289,6 +1339,7 @@ public class BufferListener extends VisPlugin {
 
   private final ActionListener bufferSelectedListener = new ActionListener() {
     @SuppressWarnings("unchecked")
+    @Override
     public void actionPerformed(ActionEvent e) {
       Class<? extends Buffer> btClass =
         (Class<? extends Buffer>)
@@ -1421,6 +1472,7 @@ public class BufferListener extends VisPlugin {
   }
   public static abstract class GraphicalParser implements Parser {
     BufferAccess ba = null;
+    @Override
     public Object parse(BufferAccess ba) {
       this.ba = ba;
       return ba;
@@ -1430,6 +1482,7 @@ public class BufferListener extends VisPlugin {
   }
 
   public static abstract class StringParser implements Parser {
+    @Override
     public Object parse(BufferAccess ba) {
       return parseString(ba);
     }
@@ -1459,13 +1512,17 @@ public class BufferListener extends VisPlugin {
     public void writeConfig(Element element);
   }
   public static abstract class AbstractBuffer implements Buffer {
+    @Override
     public String getStatusString() {
       return null;
     }
+    @Override
     public void writeConfig(Element element) {
     }
+    @Override
     public void applyConfig(Element element) {
     }
+    @Override
     public boolean configure(BufferListener bl) {
       return true;
     }
@@ -1474,6 +1531,7 @@ public class BufferListener extends VisPlugin {
   public static abstract class PointerBuffer extends AbstractBuffer {
     public abstract int getPointerAddress(Mote mote);
 
+    @Override
     public SegmentMemoryMonitor createMemoryMonitor(BufferListener bl, Mote mote)
     throws Exception {
       return new PointerMemoryMonitor(
@@ -1486,6 +1544,7 @@ public class BufferListener extends VisPlugin {
     }
   }
   public static abstract class SegmentBuffer extends AbstractBuffer {
+    @Override
     public SegmentMemoryMonitor createMemoryMonitor(BufferListener bl, Mote mote)
     throws Exception {
       return new SegmentMemoryMonitor(
@@ -1521,6 +1580,7 @@ public class BufferListener extends VisPlugin {
 
   @ClassDescription("Byte array")
   public static class ByteArrayParser extends StringParser {
+    @Override
     public String parseString(BufferAccess ba) {
       boolean[] diff = ba.getAccessedBitpattern();
       if (diff == null) {
@@ -1562,6 +1622,7 @@ public class BufferListener extends VisPlugin {
 
   @ClassDescription("Integer array")
   public static class IntegerParser extends StringParser {
+    @Override
     public String parseString(BufferAccess ba) {
       StringBuilder sb = new StringBuilder();
 
@@ -1592,6 +1653,7 @@ public class BufferListener extends VisPlugin {
 
   @ClassDescription("Terminated string")
   public static class TerminatedStringParser extends StringParser {
+    @Override
     public String parseString(BufferAccess ba) {
       /* TODO Diff? */
       int i;
@@ -1608,6 +1670,7 @@ public class BufferListener extends VisPlugin {
 
   @ClassDescription("Printable characters")
   public static class PrintableCharactersParser extends StringParser {
+    @Override
     public String parseString(BufferAccess ba) {
       /* TODO Diff? */
       return new String(ba.mem).replaceAll("[^\\p{Print}]", "");
@@ -1616,6 +1679,7 @@ public class BufferListener extends VisPlugin {
 
   @ClassDescription("IPv6 address")
   public static class IPv6AddressParser extends StringParser {
+    @Override
     public String parseString(BufferAccess ba) {
       /* TODO Diff? */
       if (ba.mem.length < 16) {
@@ -1634,6 +1698,7 @@ public class BufferListener extends VisPlugin {
 
   @ClassDescription("IPv4 address")
   public static class IPv4AddressParser extends StringParser {
+    @Override
     public String parseString(BufferAccess ba) {
       /* TODO Diff? */
       if (ba.mem.length < 4) {
@@ -1664,6 +1729,7 @@ public class BufferListener extends VisPlugin {
       parser.ba = ba;
       setPreferredSize(new Dimension(parser.getUnscaledWidth() + 2*XOFFSET, HEIGHT));
     }
+    @Override
     public void paintComponent(Graphics g) {
       super.paintComponent(g);
       g.translate(XOFFSET, 0);
@@ -1681,9 +1747,11 @@ public class BufferListener extends VisPlugin {
 
   @ClassDescription("Graphical: Height")
   public static class GraphicalHeight4BitsParser extends GraphicalParser {
+    @Override
     public int getUnscaledWidth() {
       return ba.mem.length*2;
     }
+    @Override
     public void paintComponent(Graphics g, JComponent c) {
       g.setColor(Color.GRAY);
       boolean[] diff = ba.getAccessedBitpattern();
@@ -1707,9 +1775,11 @@ public class BufferListener extends VisPlugin {
 
   @ClassDescription("Graphical: Grayscale")
   public static class GraphicalGrayscale4BitsParser extends GraphicalParser {
+    @Override
     public int getUnscaledWidth() {
       return ba.mem.length*2;
     }
+    @Override
     public void paintComponent(Graphics g, JComponent c) {
       boolean[] diff = ba.getAccessedBitpattern();
       for (int x=0; x < ba.mem.length; x++) {
@@ -1730,12 +1800,14 @@ public class BufferListener extends VisPlugin {
 
   @ClassDescription("Variable: node_id")
   public static class NodeIDBuffer extends SegmentBuffer {
+    @Override
     public int getAddress(Mote mote) {
       if (!mote.getMemory().variableExists("node_id")) {
         return -1;
       }
       return mote.getMemory().getVariableAddress("node_id");
     }
+    @Override
     public int getSize(Mote mote) {
       return mote.getMemory().getIntegerLength();
     }
@@ -1744,6 +1816,7 @@ public class BufferListener extends VisPlugin {
 
   @ClassDescription("Queuebuf 0 RAM")
   public static class Queuebuf0Buffer extends SegmentBuffer {
+    @Override
     public int getAddress(Mote mote) {
       if (!mote.getMemory().variableExists("buframmem")) {
         return -1;
@@ -1751,6 +1824,7 @@ public class BufferListener extends VisPlugin {
       int offset = 0;
       return mote.getMemory().getVariableAddress("buframmem") + offset;
     }
+    @Override
     public int getSize(Mote mote) {
       return 128;
     }
@@ -1758,12 +1832,14 @@ public class BufferListener extends VisPlugin {
 
   @ClassDescription("packetbuf_aligned")
   public static class PacketbufBuffer extends SegmentBuffer {
+    @Override
     public int getAddress(Mote mote) {
       if (!mote.getMemory().variableExists("packetbuf_aligned")) {
         return -1;
       }
       return mote.getMemory().getVariableAddress("packetbuf_aligned");
     }
+    @Override
     public int getSize(Mote mote) {
       return 128;
     }
@@ -1771,18 +1847,21 @@ public class BufferListener extends VisPlugin {
 
   @ClassDescription("*packetbufptr")
   public static class PacketbufPointerBuffer extends PointerBuffer {
+    @Override
     public int getPointerAddress(Mote mote) {
       if (!mote.getMemory().variableExists("packetbufptr")) {
         return -1;
       }
       return mote.getMemory().getVariableAddress("packetbufptr");
     }
+    @Override
     public int getAddress(Mote mote) {
       if (!mote.getMemory().variableExists("packetbufptr")) {
         return -1;
       }
       return mote.getMemory().getIntValueOf("packetbufptr");
     }
+    @Override
     public int getSize(Mote mote) {
       return 128;
     }
@@ -1793,18 +1872,21 @@ public class BufferListener extends VisPlugin {
     public String variable;
     public int size;
     public int offset;
+    @Override
     public int getPointerAddress(Mote mote) {
       if (!mote.getMemory().variableExists(variable)) {
         return -1;
       }
       return mote.getMemory().getVariableAddress(variable);
     }
+    @Override
     public int getAddress(Mote mote) {
       if (!mote.getMemory().variableExists(variable)) {
         return -1;
       }
       return mote.getMemory().getIntValueOf(variable)+offset;
     }
+    @Override
     public int getSize(Mote mote) {
       if (!mote.getMemory().variableExists(variable)) {
         return -1;
@@ -1812,6 +1894,7 @@ public class BufferListener extends VisPlugin {
       return size;
     }
 
+    @Override
     public String getStatusString() {
       if (offset > 0) {
         return "Pointer *" + variable + "[" + offset + "] (" + size + ")";
@@ -1820,16 +1903,19 @@ public class BufferListener extends VisPlugin {
       }
     }
 
+    @Override
     public void writeConfig(Element element) {
       element.setAttribute("variable", variable);
       element.setAttribute("size", "" + size);
       element.setAttribute("offset", "" + offset);
     }
+    @Override
     public void applyConfig(Element element) {
       variable = element.getAttributeValue("variable");
       size = Integer.parseInt(element.getAttributeValue("size"));
       offset = Integer.parseInt(element.getAttributeValue("offset"));
     }
+    @Override
     public boolean configure(BufferListener bl) {
       String suggestName = Cooja.getExternalToolsSetting("BUFFER_LISTENER_VARNAME", "node_id");
       String suggestSize = Cooja.getExternalToolsSetting("BUFFER_LISTENER_VARSIZE", "2");
@@ -1880,12 +1966,14 @@ public class BufferListener extends VisPlugin {
     public String variable;
     public int size;
     public int offset;
+    @Override
     public int getAddress(Mote mote) {
       if (!mote.getMemory().variableExists(variable)) {
         return -1;
       }
       return mote.getMemory().getVariableAddress(variable)+offset;
     }
+    @Override
     public int getSize(Mote mote) {
       if (!mote.getMemory().variableExists(variable)) {
         return -1;
@@ -1893,6 +1981,7 @@ public class BufferListener extends VisPlugin {
       return size;
     }
 
+    @Override
     public String getStatusString() {
       if (offset > 0) {
         return "Symbol &" + variable + "[" + offset + "] (" + size + ")";
@@ -1901,16 +1990,19 @@ public class BufferListener extends VisPlugin {
       }
     }
 
+    @Override
     public void writeConfig(Element element) {
       element.setAttribute("variable", variable);
       element.setAttribute("size", "" + size);
       element.setAttribute("offset", "" + offset);
     }
+    @Override
     public void applyConfig(Element element) {
       variable = element.getAttributeValue("variable");
       size = Integer.parseInt(element.getAttributeValue("size"));
       offset = Integer.parseInt(element.getAttributeValue("offset"));
     }
+    @Override
     public boolean configure(BufferListener bl) {
       String suggestName = Cooja.getExternalToolsSetting("BUFFER_LISTENER_VARNAME", "node_id");
       String suggestSize = Cooja.getExternalToolsSetting("BUFFER_LISTENER_VARSIZE", "2");
@@ -1958,26 +2050,32 @@ public class BufferListener extends VisPlugin {
   @ClassDescription("Integer...")
   public static class CustomIntegerBuffer extends SegmentBuffer {
     public String variable;
+    @Override
     public int getAddress(Mote mote) {
       if (!mote.getMemory().variableExists(variable)) {
         return -1;
       }
       return mote.getMemory().getVariableAddress(variable);
     }
+    @Override
     public int getSize(Mote mote) {
       return mote.getMemory().getIntegerLength();
     }
 
+    @Override
     public String getStatusString() {
       return "Integer " + variable;
     }
 
+    @Override
     public void writeConfig(Element element) {
       element.setAttribute("variable", variable);
     }
+    @Override
     public void applyConfig(Element element) {
       variable = element.getAttributeValue("variable");
     }
+    @Override
     public boolean configure(BufferListener bl) {
       String suggestName = Cooja.getExternalToolsSetting("BUFFER_LISTENER_VARNAME", "node_id");
       BufferInput infoComponent =

From 579f0a9a935e2272f1c9362553b17fcf871cd483 Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Fri, 11 Apr 2014 10:13:35 +0200
Subject: [PATCH 02/28] [cooja] Added MemoryLayout class to represent basic
 information about motes memory such as word size or endianess

---
 .../contikios/cooja/avrmote/MicaZMote.java    |   3 +
 .../org/contikios/cooja/mspmote/MspMote.java  |   3 +
 .../cooja/mote/memory/MemoryLayout.java       | 188 ++++++++++++++++++
 .../cooja/motes/AbstractApplicationMote.java  |   2 +
 4 files changed, 196 insertions(+)
 create mode 100644 tools/cooja/java/org/contikios/cooja/mote/memory/MemoryLayout.java

diff --git a/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/MicaZMote.java b/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/MicaZMote.java
index 97cca433a..5c7aa8a20 100644
--- a/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/MicaZMote.java
+++ b/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/MicaZMote.java
@@ -53,6 +53,8 @@ import avrora.sim.mcu.AtmelMicrocontroller;
 import avrora.sim.mcu.EEPROM;
 import avrora.sim.platform.MicaZ;
 import avrora.sim.platform.PlatformFactory;
+import java.nio.ByteOrder;
+import org.contikios.cooja.mote.memory.MemoryLayout;
 
 /**
  * @author Joakim Eriksson, Fredrik Osterlind
@@ -143,6 +145,7 @@ public class MicaZMote extends AbstractEmulatedMote implements Mote {
     avrProperties = (AVRProperties) myCpu.getProperties();
     Simulator sim = myCpu.getSimulator();
     interpreter = (AtmelInterpreter) sim.getInterpreter();
+    new MemoryLayout(ByteOrder.LITTLE_ENDIAN, MemoryLayout.ARCH_8BIT, 2);
 //     State state = interpreter.getState();
     myMemory = new AvrMoteMemory(program.getProgram().getSourceMapping(), avrProperties, interpreter);
   }
diff --git a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMote.java b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMote.java
index 3d66c6b08..3fb989c9c 100644
--- a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMote.java
+++ b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMote.java
@@ -34,6 +34,7 @@ import java.awt.Component;
 import java.io.File;
 import java.io.IOException;
 import java.io.PrintStream;
+import java.nio.ByteOrder;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Hashtable;
@@ -51,6 +52,7 @@ import org.contikios.cooja.Simulation;
 import org.contikios.cooja.Watchpoint;
 import org.contikios.cooja.WatchpointMote;
 import org.contikios.cooja.interfaces.IPAddress;
+import org.contikios.cooja.mote.memory.MemoryLayout;
 import org.contikios.cooja.motes.AbstractEmulatedMote;
 import org.contikios.cooja.mspmote.interfaces.Msp802154Radio;
 import org.contikios.cooja.mspmote.interfaces.MspSerial;
@@ -105,6 +107,7 @@ public abstract class MspMote extends AbstractEmulatedMote implements Mote, Watc
   public MspMote(MspMoteType moteType, Simulation simulation) {
     this.simulation = simulation;
     myMoteType = moteType;
+    new MemoryLayout(ByteOrder.LITTLE_ENDIAN, MemoryLayout.ARCH_16BIT, 2);
 
     /* Schedule us immediately */
     requestImmediateWakeup();
diff --git a/tools/cooja/java/org/contikios/cooja/mote/memory/MemoryLayout.java b/tools/cooja/java/org/contikios/cooja/mote/memory/MemoryLayout.java
new file mode 100644
index 000000000..aa3f7a743
--- /dev/null
+++ b/tools/cooja/java/org/contikios/cooja/mote/memory/MemoryLayout.java
@@ -0,0 +1,188 @@
+/*
+ * Copyright (c) 2014, TU Braunschweig
+ * All rights reserved.
+ * 
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ * 3. Neither the name of the Institute nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software
+ *    without specific prior written permission.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE INSTITUTE OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ */
+
+package org.contikios.cooja.mote.memory;
+
+import java.nio.ByteOrder;
+
+/**
+ * Holds memory layout informations such as endianess, wordsize, C int size.
+ * 
+ * @author Enrico Jorns
+ */
+public class MemoryLayout {
+
+  /** 8 bit memory architecture */
+  public static final int ARCH_8BIT = 1;
+  /** 16 bit memory architecture */
+  public static final int ARCH_16BIT = 2;
+  /** 32 bit memory architecture */
+  public static final int ARCH_32BIT = 4;
+  /** 64 bit memory architecture */
+  public static final int ARCH_64BIT = 8;
+
+  /**
+   * Size of data types in bytes.
+   */
+  public enum DataType {
+
+    BYTE(1),
+    CHAR(1),
+    SHORT(2),
+    INT(4),
+    LONG(8),
+    LONGLONG(8),
+    INT8(1),
+    INT16(2),
+    INT32(4),
+    INT64(8),
+    FLOAT(4),
+    DOUBLE(8),
+    POINTER(4);
+
+    private int size;
+
+    DataType(int size) {
+      this.size = size;
+    }
+
+    public void setSize(int size) {
+      this.size = size;
+    }
+
+    public int getSize() {
+      return this.size;
+    }
+  }
+
+  public final ByteOrder order;
+  public final int addrSize;
+  public final int intSize;
+  public final int WORD_SIZE;
+  private boolean aligned = true;
+
+  /**
+   * Creates new MemoryLayout instance.
+   *
+   * @param order either ByteOrder.BIG_ENDIAN, or ByteOrder.LITTLE_ENDIAN
+   * @param wordsize should be one of ARCH_8BIT, ARCH_16BIT, ARCH_32BIT,
+   * ARCH_64BIT
+   * @param sizeofInt
+   */
+  public MemoryLayout(ByteOrder order, int wordsize, int sizeofInt) {
+    this(order, wordsize, sizeofInt, wordsize);
+  }
+
+  /**
+   * Creates new MemoryLayout instance.
+   *
+   * @param order either ByteOrder.BIG_ENDIAN, or ByteOrder.LITTLE_ENDIAN
+   * @param wordsize should be one of ARCH_8BIT, ARCH_16BIT, ARCH_32BIT,
+   * ARCH_64BIT
+   * @param sizeofPointer
+   * @param sizeofInt
+   */
+  public MemoryLayout(ByteOrder order, int wordsize, int sizeofInt, int sizeofPointer) {
+    this.order = order;
+    this.WORD_SIZE = wordsize;
+    this.intSize = sizeofInt;
+    this.addrSize = sizeofPointer;
+    DataType.INT.setSize(this.intSize);
+    DataType.POINTER.setSize(this.addrSize);
+  }
+
+  /**
+   * Returns the MemoryLayout for the running jvm.
+   *
+   * @return MemoryLayout for the running jvm.
+   */
+  public static MemoryLayout getNative() {
+    return new MemoryLayout(
+            ByteOrder.nativeOrder(),
+            Integer.parseInt(System.getProperty("sun.arch.data.model")) / 8,
+            Integer.SIZE / 8);
+  }
+
+  /**
+   * Enable/Disable data alignment.
+   *
+   * Determines whether data alignemnt is used for packing structs.
+   * Default is enabled.
+   *
+   * @param aligned true to enable data alignment, false to disable
+   */
+  public void setAligned(boolean aligned) {
+    this.aligned = aligned;
+  }
+
+  /**
+   * Returns true if data is aligned.
+   * 
+   * @return if aligned
+   */
+  public boolean isAligned() {
+    return aligned;
+  }
+
+  /**
+   * Returns number of padding bytes between two data types.
+   * 
+   * @param currType
+   * @param nextType
+   * @return 
+   */
+  public int getPaddingBytesFor(DataType currType, DataType nextType) {
+    /* No padding bytes for unaligned memory */
+    if (!isAligned()) {
+      return 0;
+    }
+    /* get size of next element in structure */
+    int nextsize = nextType.getSize();
+    /* limit padding to word size */
+    nextsize = nextsize > WORD_SIZE ? WORD_SIZE : nextsize;
+    System.out.println("Nextsize: " + nextsize);
+    /* calc padding */
+    int pad = nextsize - currType.getSize();
+    return pad;
+  }
+
+  /**
+   * Returns information string for this MemoryLayout.
+   * 
+   * @return String that shows Endianess and word size.
+   */
+  @Override
+  public String toString() {
+    StringBuilder sb = new StringBuilder();
+    return sb.append("MemoryLayout: ")
+            .append("Endianess: ").append(order)
+            .append(", WORD_SIZE: ").append(WORD_SIZE)
+            .toString();
+  }
+}
diff --git a/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java b/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
index 7321fc0b7..5bab4e3bd 100644
--- a/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
+++ b/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
@@ -47,6 +47,7 @@ import org.contikios.cooja.Simulation;
 import org.contikios.cooja.interfaces.ApplicationRadio;
 import org.contikios.cooja.interfaces.ApplicationSerialPort;
 import org.contikios.cooja.interfaces.Radio;
+import org.contikios.cooja.mote.memory.MemoryLayout;
 
 /**
  * Abstract application mote.
@@ -89,6 +90,7 @@ public abstract class AbstractApplicationMote extends AbstractWakeupMote impleme
   public AbstractApplicationMote(MoteType moteType, Simulation sim) {
     setSimulation(sim);
     this.moteType = moteType;
+    MemoryLayout.getNative();
     this.memory = new SectionMoteMemory(new HashMap<String, Integer>(), 0);
     this.moteInterfaces = new MoteInterfaceHandler(this, moteType.getMoteInterfaceClasses());
     this.moteInterfaces.getRadio().addObserver(radioDataObserver);

From 4ac0250dc984a3d94b1c51cf94f662336d720c11 Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Fri, 18 Jul 2014 11:23:45 +0200
Subject: [PATCH 03/28] [cooja] Added base class `MemoryBuffer` for reading and
 writing both simple and complex data structures to and from memory with
 support for padding.

---
 .../cooja/mote/memory/MemoryBuffer.java       | 481 ++++++++++++++++++
 1 file changed, 481 insertions(+)
 create mode 100644 tools/cooja/java/org/contikios/cooja/mote/memory/MemoryBuffer.java

diff --git a/tools/cooja/java/org/contikios/cooja/mote/memory/MemoryBuffer.java b/tools/cooja/java/org/contikios/cooja/mote/memory/MemoryBuffer.java
new file mode 100644
index 000000000..4f645a2e0
--- /dev/null
+++ b/tools/cooja/java/org/contikios/cooja/mote/memory/MemoryBuffer.java
@@ -0,0 +1,481 @@
+/*
+ * Copyright (c) 2014, TU Braunschweig
+ * All rights reserved.
+ * 
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ * 3. Neither the name of the Institute nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software
+ *    without specific prior written permission.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE INSTITUTE OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ */
+package org.contikios.cooja.mote.memory;
+
+import java.nio.ByteBuffer;
+import org.contikios.cooja.mote.memory.MemoryLayout.DataType;
+
+/**
+ * Basic routines for memory access with multi-arch support.
+ *
+ * Handles endianess, integer size and address size.
+ *
+ * Supports padding/aligning.
+ *
+ * @author Enrico Jorns
+ */
+public class MemoryBuffer {
+
+  private final MemoryLayout memLayout;
+  private final ByteBuffer bbuf;
+  private final DataType[] structure;
+  private int structIndex;
+
+  private MemoryBuffer(MemoryLayout memLayout, ByteBuffer buffer, DataType[] structure) {
+    this.memLayout = memLayout;
+    this.bbuf = buffer;
+    this.structure = structure;
+    this.structIndex = 0;
+  }
+
+  /**
+   * Wraps a byte array into an unstructered MemoryBuffer with given MemoryLayout.
+   *<p>
+   * Note that modifications to the buffer are applied to the backed array and vice versa.
+   *
+   * @param layout MemoryLayout for memory to access array from
+   * @param array Byte array that will back this buffer
+   * @return the new MemroyBuffer
+   */
+  public static MemoryBuffer wrap(MemoryLayout layout, byte[] array) {
+    return wrap(layout, array, null);
+  }
+
+  /**
+   * Wraps a byte array into a structured MemoryBuffer with given MemoryLayout.
+   *<p>
+   * Note that modifications to the buffer are applied to the backed array and vice versa.
+   *<p>
+   * A structured MemoryBuffer can be used to simplify reading c struct data
+   * from the memory as it provides support for data aligning.
+   *<p>
+   * The structure array elements should be set to exactly the same types and order
+   * that the corresponding c struct has.
+   * 
+   * @param layout MemoryLayout for memory to access array from
+   * @param structure Array of data types representing the structure to read
+   * @param array Byte array that will back this buffer
+   * @return the new MemroyBuffer
+   */
+  public static MemoryBuffer wrap(MemoryLayout layout, byte[] array, DataType[] structure) {
+    ByteBuffer b = ByteBuffer.wrap(array);
+    b.order(layout.order); // preset endianess
+    return new MemoryBuffer(layout, b, structure);
+  }
+
+  /**
+   * Returns the byte array that backs this buffer
+   *
+   * @return  byte array that backs this buffer
+   */
+  public byte[] getBytes() {
+    if (bbuf.hasArray()) {
+      return bbuf.array();
+    }
+    else {
+      return null;
+    }
+  }
+
+  /**
+   * Calculates the padding bytes to be added/skipped between current and next
+   * element.
+   *
+   * @param type Current data type
+   */
+  private void skipPaddingBytesFor(DataType type) {
+    /* Check if we have a structure and not yet reached the last element */
+    if (structure != null && structure[structIndex + 1] != null) {
+      /* get size of next element in structure */
+      int nextsize = structure[structIndex + 1].getSize();
+      /* limit padding to word size */
+      nextsize = nextsize > memLayout.WORD_SIZE ? memLayout.WORD_SIZE : nextsize;
+      /* calc padding */
+      int pad = nextsize - type.getSize();
+      /* Skip padding bytes */
+      if (pad > 0) {
+        bbuf.position(bbuf.position() + pad);
+      }
+    }
+    structIndex++;
+  }
+
+  /**
+   * Returns current element type.
+   *
+   * @return current element type or null if no struct is used
+   */
+  public DataType getType() {
+    if (structure == null) {
+      return null;
+    }
+    return structure[structIndex];
+  }
+  
+  // --- fixed size types
+
+  /**
+   * Reads 8 bit integer from current buffer position,
+   * and then increments position.
+   * <p>
+   * Note: If structured reading is enabled,
+   * additional padding bytes may be skipped automatically.
+   *
+   * @return 8 bit integer at the buffer's current position
+   */
+  public byte getInt8() {
+    byte value = bbuf.get();
+    skipPaddingBytesFor(DataType.INT8);
+    return value;
+  }
+
+  /**
+   * Reads 16 bit integer from current buffer position,
+   * and then increments position.
+   * <p>
+   * Note: If structured reading is enabled,
+   * additional padding bytes may be skipped automatically.
+   *
+   * @return 16 bit integer at the buffer's current position
+   */
+  public short getInt16() {
+    short value = bbuf.getShort();
+    skipPaddingBytesFor(DataType.INT16);
+    return value;
+  }
+
+  /**
+   * Reads 32 bit integer from current buffer position,
+   * and then increments position.
+   * <p>
+   * Note: If structured reading is enabled,
+   * additional padding bytes may be skipped automatically.
+   *
+   * @return 32 bit integer at the buffer's current position
+   */
+  public int getInt32() {
+    int value = bbuf.getInt();
+    skipPaddingBytesFor(DataType.INT32);
+    return value;
+  }
+
+  /**
+   * Reads 64 bit integer from current buffer position,
+   * and then increments position.
+   * <p>
+   * Note: If structured reading is enabled,
+   * additional padding bytes may be skipped automatically.
+   *
+   * @return 64 bit integer at the buffer's current position
+   */
+  public long getInt64() {
+    long value = bbuf.getLong();
+    skipPaddingBytesFor(DataType.INT64);
+    return value;
+  }
+
+  // --- platform-dependent types
+
+  /**
+   * Reads byte from current buffer position,
+   * and then increments position.
+   * <p>
+   * Note: If structured reading is enabled,
+   * additional padding bytes may be skipped automatically.
+   *
+   * @return byte at the buffer's current position
+   */
+  public byte getByte() {
+    byte value = bbuf.get();
+    skipPaddingBytesFor(DataType.BYTE);
+    return value;
+  }
+
+  /**
+   * Reads short from current buffer position,
+   * and then increments position.
+   * <p>
+   * Note: If structured reading is enabled,
+   * additional padding bytes may be skipped automatically.
+   *
+   * @return short at the buffer's current position
+   */
+  public short getShort() {
+    short value = bbuf.getShort();
+    skipPaddingBytesFor(DataType.SHORT);
+    return value;
+  }
+
+  /**
+   * Reads integer from current buffer position,
+   * and then increments position.
+   * <p>
+   * Note: If structured reading is enabled,
+   * additional padding bytes may be skipped automatically.
+   *
+   * @return integer at the buffer's current position
+   */
+  public int getInt() {
+    int value;
+    switch (memLayout.intSize) {
+      case 2:
+        value = bbuf.getShort();
+        break;
+      case 4:
+      default:
+        value = bbuf.getInt();
+        break;
+    }
+    skipPaddingBytesFor(DataType.INT);
+    return value;
+  }
+
+  /**
+   * Reads long from current buffer position,
+   * and then increments position.
+   * <p>
+   * Note: If structured reading is enabled,
+   * additional padding bytes may be skipped automatically.
+   *
+   * @return long at the buffer's current position
+   */
+  public long getLong() {
+    long value = bbuf.getLong();
+    skipPaddingBytesFor(DataType.LONG);
+    return value;
+  }
+
+  /**
+   * Reads pointer from current buffer position,
+   * and then increments position.
+   * <p>
+   * Note: If structured reading is enabled,
+   * additional padding bytes may be skipped automatically.
+   *
+   * @return pointer at the buffer's current position
+   */
+  public long getAddr() {
+    long value;
+    switch (memLayout.addrSize) {
+      case 2:
+        value = bbuf.getShort();
+        break;
+      case 4:
+        value = bbuf.getInt();
+        break;
+      case 8:
+        value = bbuf.getLong();
+        break;
+      default:
+        value = bbuf.getInt();
+        break;
+    }
+    skipPaddingBytesFor(DataType.POINTER);
+    return value;
+  }
+
+  // --- fixed size types
+  
+  /**
+   * Writes 8 bit integer to current buffer position,
+   * and then increments position.
+   * <p>
+   * Note: If structured writing is enabled,
+   * additional padding bytes may be skipped automatically.
+   *
+   * @param value 8 bit integer to write
+   * @return A reference to this object
+   */
+  public MemoryBuffer putInt8(byte value) {
+    bbuf.put(value);
+    skipPaddingBytesFor(DataType.INT8);
+    return this;
+  }
+
+  /**
+   * Writes 16 bit integer to current buffer position,
+   * and then increments position.
+   * <p>
+   * Note: If structured writing is enabled,
+   * additional padding bytes may be skipped automatically.
+   *
+   * @param value 16 bit integer to write
+   * @return A reference to this object
+   */
+  public MemoryBuffer putInt16(short value) {
+    bbuf.putShort(value);
+    skipPaddingBytesFor(DataType.INT16);
+    return this;
+  }
+
+  /**
+   * Writes 32 bit integer to current buffer position,
+   * and then increments position.
+   * <p>
+   * Note: If structured writing is enabled,
+   * additional padding bytes may be skipped automatically.
+   *
+   * @param value 32 bit integer to write
+   * @return A reference to this object
+   */
+  public MemoryBuffer putInt32(int value) {
+    bbuf.putInt(value);
+    skipPaddingBytesFor(DataType.INT32);
+    return this;
+  }
+
+  /**
+   * Writes 64 bit integer to current buffer position,
+   * and then increments position.
+   * <p>
+   * Note: If structured writing is enabled,
+   * additional padding bytes may be skipped automatically.
+   *
+   * @param value 64 bit integer to write
+   * @return A reference to this object
+   */
+  public MemoryBuffer putInt64(long value) {
+    bbuf.putLong(value);
+    skipPaddingBytesFor(DataType.INT64);
+    return this;
+  }
+
+  // --- platform-dependent types
+  
+  /**
+   * Writes byte to current buffer position,
+   * and then increments position.
+   * <p>
+   * Note: If structured writing is enabled,
+   * additional padding bytes may be skipped automatically.
+   *
+   * @param value byte to write
+   * @return A reference to this object
+   */
+  public MemoryBuffer putByte(byte value) {
+    bbuf.put(value);
+    skipPaddingBytesFor(DataType.BYTE);
+    return this;
+  }
+
+  /**
+   * Writes short to current buffer position,
+   * and then increments position.
+   * <p>
+   * Note: If structured writing is enabled,
+   * additional padding bytes may be skipped automatically.
+   *
+   * @param value short to write
+   * @return A reference to this object
+   */
+  public MemoryBuffer putShort(short value) {
+    bbuf.putShort(value);
+    skipPaddingBytesFor(DataType.SHORT);
+    return this;
+  }
+
+  /**
+   * Writes integer to current buffer position,
+   * and then increments position.
+   * <p>
+   * Note: If structured writing is enabled,
+   * additional padding bytes may be skipped automatically.
+   * <p>
+   * Note: Size of integer depends on platform type
+   *
+   * @param value integer to write
+   * @return A reference to this object
+   */
+  public MemoryBuffer putInt(int value) {
+    switch (memLayout.intSize) {
+      case 2:
+        /**
+         * @TODO: check for size?
+         */
+        bbuf.putShort((short) value);
+        break;
+      case 4:
+      default:
+        bbuf.putInt(value);
+        break;
+    }
+    skipPaddingBytesFor(DataType.INT);
+    return this;
+  }
+
+  /**
+   * Writes long to current buffer position,
+   * and then increments position.
+   * <p>
+   * Note: If structured writing is enabled,
+   * additional padding bytes may be skipped automatically.
+   *
+   * @param value long to write
+   * @return A reference to this object
+   */
+  public MemoryBuffer putLong(long value) {
+    bbuf.putLong(value);
+    skipPaddingBytesFor(DataType.LONG);
+    return this;
+  }
+
+  /**
+   * Writes pointer to current buffer position,
+   * and then increments position.
+   * <p>
+   * Note: If structured writing is enabled,
+   * additional padding bytes may be skipped automatically.
+   * <p>
+   * Note: Size of pointer depends on platform type
+   *
+   * @param value pointer to write
+   * @return A reference to this object
+   */
+  public MemoryBuffer putAddr(long value) {
+    /**
+     * @TODO: check for size?
+     */
+    switch (memLayout.addrSize) {
+      case 2:
+        bbuf.putShort((short) value);
+        break;
+      case 4:
+        bbuf.putInt((int) value);
+        break;
+      case 8:
+        bbuf.putLong(value);
+        break;
+      default:
+        bbuf.putInt((int) value);
+        break;
+    }
+    skipPaddingBytesFor(DataType.POINTER);
+    return this;
+  }
+}

From 128ef572895c859219c362d0bbfce5687c6efef1 Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Thu, 31 Jul 2014 16:27:25 +0200
Subject: [PATCH 04/28] [cooja] memory: Introduce minimal memory access
 interface 'MemoryInterface'

A mote should provide access to its memory using this interface.
All high-level access methods are wrapped around this minimal interface.

Contains dummy-implementations of functions for AvrMoteMemory and MspMoteMemory
---
 .../cooja/mote/memory/MemoryInterface.java    | 192 ++++++++++++++++++
 1 file changed, 192 insertions(+)
 create mode 100644 tools/cooja/java/org/contikios/cooja/mote/memory/MemoryInterface.java

diff --git a/tools/cooja/java/org/contikios/cooja/mote/memory/MemoryInterface.java b/tools/cooja/java/org/contikios/cooja/mote/memory/MemoryInterface.java
new file mode 100644
index 000000000..3f7df09ff
--- /dev/null
+++ b/tools/cooja/java/org/contikios/cooja/mote/memory/MemoryInterface.java
@@ -0,0 +1,192 @@
+/*
+ * Copyright (c) 2014, TU Braunschweig
+ * All rights reserved.
+ * 
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ * 3. Neither the name of the Institute nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software
+ *    without specific prior written permission.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE INSTITUTE OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ */
+package org.contikios.cooja.mote.memory;
+
+import java.util.Map;
+
+/**
+ * A minimal interface to a motes memory.
+ * 
+ * Allows reading and writing memory, obtaining symbol information
+ * and provides some basic inforation about size, layout, etc.
+ *
+ * @author Enrico Jorns
+ */
+public interface MemoryInterface {
+
+  /**
+   * Represents a symbol in memory (variable / function)
+   */
+  public static class Symbol {
+
+    public final Type type;
+    public final String name;
+    public final String section;
+    public final long addr;
+    public final int size;
+
+    public enum Type {
+
+      VARIABLE,
+      FUNCTION
+    }
+
+    public Symbol(Type type, String name, String section, long addr, int size) {
+      this.type = type;
+      this.name = name;
+      this.section = section;
+      this.addr = addr;
+      this.size = size;
+    }
+
+    public Symbol(Type type, String name, long addr, int size) {
+      this(type, name, null, addr, size);
+    }
+
+    @Override
+    public String toString() {
+      return new StringBuilder("Symbol(").append(type == null ? "N/A" : type.toString())
+              .append(") '").append(name)
+              .append("' in '").append(section == null ? "N/A" : section)
+              .append("' at 0x").append(addr == -1 ? "N/A" : Long.toHexString(addr))
+              .append(" size ").append(size == -1 ? "N/A" : String.valueOf(size)).toString();
+    }
+  }
+
+  /**
+   * Class represents memory access exceptions.
+   */
+  public class MoteMemoryException extends RuntimeException {
+
+    public MoteMemoryException(String message, Object... args) {
+      super(String.format(message, args));
+    }
+  }
+
+  /**
+   * Returns entire mote memory
+   * @return Memory byte array
+   * @throws org.contikios.cooja.mote.memory.MemoryInterface.MoteMemoryException 
+   */
+  public byte[] getMemory() throws MoteMemoryException;
+
+  /**
+   * Reads a segment from memory.
+   *
+   * @param addr Start address to read from
+   * @param size Size to read [bytes]
+   * @return Byte array
+   */
+  public byte[] getMemorySegment(long addr, int size) throws MoteMemoryException;
+
+  /**
+   * Sets a segment of memory.
+   *
+   * @param addr Start address to write to
+   * @param data Size to write [bytes]
+   */
+  void setMemorySegment(long addr, byte[] data) throws MoteMemoryException;
+
+  /**
+   * Clears the memory.
+   */
+  void clearMemory();
+
+  /**
+   * 
+   * @return 
+   */
+  long getStartAddr();
+
+  /**
+   * Returns total size of memory.
+   *
+   * @return Size [bytes]
+   */
+  int getTotalSize();// XXX getSize();
+
+  /**
+   * Returns Map of all variables in memory.
+   * Map must be of typ name / symbol.
+   *
+   * @return Variables
+   */
+  Map<String, Symbol> getSymbolMap();
+
+  /**
+   * Returns the MemoryLayout for this memory.
+   * 
+   * @return Memory layout for this memory
+   */
+  MemoryLayout getLayout();
+
+  /**
+   * Monitor to listen for memory updates.
+   */
+  interface SegmentMonitor {
+
+    public static enum EventType {
+
+      READ,
+      WRITE,
+      READWRITE
+    }
+
+    /**
+     * Invoked if the monitored segment changed
+     * 
+     * @param memory Reference to the memory
+     * @param type XXX ???
+     * @param address Address in segment where modification occured
+     */
+    void memoryChanged(MemoryInterface memory, EventType type, long address);
+  }
+
+  /**
+   * Adds a SegmentMonitor for the specified address region.
+   *
+   * @param flag Select memory operation(s) to listen for
+   * (read, write, read/write)
+   * @param address Start address of monitored data region
+   * @param size Size of monitored data region
+   * @param monitor SegmentMonitor to add
+   * @return true if monitor could be added, false if not
+   */
+  boolean addSegmentMonitor(SegmentMonitor.EventType flag, long address, int size, SegmentMonitor monitor);
+
+  /**
+   * Removes SegmentMonitor assigned to the specified region.
+   *
+   * @param address Start address of Monitor data region
+   * @param size Size of Monitor data region
+   * @param monitor SegmentMonitor to remove
+   * @return true if monitor was removed, false if not
+   */
+  boolean removeSegmentMonitor(long address, int size, SegmentMonitor monitor);
+}

From d1c05300a96b510b81412ff19813c878f547dd6b Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Thu, 31 Jul 2014 16:30:05 +0200
Subject: [PATCH 05/28] [cooja] memory: AvrMoteMemory and MspMoteMemory dummy
 implementation of MemoryInterface

---
 .../cooja/avrmote/AvrMoteMemory.java          | 56 +++++++++++++++++--
 .../cooja/mspmote/MspMoteMemory.java          | 56 +++++++++++++++++--
 2 files changed, 100 insertions(+), 12 deletions(-)

diff --git a/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/AvrMoteMemory.java b/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/AvrMoteMemory.java
index ec356879c..8a371d44d 100644
--- a/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/AvrMoteMemory.java
+++ b/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/AvrMoteMemory.java
@@ -40,10 +40,13 @@ import avrora.core.SourceMapping;
 import avrora.core.SourceMapping.Location;
 import avrora.sim.AtmelInterpreter;
 import avrora.sim.Simulator.Watch;
+import java.util.Map;
+import org.contikios.cooja.mote.memory.MemoryInterface;
+import org.contikios.cooja.mote.memory.MemoryLayout;
 /**
  * @author Joakim Eriksson
  */
-public class AvrMoteMemory implements MoteMemory, AddressMemory {
+public class AvrMoteMemory implements MemoryInterface, MoteMemory, AddressMemory {
     private static Logger logger = Logger.getLogger(AvrMoteMemory.class);
 
     private SourceMapping memoryMap;
@@ -59,11 +62,6 @@ public class AvrMoteMemory implements MoteMemory, AddressMemory {
     public void insertWatch(Watch w, int address) {
         interpreter.getSimulator().insertWatch(w, address);
     }
-    
-    @Override
-    public void clearMemory() {
-        logger.fatal("not implemented");
-    }
 
     @Override
     public byte[] getMemorySegment(int address, int size) {
@@ -199,4 +197,50 @@ public class AvrMoteMemory implements MoteMemory, AddressMemory {
       logger.warn("Not implemented");
       return 0;
     }
+
+  @Override
+  public byte[] getMemory() throws MoteMemoryException {
+    throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
+  }
+
+  @Override
+  public byte[] getMemorySegment(long addr, int size) throws MoteMemoryException {
+    throw new UnsupportedOperationException("Not supported yet.");
+  }
+
+  @Override
+  public void setMemorySegment(long addr, byte[] data) throws MoteMemoryException {
+    throw new UnsupportedOperationException("Not supported yet.");
+  }
+
+  @Override
+  public void clearMemory() {
+    throw new UnsupportedOperationException("Not supported yet.");
+  }
+
+  @Override
+  public long getStartAddr() {
+    throw new UnsupportedOperationException("Not supported yet.");
+  }
+
+  @Override
+  public Map<String, Symbol> getSymbolMap() {
+    throw new UnsupportedOperationException("Not supported yet.");
+  }
+
+  @Override
+  public MemoryLayout getLayout() {
+    throw new UnsupportedOperationException("Not supported yet.");
+  }
+
+  @Override
+  public boolean addSegmentMonitor(SegmentMonitor.EventType flag, long address, int size, SegmentMonitor monitor) {
+    throw new UnsupportedOperationException("Not supported yet.");
+  }
+
+  @Override
+  public boolean removeSegmentMonitor(long address, int size, SegmentMonitor monitor) {
+    throw new UnsupportedOperationException("Not supported yet.");
+  }
+
 }
diff --git a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMoteMemory.java b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMoteMemory.java
index 824dd6c08..ce41b33d6 100644
--- a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMoteMemory.java
+++ b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMoteMemory.java
@@ -29,18 +29,21 @@
 package org.contikios.cooja.mspmote;
 
 import java.util.ArrayList;
+import java.util.Map;
 
 import org.apache.log4j.Logger;
 
 import org.contikios.cooja.AddressMemory;
 import org.contikios.cooja.Mote;
 import org.contikios.cooja.MoteMemory;
+import org.contikios.cooja.mote.memory.MemoryInterface;
+import org.contikios.cooja.mote.memory.MemoryLayout;
 import se.sics.mspsim.core.MSP430;
 import se.sics.mspsim.core.Memory.AccessMode;
 import se.sics.mspsim.core.Memory.AccessType;
 import se.sics.mspsim.util.MapEntry;
 
-public class MspMoteMemory implements MoteMemory, AddressMemory {
+public class MspMoteMemory implements MemoryInterface, MoteMemory, AddressMemory {
   private static Logger logger = Logger.getLogger(MspMoteMemory.class);
   private final ArrayList<MapEntry> mapEntries;
 
@@ -87,11 +90,6 @@ public class MspMoteMemory implements MoteMemory, AddressMemory {
     return 2;
   }
 
-  @Override
-  public void clearMemory() {
-    logger.fatal("clearMemory() not implemented");
-  }
-
   @Override
   public byte[] getMemorySegment(int address, int size) {
     int[] memInts = new int[size];
@@ -201,6 +199,52 @@ public class MspMoteMemory implements MoteMemory, AddressMemory {
   }
 
   private ArrayList<MemoryCPUMonitor> cpuMonitorArray = new ArrayList<MemoryCPUMonitor>();
+
+  @Override
+  public byte[] getMemory() throws MoteMemoryException {
+    throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
+  }
+
+  @Override
+  public byte[] getMemorySegment(long addr, int size) throws MoteMemoryException {
+    throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
+  }
+
+  @Override
+  public void setMemorySegment(long addr, byte[] data) throws MoteMemoryException {
+    throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
+  }
+
+  @Override
+  public void clearMemory() {
+    throw new UnsupportedOperationException("Not supported yet.");
+  }
+
+  @Override
+  public long getStartAddr() {
+    throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
+  }
+
+  @Override
+  public Map<String, Symbol> getSymbolMap() {
+    throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
+  }
+
+  @Override
+  public MemoryLayout getLayout() {
+    throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
+  }
+
+  @Override
+  public boolean addSegmentMonitor(SegmentMonitor.EventType flag, long address, int size, SegmentMonitor monitor) {
+    throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
+  }
+
+  @Override
+  public boolean removeSegmentMonitor(long address, int size, SegmentMonitor monitor) {
+    throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
+  }
+
   class MemoryCPUMonitor extends se.sics.mspsim.core.MemoryMonitor.Adapter {
     public final MemoryMonitor mm;
     public final int address;

From 6b15e7837ddeea458ad1e405ed3399729a8ab958 Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Tue, 22 Jul 2014 18:10:30 +0200
Subject: [PATCH 06/28] [cooja] memory: Added address and symbol based memory
 access classes

---
 .../contikios/cooja/mote/memory/Memory.java   | 256 ++++++++++++
 .../cooja/mote/memory/VarMemory.java          | 383 ++++++++++++++++++
 2 files changed, 639 insertions(+)
 create mode 100644 tools/cooja/java/org/contikios/cooja/mote/memory/Memory.java
 create mode 100644 tools/cooja/java/org/contikios/cooja/mote/memory/VarMemory.java

diff --git a/tools/cooja/java/org/contikios/cooja/mote/memory/Memory.java b/tools/cooja/java/org/contikios/cooja/mote/memory/Memory.java
new file mode 100644
index 000000000..4f405a07c
--- /dev/null
+++ b/tools/cooja/java/org/contikios/cooja/mote/memory/Memory.java
@@ -0,0 +1,256 @@
+/*
+ * Copyright (c) 2014, TU Braunschweig.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ * 3. Neither the name of the Institute nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software
+ *    without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE INSTITUTE OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ *
+ */
+package org.contikios.cooja.mote.memory;
+
+import org.contikios.cooja.mote.memory.MemoryLayout.DataType;
+
+/**
+ * Represents memory that can be accessed with address and size informations.
+ *
+ * @author Enrico Jorns
+ */
+public abstract class Memory {
+
+  private final MemoryInterface memIntf;
+
+  /**
+   * Creates new memory for given MemoryLayout.
+   *
+   * @param intf
+   */
+  public Memory(MemoryInterface intf) {
+    memIntf = intf;
+  }
+
+  // -- Get fixed size types
+  /**
+   * Read 8 bit integer from address.
+   *
+   * @param addr Address to read from
+   * @return 8 bit value read from address
+   */
+  public byte getInt8ValueOf(long addr) {
+    return memIntf.getMemorySegment(addr, DataType.INT8.getSize())[0];
+  }
+
+  /**
+   * Read 16 bit integer from address.
+   *
+   * @param addr Address to read from
+   * @return 16 bit value read from address
+   */
+  public short getInt16ValueOf(long addr) {
+    return MemoryBuffer.wrap(
+            memIntf.getLayout(),
+            memIntf.getMemorySegment(addr, DataType.INT16.getSize())).getInt16();
+  }
+
+  /**
+   * Read 32 bit integer from address.
+   *
+   * @param addr Address to read from
+   * @return 32 bit value read from address
+   */
+  public int getInt32ValueOf(long addr) {
+    return MemoryBuffer.wrap(
+            memIntf.getLayout(),
+            memIntf.getMemorySegment(addr, DataType.INT32.getSize())).getInt32();
+  }
+
+  /**
+   * Read 64 bit integer from address.
+   *
+   * @param addr Address to read from
+   * @return 64 bit value read from address
+   */
+  public long getInt64ValueOf(long addr) {
+    return MemoryBuffer.wrap(
+            memIntf.getLayout(),
+            memIntf.getMemorySegment(addr, DataType.INT64.getSize())).getInt64();
+  }
+
+  // -- Get compiler-dependent types
+  /**
+   * Read byte from address.
+   *
+   * @param addr Address to read from
+   * @return byte read from address
+   */
+  public byte getByteValueOf(long addr) {
+    return memIntf.getMemorySegment(addr, DataType.BYTE.getSize())[0];
+  }
+
+  /**
+   * Read short from address.
+   *
+   * @param addr Address to read from
+   * @return short read from address
+   */
+  public short getShortValueOf(long addr) {
+    return MemoryBuffer.wrap(memIntf.getLayout(), memIntf.getMemorySegment(addr, 2)).getShort();
+  }
+
+  /**
+   * Read integer from address.
+   * <p>
+   * Note: Size of integer depends on platform type.
+   *
+   * @param addr Address to read from
+   * @return integer read from address
+   */
+  public int getIntValueOf(long addr) {
+    return MemoryBuffer.wrap(memIntf.getLayout(), memIntf.getMemorySegment(addr, memIntf.getLayout().intSize)).getInt();
+  }
+
+  /**
+   * Read long from address.
+   *
+   * @param addr Address to read from
+   * @return long read from address
+   */
+  public long getLongValueOf(long addr) {
+    return MemoryBuffer.wrap(memIntf.getLayout(), memIntf.getMemorySegment(addr, 4)).getLong();
+  }
+
+  /**
+   * Read pointer from address.
+   * <p>
+   * Note: Size of pointer depends on platform type.
+   *
+   * @param addr Address to read from
+   * @return pointer read from address
+   */
+  public long getAddrValueOf(long addr) {
+    return MemoryBuffer.wrap(memIntf.getLayout(), memIntf.getMemorySegment(addr, memIntf.getLayout().addrSize)).getAddr();
+  }
+
+  // -- Set fixed size types
+  /**
+   * Write 8 bit integer to address.
+   *
+   * @param addr Address to write to
+   * @param value 8 bit value to write
+   */
+  public void setInt8ValueOf(long addr, byte value) {
+    memIntf.setMemorySegment(addr, new byte[]{value});
+  }
+
+  /**
+   * Write 16 bit integer to address.
+   *
+   * @param addr Address to write to
+   * @param value 16 bit value to write
+   */
+  public void setInt16ValueOf(long addr, short value) {
+    memIntf.setMemorySegment(addr, MemoryBuffer.wrap(
+            memIntf.getLayout(),
+            new byte[DataType.INT16.getSize()]).putShort(value).getBytes());
+  }
+
+  /**
+   * Write 32 bit integer to address.
+   *
+   * @param addr Address to write to
+   * @param value 32 bit value to write
+   */
+  public void setInt32ValueOf(long addr, int value) {
+    memIntf.setMemorySegment(addr, MemoryBuffer.wrap(
+            memIntf.getLayout(),
+            new byte[DataType.INT32.getSize()]).putInt(value).getBytes());
+  }
+
+  /**
+   * Write 64 bit integer to address.
+   *
+   * @param addr Address to write to
+   * @param value 64 bit value to write
+   */
+  public void setInt64ValueOf(long addr, long value) {
+    memIntf.setMemorySegment(addr, MemoryBuffer.wrap(
+            memIntf.getLayout(),
+            new byte[DataType.INT64.getSize()]).putLong(value).getBytes());
+  }
+
+  // -- Set compiler-dependent types
+  /**
+   * Write byte to address.
+   *
+   * @param addr Address to write to
+   * @param value byte to write
+   */
+  public void setByteValueOf(long addr, byte value) {
+    memIntf.setMemorySegment(addr, new byte[]{value});
+  }
+
+  /**
+   * Write short to address.
+   *
+   * @param addr Address to write to
+   * @param value short to write
+   */
+  public void setShortValueOf(long addr, short value) {
+    memIntf.setMemorySegment(addr, MemoryBuffer.wrap(memIntf.getLayout(), new byte[2]).putShort(value).getBytes());
+  }
+
+  /**
+   * Write integer to address.
+   * <p>
+   * Note: Size of integer depends on platform type.
+   *
+   * @param addr Address to write to
+   * @param value integer to write
+   */
+  public void setIntValueOf(long addr, int value) {
+    memIntf.setMemorySegment(addr, MemoryBuffer.wrap(memIntf.getLayout(), new byte[memIntf.getLayout().intSize]).putInt(value).getBytes());
+  }
+
+  /**
+   * Write long to address.
+   *
+   * @param addr Address to write to
+   * @param value long to write
+   */
+  public void setLongValueOf(long addr, long value) {
+    memIntf.setMemorySegment(addr, MemoryBuffer.wrap(memIntf.getLayout(), new byte[4]).putLong(value).getBytes());
+  }
+
+  /**
+   * Write pointer to address.
+   * <p>
+   * Note: Size of pointer depends on platform type.
+   *
+   * @param addr Address to write to
+   * @param value pointer to write
+   */
+  public void setAddrValueOf(long addr, long value) {
+    memIntf.setMemorySegment(addr, MemoryBuffer.wrap(memIntf.getLayout(), new byte[memIntf.getLayout().addrSize]).putAddr(value).getBytes());
+  }
+
+}
diff --git a/tools/cooja/java/org/contikios/cooja/mote/memory/VarMemory.java b/tools/cooja/java/org/contikios/cooja/mote/memory/VarMemory.java
new file mode 100644
index 000000000..c8866eeef
--- /dev/null
+++ b/tools/cooja/java/org/contikios/cooja/mote/memory/VarMemory.java
@@ -0,0 +1,383 @@
+/*
+ * Copyright (c) 2014, TU Braunschweig.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ * 3. Neither the name of the Institute nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software
+ *    without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE INSTITUTE OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ *
+ */
+package org.contikios.cooja.mote.memory;
+
+import java.util.Collection;
+import java.util.Set;
+
+import org.contikios.cooja.mote.memory.MemoryInterface.Symbol;
+import org.contikios.cooja.mote.memory.MemoryInterface.SegmentMonitor;
+import org.contikios.cooja.mote.memory.MemoryInterface.SegmentMonitor.EventType;
+
+/**
+ * Represents memory that can be accessed with names of variables.
+ *
+ * @author Enrico Jorns
+ */
+public class VarMemory extends Memory {
+
+  private MemoryInterface memIntf;
+
+  /**
+   * Creates new VarMemory.
+   *
+   * @param intf
+   */
+  public VarMemory(MemoryInterface intf) {
+    super(intf);
+    memIntf = intf;
+  }
+
+  /**
+   * Allows to change the MemoryInterface associated with this access class.
+   *
+   * @param intf Interface to associate with
+   */
+  public void associateMemory(MemoryInterface intf) {
+    memIntf = intf;
+  }
+
+  /**
+   * Generates and returns an array of all variables in this memory
+   *
+   * @return All variables located in this memory
+   */
+  public Collection<Symbol> getVariables() {
+    return memIntf.getSymbolMap().values();
+  }
+
+  /**
+   * Generates an array of all variable names in this memory.
+   *
+   * @return All variable names located in this memory
+   */
+  public Set<String> getVariableNames() {
+    return memIntf.getSymbolMap().keySet();
+  }
+
+  /**
+   * Checks if given variable exists in memory.
+   *
+   * @param varName Variable name
+   * @return True if variable exists, false otherwise
+   */
+  public boolean variableExists(String varName) {
+    return memIntf.getSymbolMap().containsKey(varName);
+  }
+
+  /**
+   * Returns address of variable with given name.
+   *
+   * @param varName Variable name
+   * @return Variable address
+   */
+  public Symbol getVariable(String varName) throws UnknownVariableException {
+    return memIntf.getSymbolMap().get(varName);
+  }
+
+  /**
+   * Returns address of variable with given name.
+   *
+   * @param varName Variable name
+   * @return Address of variable
+   * @throws UnknownVariableException If variable not found
+   */
+  public long getVariableAddress(String varName) throws UnknownVariableException {
+    return getVariable(varName).addr;
+  }
+
+  /**
+   * Return size of variable with given name.
+   *
+   * @param varName Variable name
+   * @return Size of variable, -1 if unknown size
+   * @throws UnknownVariableException If variable not found
+   */
+  public int getVariableSize(String varName) throws UnknownVariableException {
+    return getVariable(varName).size;
+  }
+
+  /**
+   * Read 8 bit integer from location associated with this variable name.
+   *
+   * @param varName Variable name
+   * @return 8 bit integer value read from location assigned to variable name
+   */
+  public byte getInt8ValueOf(String varName)
+          throws UnknownVariableException {
+    return getInt8ValueOf(getVariable(varName).addr);
+  }
+
+  /**
+   * Read 16 bit integer from location associated with this variable name.
+   *
+   * @param varName Variable name
+   * @return 16 bit integer value read from location assigned to variable name
+   */
+  public short getInt16ValueOf(String varName)
+          throws UnknownVariableException {
+    return getInt16ValueOf(getVariable(varName).addr);
+  }
+
+  /**
+   * Read 32 bit integer from location associated with this variable name.
+   *
+   * @param varName Variable name
+   * @return 32 bit integer value read from location assigned to variable name
+   */
+  public int getInt32ValueOf(String varName)
+          throws UnknownVariableException {
+    return getInt32ValueOf(getVariable(varName).addr);
+  }
+
+  /**
+   * Read 64 bit integer from location associated with this variable name.
+   *
+   * @param varName Variable name
+   * @return 64 bit integer value read from location assigned to variable name
+   */
+  public long getInt64ValueOf(String varName)
+          throws UnknownVariableException {
+    return getInt64ValueOf(getVariable(varName).addr);
+  }
+
+  /**
+   * Read byte from location associated with this variable name.
+   *
+   * @param varName Variable name
+   * @return byte value read from location assigned to variable name
+   */
+  public byte getByteValueOf(String varName)
+          throws UnknownVariableException {
+    return getByteValueOf(getVariable(varName).addr);
+  }
+
+  /**
+   * Read short from location associated with this variable name.
+   *
+   * @param varName Variable name
+   * @return short value read from location assigned to variable name
+   */
+  public short getShortValueOf(String varName)
+          throws UnknownVariableException {
+    short val = getShortValueOf(getVariable(varName).addr);
+    return val;
+  }
+
+  /**
+   * Read integer from location associated with this variable name.
+   *
+   * @param varName Variable name
+   * @return integer value read from location assigned to variable name
+   */
+  public int getIntValueOf(String varName)
+          throws UnknownVariableException {
+    int val = getIntValueOf(getVariable(varName).addr);
+    return val;
+  }
+
+  /**
+   * Read long from location associated with this variable name.
+   *
+   * @param varName Variable name
+   * @return long value read from location assigned to variable name
+   */
+  public long getLongValueOf(String varName)
+          throws UnknownVariableException {
+    long val = getLongValueOf(getVariable(varName).addr);
+    return val;
+  }
+
+  /**
+   * Read pointer from location associated with this variable name.
+   *
+   * The number of bytes actually read depends on the pointer size
+   * defined in memory layout.
+   *
+   * @param varName Variable name
+   * @return pointer value read from location assigned to variable name
+   */
+  public long getAddrValueOf(String varName)
+          throws UnknownVariableException {
+    long val = getAddrValueOf(getVariable(varName).addr);
+    return val;
+  }
+
+  /**
+   * Read byte array starting at location associated with this variable name.
+   *
+   * @param varName Variable name
+   * @param length Numbe of bytes to read
+   * @return byte array read from location assigned to variable name
+   */
+  public byte[] getByteArray(String varName, int length)
+          throws UnknownVariableException {
+    return memIntf.getMemorySegment(getVariable(varName).addr, length);
+  }
+
+  /**
+   * Write 8 bit integer value to location associated with this variable name.
+   *
+   * @param varName Variable name
+   * @param value 8 bit integer value to write
+   */
+  public void setInt8ValueOf(String varName, byte value)
+          throws UnknownVariableException {
+    setInt8ValueOf(getVariable(varName).addr, value);
+  }
+
+  /**
+   * Write 16 bit integer value to location associated with this variable name.
+   *
+   * @param varName Variable name
+   * @param value 16 bit integer value to write
+   */
+  public void setInt16ValueOf(String varName, byte value)
+          throws UnknownVariableException {
+    setInt16ValueOf(getVariable(varName).addr, value);
+  }
+
+  /**
+   * Write 32 bit integer value to location associated with this variable name.
+   *
+   * @param varName Variable name
+   * @param value 32 bit integer value to write
+   */
+  public void setInt32ValueOf(String varName, byte value)
+          throws UnknownVariableException {
+    setInt32ValueOf(getVariable(varName).addr, value);
+  }
+
+  /**
+   * Write 64 bit integer value to location associated with this variable name.
+   *
+   * @param varName Variable name
+   * @param value 64 bit integer value to write
+   */
+  public void setInt64ValueOf(String varName, byte value)
+          throws UnknownVariableException {
+    setInt64ValueOf(getVariable(varName).addr, value);
+  }
+
+  /**
+   * Write byte value to location associated with this variable name.
+   *
+   * @param varName Variable name
+   * @param value byte value to write
+   */
+  public void setByteValueOf(String varName, byte value)
+          throws UnknownVariableException {
+    setByteValueOf(getVariable(varName).addr, value);
+  }
+
+  /**
+   * Write short value to location associated with this variable name.
+   *
+   * @param varName Variable name
+   * @param value short value to write
+   */
+  public void setShortValueOf(String varName, short value)
+          throws UnknownVariableException {
+    setShortValueOf(getVariable(varName).addr, value);
+  }
+
+  /**
+   * Write int value to location associated with this variable name.
+   *
+   * @param varName Variable name
+   * @param value int value to write
+   */
+  public void setIntValueOf(String varName, int value)
+          throws UnknownVariableException {
+    setIntValueOf(getVariable(varName).addr, value);
+  }
+
+  /**
+   * Write long value to location associated with this variable name.
+   *
+   * @param varName Variable name
+   * @param value long value to write
+   */
+  public void setLongValueOf(String varName, long value)
+          throws UnknownVariableException {
+    setLongValueOf(getVariable(varName).addr, value);
+  }
+
+  /**
+   * Write pointer value to location associated with this variable name.
+   *
+   * The number of bytes actually written depends on the pointer size
+   * defined in memory layout.
+   *
+   * @param varName Variable name
+   * @param value Value to write
+   */
+  public void setAddrValueOf(String varName, long value)
+          throws UnknownVariableException {
+    setAddrValueOf(getVariable(varName).addr, value);
+  }
+
+  /**
+   *
+   * @param varName
+   * @param data
+   */
+  public void setByteArray(String varName, byte[] data)
+          throws UnknownVariableException {
+    memIntf.setMemorySegment(getVariable(varName).addr, data);
+  }
+
+  /**
+   * Adds a MemoryMonitor for the specified address region.
+   *
+   * @param flag Select memory operation(s) to listen for (read, write,
+   * read/write)
+   * @param varName
+   * @param mm
+   * @return
+   */
+  public boolean addVarMonitor(EventType flag, final String varName, final SegmentMonitor mm) {
+    return memIntf.addSegmentMonitor(
+            flag,
+            getVariable(varName).addr,
+            getVariable(varName).size,
+            mm);
+  }
+
+  /**
+   * Removes MemoryMonitor assigned to the specified region.
+   *
+   * @param varName
+   * @param mm MemoryMonitor to remove
+   */
+  public void removeVarMonitor(String varName, SegmentMonitor mm) {
+    memIntf.removeSegmentMonitor(getVariable(varName).addr, getVariable(varName).size, mm);
+  }
+}

From 19d07beb1630393619c82983fb1d099ffda667f6 Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Tue, 22 Jul 2014 22:47:54 +0200
Subject: [PATCH 07/28] [cooja] memory: SectionMoteMemory dummy implementation
 of MemoryInterface

---
 .../contikios/cooja/SectionMoteMemory.java    | 40 ++++++++++++++++++-
 1 file changed, 39 insertions(+), 1 deletion(-)

diff --git a/tools/cooja/java/org/contikios/cooja/SectionMoteMemory.java b/tools/cooja/java/org/contikios/cooja/SectionMoteMemory.java
index 79f32a15b..7f7a7d92b 100644
--- a/tools/cooja/java/org/contikios/cooja/SectionMoteMemory.java
+++ b/tools/cooja/java/org/contikios/cooja/SectionMoteMemory.java
@@ -30,8 +30,11 @@ package org.contikios.cooja;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
+import java.util.Map;
 
 import org.apache.log4j.Logger;
+import org.contikios.cooja.mote.memory.MemoryInterface;
+import org.contikios.cooja.mote.memory.MemoryLayout;
 
 /**
  * Represents a mote memory consisting of non-overlapping memory sections with
@@ -43,7 +46,7 @@ import org.apache.log4j.Logger;
  *
  * @author Fredrik Osterlind
  */
-public class SectionMoteMemory implements MoteMemory, AddressMemory {
+public class SectionMoteMemory implements MemoryInterface, MoteMemory, AddressMemory {
   private static Logger logger = Logger.getLogger(SectionMoteMemory.class);
 
   private ArrayList<MoteMemorySection> sections = new ArrayList<MoteMemorySection>();
@@ -268,6 +271,41 @@ public class SectionMoteMemory implements MoteMemory, AddressMemory {
     setMemorySegment(varAddr, data);
   }
 
+  @Override
+  public byte[] getMemorySegment(long addr, int size) throws MoteMemoryException {
+    throw new UnsupportedOperationException("Not supported yet.");
+  }
+
+  @Override
+  public void setMemorySegment(long addr, byte[] data) throws MoteMemoryException {
+    throw new UnsupportedOperationException("Not supported yet.");
+  }
+
+  @Override
+  public long getStartAddr() {
+    throw new UnsupportedOperationException("Not supported yet.");
+  }
+
+  @Override
+  public Map<String, Symbol> getSymbolMap() {
+    throw new UnsupportedOperationException("Not supported yet.");
+  }
+
+  @Override
+  public MemoryLayout getLayout() {
+    throw new UnsupportedOperationException("Not supported yet.");
+  }
+
+  @Override
+  public boolean addSegmentMonitor(SegmentMonitor.EventType flag, long address, int size, SegmentMonitor monitor) {
+    throw new UnsupportedOperationException("Not supported yet.");
+  }
+
+  @Override
+  public boolean removeSegmentMonitor(long address, int size, SegmentMonitor monitor) {
+    throw new UnsupportedOperationException("Not supported yet.");
+  }
+
   /**
    * A memory section contains a byte array and a start address.
    *

From 9dd29d56c9e2732095fb8d518ddd24c989a29946 Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Wed, 23 Jul 2014 00:01:19 +0200
Subject: [PATCH 08/28] [cooja] getMemory() now returns MemoryInterface

Including code adaptions based on new memory methods to keep code compilable
---
 .../contikios/cooja/avrmote/MicaZMote.java    |  6 +-
 .../org/contikios/cooja/mspmote/MspMote.java  |  4 +-
 .../cooja/java/org/contikios/cooja/Mote.java  |  3 +-
 .../cooja/contikimote/ContikiMote.java        |  3 +-
 .../contikios/cooja/interfaces/IPAddress.java | 35 ++++----
 .../cooja/interfaces/RimeAddress.java         | 23 ++---
 .../cooja/motes/AbstractApplicationMote.java  |  3 +-
 .../cooja/plugins/BufferListener.java         | 88 +++++++++++--------
 8 files changed, 92 insertions(+), 73 deletions(-)

diff --git a/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/MicaZMote.java b/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/MicaZMote.java
index 5c7aa8a20..e82c86384 100644
--- a/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/MicaZMote.java
+++ b/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/MicaZMote.java
@@ -43,6 +43,8 @@ import org.contikios.cooja.MoteInterfaceHandler;
 import org.contikios.cooja.MoteMemory;
 import org.contikios.cooja.MoteType;
 import org.contikios.cooja.Simulation;
+import org.contikios.cooja.mote.memory.MemoryInterface;
+import org.contikios.cooja.mote.memory.MemoryLayout;
 import org.contikios.cooja.motes.AbstractEmulatedMote;
 import avrora.arch.avr.AVRProperties;
 import avrora.core.LoadableProgram;
@@ -54,7 +56,6 @@ import avrora.sim.mcu.EEPROM;
 import avrora.sim.platform.MicaZ;
 import avrora.sim.platform.PlatformFactory;
 import java.nio.ByteOrder;
-import org.contikios.cooja.mote.memory.MemoryLayout;
 
 /**
  * @author Joakim Eriksson, Fredrik Osterlind
@@ -267,7 +268,8 @@ public class MicaZMote extends AbstractEmulatedMote implements Mote {
     return config;
   }
 
-  public MoteMemory getMemory() {
+  @Override
+  public MemoryInterface getMemory() {
     return myMemory;
   }
 
diff --git a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMote.java b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMote.java
index 3fb989c9c..b76651bce 100644
--- a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMote.java
+++ b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMote.java
@@ -52,6 +52,7 @@ import org.contikios.cooja.Simulation;
 import org.contikios.cooja.Watchpoint;
 import org.contikios.cooja.WatchpointMote;
 import org.contikios.cooja.interfaces.IPAddress;
+import org.contikios.cooja.mote.memory.MemoryInterface;
 import org.contikios.cooja.mote.memory.MemoryLayout;
 import org.contikios.cooja.motes.AbstractEmulatedMote;
 import org.contikios.cooja.mspmote.interfaces.Msp802154Radio;
@@ -188,7 +189,8 @@ public abstract class MspMote extends AbstractEmulatedMote implements Mote, Watc
     myCpu = cpu;
   }
 
-  public MoteMemory getMemory() {
+  @Override
+  public MemoryInterface getMemory() {
     return myMemory;
   }
 
diff --git a/tools/cooja/java/org/contikios/cooja/Mote.java b/tools/cooja/java/org/contikios/cooja/Mote.java
index 7eeb326a0..167a24ff4 100644
--- a/tools/cooja/java/org/contikios/cooja/Mote.java
+++ b/tools/cooja/java/org/contikios/cooja/Mote.java
@@ -28,6 +28,7 @@
 package org.contikios.cooja;
 
 import java.util.Collection;
+import org.contikios.cooja.mote.memory.MemoryInterface;
 
 import org.jdom.Element;
 
@@ -63,7 +64,7 @@ public interface Mote {
    * @see #setMemory(MoteMemory)
    * @return Mote memory
    */
-  public MoteMemory getMemory();
+  public MemoryInterface getMemory();
 
   /**
    * Returns mote type.
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMote.java b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMote.java
index 0567f3cac..b16b8a95d 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMote.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMote.java
@@ -42,6 +42,7 @@ import org.contikios.cooja.MoteMemory;
 import org.contikios.cooja.MoteType;
 import org.contikios.cooja.SectionMoteMemory;
 import org.contikios.cooja.Simulation;
+import org.contikios.cooja.mote.memory.MemoryInterface;
 import org.contikios.cooja.motes.AbstractWakeupMote;
 
 /**
@@ -98,7 +99,7 @@ public class ContikiMote extends AbstractWakeupMote implements Mote {
   }
 
   @Override
-  public MoteMemory getMemory() {
+  public MemoryInterface getMemory() {
     return myMemory;
   }
 
diff --git a/tools/cooja/java/org/contikios/cooja/interfaces/IPAddress.java b/tools/cooja/java/org/contikios/cooja/interfaces/IPAddress.java
index 7216f8010..a0263d077 100644
--- a/tools/cooja/java/org/contikios/cooja/interfaces/IPAddress.java
+++ b/tools/cooja/java/org/contikios/cooja/interfaces/IPAddress.java
@@ -42,9 +42,9 @@ import org.jdom.Element;
 import org.contikios.cooja.ClassDescription;
 import org.contikios.cooja.Mote;
 import org.contikios.cooja.MoteInterface;
-import org.contikios.cooja.MoteMemory;
-import org.contikios.cooja.MoteMemory.MemoryEventType;
-import org.contikios.cooja.MoteMemory.MemoryMonitor;
+import org.contikios.cooja.mote.memory.MemoryInterface;
+import org.contikios.cooja.mote.memory.MemoryInterface.SegmentMonitor;
+import org.contikios.cooja.mote.memory.VarMemory;
 
 /**
  * Read-only interface to IPv4 or IPv6 address.
@@ -54,21 +54,22 @@ import org.contikios.cooja.MoteMemory.MemoryMonitor;
 @ClassDescription("IP Address")
 public class IPAddress extends MoteInterface {
   private static Logger logger = Logger.getLogger(IPAddress.class);
-  private final MoteMemory moteMem;
+  private final VarMemory moteMem;
 
   private static final int IPv6_MAX_ADDRESSES = 4;
   private boolean ipv6IsGlobal = false;
   private int ipv6AddressIndex = -1;
 
   private static final int MONITORED_SIZE = 150;
-  private MemoryMonitor memMonitor;
+  private SegmentMonitor memMonitor;
 
   public IPAddress(final Mote mote) {
-    moteMem = mote.getMemory();
+    moteMem = new VarMemory(mote.getMemory());
 
-    memMonitor = new MemoryMonitor() {
-      public void memoryChanged(MoteMemory memory, MemoryEventType type, int address) {
-        if (type != MemoryEventType.WRITE) {
+    memMonitor = new MemoryInterface.SegmentMonitor() {
+      @Override
+      public void memoryChanged(MemoryInterface memory, SegmentMonitor.EventType type, long address) {
+        if (type != SegmentMonitor.EventType.WRITE) {
           return;
         }
         setChanged();
@@ -76,11 +77,11 @@ public class IPAddress extends MoteInterface {
       }
     };
     if (isVersion4()) {
-      moteMem.addMemoryMonitor(moteMem.getVariableAddress("uip_hostaddr"), 4, memMonitor);
+      moteMem.addVarMonitor(SegmentMonitor.EventType.WRITE, "uip_hostaddr", memMonitor);
     } else if (isVersion6()) {
-      moteMem.addMemoryMonitor(moteMem.getVariableAddress("uip_ds6_netif_addr_list_offset"), 1, memMonitor);
-      moteMem.addMemoryMonitor(moteMem.getVariableAddress("uip_ds6_addr_size"), 1, memMonitor);
-      moteMem.addMemoryMonitor(moteMem.getVariableAddress("uip_ds6_if"), MONITORED_SIZE, memMonitor);
+      moteMem.addVarMonitor(SegmentMonitor.EventType.WRITE, "uip_ds6_netif_addr_list_offset", memMonitor);
+      moteMem.addVarMonitor(SegmentMonitor.EventType.WRITE, "uip_ds6_addr_size", memMonitor);
+      moteMem.addVarMonitor(SegmentMonitor.EventType.WRITE, "uip_ds6_if", memMonitor);
     }
   }
 
@@ -205,11 +206,11 @@ public class IPAddress extends MoteInterface {
     super.removed();
     if (memMonitor != null) {
       if (isVersion4()) {
-        moteMem.removeMemoryMonitor(moteMem.getVariableAddress("rimeaddr_node_addr"), 4, memMonitor);
+        moteMem.removeVarMonitor("rimeaddr_node_addr", memMonitor);
       } else if (isVersion6()) {
-        moteMem.removeMemoryMonitor(moteMem.getVariableAddress("uip_ds6_netif_addr_list_offset"), 1, memMonitor);
-        moteMem.removeMemoryMonitor(moteMem.getVariableAddress("uip_ds6_addr_size"), 1, memMonitor);
-        moteMem.removeMemoryMonitor(moteMem.getVariableAddress("uip_ds6_if"), MONITORED_SIZE, memMonitor);
+        moteMem.removeVarMonitor("uip_ds6_netif_addr_list_offset", memMonitor);
+        moteMem.removeVarMonitor("uip_ds6_addr_size", memMonitor);
+        moteMem.removeVarMonitor("uip_ds6_if", memMonitor);
       }
     }
   }
diff --git a/tools/cooja/java/org/contikios/cooja/interfaces/RimeAddress.java b/tools/cooja/java/org/contikios/cooja/interfaces/RimeAddress.java
index 405aca506..09031b44d 100644
--- a/tools/cooja/java/org/contikios/cooja/interfaces/RimeAddress.java
+++ b/tools/cooja/java/org/contikios/cooja/interfaces/RimeAddress.java
@@ -43,9 +43,9 @@ import org.jdom.Element;
 import org.contikios.cooja.ClassDescription;
 import org.contikios.cooja.Mote;
 import org.contikios.cooja.MoteInterface;
-import org.contikios.cooja.MoteMemory;
-import org.contikios.cooja.MoteMemory.MemoryEventType;
-import org.contikios.cooja.MoteMemory.MemoryMonitor;
+import org.contikios.cooja.mote.memory.MemoryInterface;
+import org.contikios.cooja.mote.memory.MemoryInterface.SegmentMonitor;
+import org.contikios.cooja.mote.memory.VarMemory;
 
 /**
  * Read-only interface to Rime address read from Contiki variable: linkaddr_node_addr.
@@ -57,18 +57,19 @@ import org.contikios.cooja.MoteMemory.MemoryMonitor;
 @ClassDescription("Rime address")
 public class RimeAddress extends MoteInterface {
   private static Logger logger = Logger.getLogger(RimeAddress.class);
-  private MoteMemory moteMem;
+  private VarMemory moteMem;
 
   public static final int RIME_ADDR_LENGTH = 2;
 
-  private MemoryMonitor memMonitor = null;
+  private SegmentMonitor memMonitor = null;
 
   public RimeAddress(final Mote mote) {
-    moteMem = mote.getMemory();
+    moteMem = new VarMemory(mote.getMemory());
     if (hasRimeAddress()) {
-      memMonitor = new MemoryMonitor() {
-        public void memoryChanged(MoteMemory memory, MemoryEventType type, int address) {
-          if (type != MemoryEventType.WRITE) {
+      memMonitor = new SegmentMonitor() {
+        @Override
+        public void memoryChanged(MemoryInterface memory, SegmentMonitor.EventType type, long address) {
+          if (type != SegmentMonitor.EventType.WRITE) {
             return;
           }
           setChanged();
@@ -76,7 +77,7 @@ public class RimeAddress extends MoteInterface {
         }
       };
       /* TODO XXX Timeout? */
-      moteMem.addMemoryMonitor(moteMem.getVariableAddress("linkaddr_node_addr"), RIME_ADDR_LENGTH, memMonitor);
+      moteMem.addVarMonitor(SegmentMonitor.EventType.WRITE, "linkaddr_node_addr", memMonitor);
     }
   }
 
@@ -131,7 +132,7 @@ public class RimeAddress extends MoteInterface {
   public void removed() {
     super.removed();
     if (memMonitor != null) {
-      moteMem.removeMemoryMonitor(moteMem.getVariableAddress("linkaddr_node_addr"), RIME_ADDR_LENGTH, memMonitor);
+      moteMem.removeVarMonitor("linkaddr_node_addr", memMonitor);
     }
   }
 
diff --git a/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java b/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
index 5bab4e3bd..11025c183 100644
--- a/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
+++ b/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
@@ -47,6 +47,7 @@ import org.contikios.cooja.Simulation;
 import org.contikios.cooja.interfaces.ApplicationRadio;
 import org.contikios.cooja.interfaces.ApplicationSerialPort;
 import org.contikios.cooja.interfaces.Radio;
+import org.contikios.cooja.mote.memory.MemoryInterface;
 import org.contikios.cooja.mote.memory.MemoryLayout;
 
 /**
@@ -111,7 +112,7 @@ public abstract class AbstractApplicationMote extends AbstractWakeupMote impleme
   }
 
   @Override
-  public MoteMemory getMemory() {
+  public MemoryInterface getMemory() {
     return memory;
   }
 
diff --git a/tools/cooja/java/org/contikios/cooja/plugins/BufferListener.java b/tools/cooja/java/org/contikios/cooja/plugins/BufferListener.java
index 9930184b5..8b2ab1327 100644
--- a/tools/cooja/java/org/contikios/cooja/plugins/BufferListener.java
+++ b/tools/cooja/java/org/contikios/cooja/plugins/BufferListener.java
@@ -100,6 +100,10 @@ import org.contikios.cooja.VisPlugin;
 import org.contikios.cooja.dialogs.TableColumnAdjuster;
 import org.contikios.cooja.dialogs.UpdateAggregator;
 import org.contikios.cooja.interfaces.IPAddress;
+import org.contikios.cooja.mote.memory.MemoryBuffer;
+import org.contikios.cooja.mote.memory.MemoryInterface;
+import org.contikios.cooja.mote.memory.MemoryInterface.SegmentMonitor;
+import org.contikios.cooja.mote.memory.VarMemory;
 import org.contikios.cooja.motes.AbstractEmulatedMote;
 import org.contikios.cooja.util.ArrayQueue;
 import org.contikios.cooja.util.StringUtils;
@@ -695,24 +699,24 @@ public class BufferListener extends VisPlugin {
 
     private void registerSegmentMonitor(int size, boolean notify) throws Exception {
       byte[] pointerValue = mote.getMemory().getMemorySegment(pointerAddress, pointerSize);
-      int segmentAddress = mote.getMemory().parseInt(pointerValue);
+      int segmentAddress = MemoryBuffer.wrap(mote.getMemory().getLayout(), pointerValue).getInt();
 
       segmentMonitor = new SegmentMemoryMonitor(bl, mote, segmentAddress, size);
       if (notify) {
-        segmentMonitor.memoryChanged(mote.getMemory(), MemoryEventType.WRITE, -1);
+        segmentMonitor.memoryChanged(mote.getMemory(), EventType.WRITE, -1);
       }
       lastSegmentAddress = segmentAddress;
     }
 
     @Override
-    final public void memoryChanged(MoteMemory memory,
-        org.contikios.cooja.MoteMemory.MemoryEventType type, int address) {
-      if (type == MemoryEventType.READ) {
+    final public void memoryChanged(MemoryInterface memory,
+        EventType type, long address) {
+      if (type == EventType.READ) {
         return;
       }
 
       byte[] pointerValue = mote.getMemory().getMemorySegment(pointerAddress, pointerSize);
-      int segmentAddress = mote.getMemory().parseInt(pointerValue);
+      int segmentAddress = MemoryBuffer.wrap(mote.getMemory().getLayout(), pointerValue).getInt();
       if (segmentAddress == lastSegmentAddress) {
         return;
       }
@@ -738,7 +742,7 @@ public class BufferListener extends VisPlugin {
     }
   }
 
-  static class SegmentMemoryMonitor implements org.contikios.cooja.MoteMemory.MemoryMonitor {
+  static class SegmentMemoryMonitor implements SegmentMonitor {
     protected final BufferListener bl;
     protected final Mote mote;
 
@@ -755,7 +759,7 @@ public class BufferListener extends VisPlugin {
       this.size = size;
 
       if (address != 0) {
-        if (!mote.getMemory().addMemoryMonitor(address, size, this)) {
+        if (!mote.getMemory().addSegmentMonitor(SegmentMonitor.EventType.WRITE, address, size, this)) {
           throw new Exception("Could not register memory monitor on: " + mote);
         }
       }
@@ -776,18 +780,18 @@ public class BufferListener extends VisPlugin {
 
     public void dispose() {
       if (address != 0) {
-        mote.getMemory().removeMemoryMonitor(address, size, this);
+        mote.getMemory().removeSegmentMonitor(address, size, this);
       }
     }
 
     @Override
-    public void memoryChanged(MoteMemory memory, MemoryEventType type, int address) {
+    public void memoryChanged(MemoryInterface memory, EventType type, long address) {
       byte[] newData = getAddress()==0?null:mote.getMemory().getMemorySegment(getAddress(), getSize());
       addBufferAccess(bl, mote, oldData, newData, type, this.address);
       oldData = newData;
     }
 
-    void addBufferAccess(BufferListener bl, Mote mote, byte[] oldData, byte[] newData, MemoryEventType type, int address) {
+    void addBufferAccess(BufferListener bl, Mote mote, byte[] oldData, byte[] newData, EventType type, int address) {
       BufferAccess ba = new BufferAccess(
           mote,
           mote.getSimulation().getSimulationTime(),
@@ -957,7 +961,7 @@ public class BufferListener extends VisPlugin {
         public boolean include(RowFilter.Entry<? extends Object, ? extends Object> entry) {
           if (hideReads) {
             int row = (Integer) entry.getIdentifier();
-            if (logs.get(row).type == MemoryEventType.READ) {
+            if (logs.get(row).type == SegmentMonitor.EventType.READ) {
               return false;
             }
           }
@@ -1013,13 +1017,13 @@ public class BufferListener extends VisPlugin {
     public final byte[] mem;
     private boolean[] accessedBitpattern = null;
 
-    public final MemoryEventType type;
+    public final SegmentMonitor.EventType type;
     public final String sourceStr;
     public final String stackTrace;
     public final int address;
 
     public BufferAccess(
-        Mote mote, long time, int address, byte[] newData, byte[] oldData, MemoryEventType type, boolean withStackTrace) {
+        Mote mote, long time, int address, byte[] newData, byte[] oldData, SegmentMonitor.EventType type, boolean withStackTrace) {
       this.mote = mote;
       this.time = time;
       this.mem = newData==null?NULL_DATA:newData;
@@ -1538,7 +1542,7 @@ public class BufferListener extends VisPlugin {
           bl,
           mote,
           getPointerAddress(mote),
-          mote.getMemory().getIntegerLength(),
+          mote.getMemory().getLayout().intSize,
           getSize(mote)
       );
     }
@@ -1622,16 +1626,18 @@ public class BufferListener extends VisPlugin {
 
   @ClassDescription("Integer array")
   public static class IntegerParser extends StringParser {
+    private VarMemory varMem = new VarMemory(null);
     @Override
     public String parseString(BufferAccess ba) {
       StringBuilder sb = new StringBuilder();
+      varMem.associateMemory(ba.mote.getMemory());
 
-      int intLen = ba.mote.getMemory().getIntegerLength();
+      int intLen = ba.mote.getMemory().getLayout().intSize;
       sb.append("<html>");
       for (int i=0; i < ba.mem.length/intLen; i++) {
         byte[] mem = Arrays.copyOfRange(ba.mem, i*intLen,(i+1)*intLen);
         boolean[] diff = Arrays.copyOfRange(ba.getAccessedBitpattern(), i*intLen,(i+1)*intLen);
-        int val = ba.mote.getMemory().parseInt(mem);
+        int val = MemoryBuffer.wrap(ba.mote.getMemory().getLayout(), mem).getInt();
 
         boolean red = false;
         for (boolean changed: diff) {
@@ -1802,14 +1808,14 @@ public class BufferListener extends VisPlugin {
   public static class NodeIDBuffer extends SegmentBuffer {
     @Override
     public int getAddress(Mote mote) {
-      if (!mote.getMemory().variableExists("node_id")) {
+      if (!mote.getMemory().getSymbolMap().containsKey("node_id")) {
         return -1;
       }
-      return mote.getMemory().getVariableAddress("node_id");
+      return (int) mote.getMemory().getSymbolMap().get("node_id").addr;
     }
     @Override
     public int getSize(Mote mote) {
-      return mote.getMemory().getIntegerLength();
+      return mote.getMemory().getLayout().intSize;
     }
 
   }
@@ -1818,11 +1824,11 @@ public class BufferListener extends VisPlugin {
   public static class Queuebuf0Buffer extends SegmentBuffer {
     @Override
     public int getAddress(Mote mote) {
-      if (!mote.getMemory().variableExists("buframmem")) {
+      if (!mote.getMemory().getSymbolMap().containsKey("buframmem")) {
         return -1;
       }
       int offset = 0;
-      return mote.getMemory().getVariableAddress("buframmem") + offset;
+      return (int) mote.getMemory().getSymbolMap().get("buframmem").addr + offset;
     }
     @Override
     public int getSize(Mote mote) {
@@ -1834,10 +1840,10 @@ public class BufferListener extends VisPlugin {
   public static class PacketbufBuffer extends SegmentBuffer {
     @Override
     public int getAddress(Mote mote) {
-      if (!mote.getMemory().variableExists("packetbuf_aligned")) {
+      if (!mote.getMemory().getSymbolMap().containsKey("packetbuf_aligned")) {
         return -1;
       }
-      return mote.getMemory().getVariableAddress("packetbuf_aligned");
+      return (int) mote.getMemory().getSymbolMap().get("packetbuf_aligned").addr;
     }
     @Override
     public int getSize(Mote mote) {
@@ -1847,19 +1853,21 @@ public class BufferListener extends VisPlugin {
 
   @ClassDescription("*packetbufptr")
   public static class PacketbufPointerBuffer extends PointerBuffer {
+    VarMemory varMem =  new VarMemory(null);
     @Override
     public int getPointerAddress(Mote mote) {
-      if (!mote.getMemory().variableExists("packetbufptr")) {
+      if (!mote.getMemory().getSymbolMap().containsKey("packetbufptr")) {
         return -1;
       }
-      return mote.getMemory().getVariableAddress("packetbufptr");
+      return (int) mote.getMemory().getSymbolMap().get("packetbufptr").addr;
     }
     @Override
     public int getAddress(Mote mote) {
-      if (!mote.getMemory().variableExists("packetbufptr")) {
+      if (!mote.getMemory().getSymbolMap().containsKey("packetbufptr")) {
         return -1;
       }
-      return mote.getMemory().getIntValueOf("packetbufptr");
+      varMem.associateMemory(mote.getMemory());
+      return varMem.getIntValueOf("packetbufptr");
     }
     @Override
     public int getSize(Mote mote) {
@@ -1872,23 +1880,25 @@ public class BufferListener extends VisPlugin {
     public String variable;
     public int size;
     public int offset;
+    VarMemory varMem =  new VarMemory(null);
     @Override
     public int getPointerAddress(Mote mote) {
-      if (!mote.getMemory().variableExists(variable)) {
+      if (!mote.getMemory().getSymbolMap().containsKey(variable)) {
         return -1;
       }
-      return mote.getMemory().getVariableAddress(variable);
+      return (int) mote.getMemory().getSymbolMap().get(variable).addr;
     }
     @Override
     public int getAddress(Mote mote) {
-      if (!mote.getMemory().variableExists(variable)) {
+      if (!mote.getMemory().getSymbolMap().containsKey(variable)) {
         return -1;
       }
-      return mote.getMemory().getIntValueOf(variable)+offset;
+      varMem.associateMemory(mote.getMemory());
+      return varMem.getIntValueOf(variable)+offset;
     }
     @Override
     public int getSize(Mote mote) {
-      if (!mote.getMemory().variableExists(variable)) {
+      if (!mote.getMemory().getSymbolMap().containsKey(variable)) {
         return -1;
       }
       return size;
@@ -1968,14 +1978,14 @@ public class BufferListener extends VisPlugin {
     public int offset;
     @Override
     public int getAddress(Mote mote) {
-      if (!mote.getMemory().variableExists(variable)) {
+      if (!mote.getMemory().getSymbolMap().containsKey(variable)) {
         return -1;
       }
-      return mote.getMemory().getVariableAddress(variable)+offset;
+      return (int) mote.getMemory().getSymbolMap().get(variable).addr+offset;
     }
     @Override
     public int getSize(Mote mote) {
-      if (!mote.getMemory().variableExists(variable)) {
+      if (!mote.getMemory().getSymbolMap().containsKey(variable)) {
         return -1;
       }
       return size;
@@ -2052,14 +2062,14 @@ public class BufferListener extends VisPlugin {
     public String variable;
     @Override
     public int getAddress(Mote mote) {
-      if (!mote.getMemory().variableExists(variable)) {
+      if (!mote.getMemory().getSymbolMap().containsKey(variable)) {
         return -1;
       }
-      return mote.getMemory().getVariableAddress(variable);
+      return (int) mote.getMemory().getSymbolMap().get(variable).addr;
     }
     @Override
     public int getSize(Mote mote) {
-      return mote.getMemory().getIntegerLength();
+      return mote.getMemory().getLayout().intSize;
     }
 
     @Override

From 482dab5d16f97baf94be6b274fac77332215ec07 Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Wed, 23 Jul 2014 10:12:19 +0200
Subject: [PATCH 09/28] [cooja] memory: Removed MoteMemory class including all
 references

---
 .../cooja/avrmote/AvrMoteMemory.java          |  30 +----
 .../contikios/cooja/avrmote/MicaZMote.java    |   3 +-
 .../org/contikios/cooja/mspmote/MspMote.java  |   5 +-
 .../cooja/mspmote/MspMoteMemory.java          | 106 +++++-------------
 .../java/org/contikios/cooja/MoteMemory.java  |  90 ---------------
 .../contikios/cooja/SectionMoteMemory.java    |  99 ++++++++--------
 .../cooja/contikimote/ContikiMote.java        |   5 +-
 .../mote/memory/UnknownVariableException.java |  41 +++++++
 .../cooja/motes/AbstractApplicationMote.java  |   3 +-
 .../cooja/plugins/BufferListener.java         |   2 -
 10 files changed, 127 insertions(+), 257 deletions(-)
 delete mode 100644 tools/cooja/java/org/contikios/cooja/MoteMemory.java
 create mode 100644 tools/cooja/java/org/contikios/cooja/mote/memory/UnknownVariableException.java

diff --git a/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/AvrMoteMemory.java b/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/AvrMoteMemory.java
index 8a371d44d..83e5203e0 100644
--- a/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/AvrMoteMemory.java
+++ b/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/AvrMoteMemory.java
@@ -34,7 +34,6 @@ import java.util.Iterator;
 import org.apache.log4j.Logger;
 
 import org.contikios.cooja.AddressMemory;
-import org.contikios.cooja.MoteMemory;
 import avrora.arch.avr.AVRProperties;
 import avrora.core.SourceMapping;
 import avrora.core.SourceMapping.Location;
@@ -46,7 +45,7 @@ import org.contikios.cooja.mote.memory.MemoryLayout;
 /**
  * @author Joakim Eriksson
  */
-public class AvrMoteMemory implements MemoryInterface, MoteMemory, AddressMemory {
+public class AvrMoteMemory implements MemoryInterface, AddressMemory {
     private static Logger logger = Logger.getLogger(AvrMoteMemory.class);
 
     private SourceMapping memoryMap;
@@ -63,22 +62,11 @@ public class AvrMoteMemory implements MemoryInterface, MoteMemory, AddressMemory
         interpreter.getSimulator().insertWatch(w, address);
     }
 
-    @Override
-    public byte[] getMemorySegment(int address, int size) {
-        logger.fatal("getMemorySegment is not implemented");
-        return null;
-    }
-
     @Override
     public int getTotalSize() {
         return 0;
     }
 
-    @Override
-    public void setMemorySegment(int address, byte[] data) {
-        logger.fatal("setMemorySegment is not implemented");
-    }
-
     @Override
     public byte[] getByteArray(String varName, int length)
             throws UnknownVariableException {
@@ -182,22 +170,6 @@ public class AvrMoteMemory implements MemoryInterface, MoteMemory, AddressMemory
         return memoryMap.getLocation(varName) != null;
     }
 
-    @Override
-    public boolean addMemoryMonitor(int address, int size, MemoryMonitor mm) {
-      logger.warn("Not implemented");
-      return false;
-    }
-
-    @Override
-    public void removeMemoryMonitor(int address, int size, MemoryMonitor mm) {
-    }
-
-    @Override
-    public int parseInt(byte[] memorySegment) {
-      logger.warn("Not implemented");
-      return 0;
-    }
-
   @Override
   public byte[] getMemory() throws MoteMemoryException {
     throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
diff --git a/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/MicaZMote.java b/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/MicaZMote.java
index e82c86384..1c45e12ef 100644
--- a/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/MicaZMote.java
+++ b/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/MicaZMote.java
@@ -40,7 +40,6 @@ import org.jdom.Element;
 import org.contikios.cooja.Mote;
 import org.contikios.cooja.MoteInterface;
 import org.contikios.cooja.MoteInterfaceHandler;
-import org.contikios.cooja.MoteMemory;
 import org.contikios.cooja.MoteType;
 import org.contikios.cooja.Simulation;
 import org.contikios.cooja.mote.memory.MemoryInterface;
@@ -273,7 +272,7 @@ public class MicaZMote extends AbstractEmulatedMote implements Mote {
     return myMemory;
   }
 
-  public void setMemory(MoteMemory memory) {
+  public void setMemory(AvrMoteMemory memory) {
     myMemory = (AvrMoteMemory) memory;
   }
 
diff --git a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMote.java b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMote.java
index b76651bce..1b0d5be11 100644
--- a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMote.java
+++ b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMote.java
@@ -46,7 +46,6 @@ import org.contikios.cooja.Cooja;
 import org.contikios.cooja.Mote;
 import org.contikios.cooja.MoteInterface;
 import org.contikios.cooja.MoteInterfaceHandler;
-import org.contikios.cooja.MoteMemory;
 import org.contikios.cooja.MoteType;
 import org.contikios.cooja.Simulation;
 import org.contikios.cooja.Watchpoint;
@@ -194,8 +193,8 @@ public abstract class MspMote extends AbstractEmulatedMote implements Mote, Watc
     return myMemory;
   }
 
-  public void setMemory(MoteMemory memory) {
-    myMemory = (MspMoteMemory) memory;
+  public void setMemory(MspMoteMemory memory) {
+    myMemory = memory;
   }
 
   /**
diff --git a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMoteMemory.java b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMoteMemory.java
index ce41b33d6..834fb70a6 100644
--- a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMoteMemory.java
+++ b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMoteMemory.java
@@ -35,15 +35,12 @@ import org.apache.log4j.Logger;
 
 import org.contikios.cooja.AddressMemory;
 import org.contikios.cooja.Mote;
-import org.contikios.cooja.MoteMemory;
 import org.contikios.cooja.mote.memory.MemoryInterface;
 import org.contikios.cooja.mote.memory.MemoryLayout;
 import se.sics.mspsim.core.MSP430;
-import se.sics.mspsim.core.Memory.AccessMode;
-import se.sics.mspsim.core.Memory.AccessType;
 import se.sics.mspsim.util.MapEntry;
 
-public class MspMoteMemory implements MemoryInterface, MoteMemory, AddressMemory {
+public class MspMoteMemory implements MemoryInterface, AddressMemory {
   private static Logger logger = Logger.getLogger(MspMoteMemory.class);
   private final ArrayList<MapEntry> mapEntries;
 
@@ -90,31 +87,31 @@ public class MspMoteMemory implements MemoryInterface, MoteMemory, AddressMemory
     return 2;
   }
 
-  @Override
-  public byte[] getMemorySegment(int address, int size) {
-    int[] memInts = new int[size];
-
-    System.arraycopy(cpu.memory, address, memInts, 0, size);
-
-    /* Convert to byte array */
-    byte[] memBytes = new byte[size];
-    for (int i=0; i < size; i++) {
-      memBytes[i] = (byte) memInts[i];
-    }
-
-    return memBytes;
-  }
-
-  @Override
-  public void setMemorySegment(int address, byte[] data) {
-    /* Convert to int array */
-    int[] memInts = new int[data.length];
-    for (int i=0; i < data.length; i++) {
-      memInts[i] = data[i];
-    }
-
-    System.arraycopy(memInts, 0, cpu.memory, address, data.length);
-  }
+//  @Override
+//  public byte[] getMemorySegment(int address, int size) {
+//    int[] memInts = new int[size];
+//
+//    System.arraycopy(cpu.memory, address, memInts, 0, size);
+//
+//    /* Convert to byte array */
+//    byte[] memBytes = new byte[size];
+//    for (int i=0; i < size; i++) {
+//      memBytes[i] = (byte) memInts[i];
+//    }
+//
+//    return memBytes;
+//  }
+//
+//  @Override
+//  public void setMemorySegment(int address, byte[] data) {
+//    /* Convert to int array */
+//    int[] memInts = new int[data.length];
+//    for (int i=0; i < data.length; i++) {
+//      memInts[i] = data[i];
+//    }
+//
+//    System.arraycopy(memInts, 0, cpu.memory, address, data.length);
+//  }
 
   @Override
   public int getTotalSize() {
@@ -198,7 +195,7 @@ public class MspMoteMemory implements MemoryInterface, MoteMemory, AddressMemory
     setMemorySegment(varAddr, data);
   }
 
-  private ArrayList<MemoryCPUMonitor> cpuMonitorArray = new ArrayList<MemoryCPUMonitor>();
+//  private ArrayList<MemoryCPUMonitor> cpuMonitorArray = new ArrayList<MemoryCPUMonitor>();
 
   @Override
   public byte[] getMemory() throws MoteMemoryException {
@@ -245,55 +242,6 @@ public class MspMoteMemory implements MemoryInterface, MoteMemory, AddressMemory
     throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
   }
 
-  class MemoryCPUMonitor extends se.sics.mspsim.core.MemoryMonitor.Adapter {
-    public final MemoryMonitor mm;
-    public final int address;
-    public final int size;
-
-    public MemoryCPUMonitor(MemoryMonitor mm, int address, int size) {
-      this.mm = mm;
-      this.address = address;
-      this.size = size;
-    }
-
-    @Override
-    public void notifyReadAfter(int address, AccessMode mode, AccessType type) {
-        mm.memoryChanged(MspMoteMemory.this, MemoryEventType.READ, address);
-    }
-
-    @Override
-    public void notifyWriteAfter(int dstAddress, int data, AccessMode mode) {
-        mm.memoryChanged(MspMoteMemory.this, MemoryEventType.WRITE, dstAddress);
-    }
-  }
-
-  @Override
-  public boolean addMemoryMonitor(int address, int size, MemoryMonitor mm) {
-    MemoryCPUMonitor t = new MemoryCPUMonitor(mm, address, size);
-    cpuMonitorArray.add(t);
-
-    for (int a = address; a < address+size; a++) {
-      cpu.addWatchPoint(a, t);
-    }
-
-    return true;
-  }
-
-  @Override
-  public void removeMemoryMonitor(int address, int size, MemoryMonitor mm) {
-    for (MemoryCPUMonitor mcm: cpuMonitorArray) {
-      if (mcm.mm != mm || mcm.address != address || mcm.size != size) {
-        continue;
-      }
-      for (int a = address; a < address+size; a++) {
-        cpu.removeWatchPoint(a, mcm);
-      }
-      cpuMonitorArray.remove(mcm);
-      break;
-    }
-  }
-
-  @Override
   public int parseInt(byte[] memorySegment) {
     if (memorySegment.length < 2) {
       return -1;
diff --git a/tools/cooja/java/org/contikios/cooja/MoteMemory.java b/tools/cooja/java/org/contikios/cooja/MoteMemory.java
deleted file mode 100644
index a730bee4f..000000000
--- a/tools/cooja/java/org/contikios/cooja/MoteMemory.java
+++ /dev/null
@@ -1,90 +0,0 @@
-/*
- * Copyright (c) 2006, Swedish Institute of Computer Science.
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- * 1. Redistributions of source code must retain the above copyright
- *    notice, this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright
- *    notice, this list of conditions and the following disclaimer in the
- *    documentation and/or other materials provided with the distribution.
- * 3. Neither the name of the Institute nor the names of its contributors
- *    may be used to endorse or promote products derived from this software
- *    without specific prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND
- * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED.  IN NO EVENT SHALL THE INSTITUTE OR CONTRIBUTORS BE LIABLE
- * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
- * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
- * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
- * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
- * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
- * SUCH DAMAGE.
- *
- */
-
-package org.contikios.cooja;
-
-
-/**
- * This interface represents a mote memory.
- * 
- * Mote memory is represented by byte arrays and this
- * interface provides a few of basic operations.
- * 
- * Note that this memory internally may consist of several
- * different memory sections, not covering the entire range
- * between the start address and the end address of this memory.
- *
- * @see org.contikios.cooja.SectionMoteMemory
- * @author Fredrik Osterlind
- */
-public interface MoteMemory extends AddressMemory {
-
-  /**
-   * Clears the entire memory.
-   */
-  public void clearMemory();
-
-  /**
-   * Returns a memory segment.
-   * 
-   * @param address Start address of memory segment
-   * @param size Size of memory segment
-   * @return Memory segment or null if segment not available
-   */
-  public byte[] getMemorySegment(int address, int size);
-
-  /**
-   * Sets a memory segment.
-   * 
-   * @param address Start address of memory segment
-   * @param data Data
-   */
-  public void setMemorySegment(int address, byte[] data);
-
-  /**
-   * Returns the sum of all byte array sizes in this memory.
-   * This is not neccessarily the the same as the total memory range,
-   * since the entire memory range may not be handled by this memory.
-   * 
-   * @return Total size
-   */
-  public int getTotalSize();
-
-  public abstract int parseInt(byte[] memorySegment);
-
-  public enum MemoryEventType { READ, WRITE };
-
-  public interface MemoryMonitor {
-    public void memoryChanged(MoteMemory memory, MemoryEventType type, int address);
-  }
-
-  public boolean addMemoryMonitor(int address, int size, MemoryMonitor mm);
-  public void removeMemoryMonitor(int address, int size, MemoryMonitor mm);
-}
diff --git a/tools/cooja/java/org/contikios/cooja/SectionMoteMemory.java b/tools/cooja/java/org/contikios/cooja/SectionMoteMemory.java
index 7f7a7d92b..e772f9f7c 100644
--- a/tools/cooja/java/org/contikios/cooja/SectionMoteMemory.java
+++ b/tools/cooja/java/org/contikios/cooja/SectionMoteMemory.java
@@ -46,7 +46,7 @@ import org.contikios.cooja.mote.memory.MemoryLayout;
  *
  * @author Fredrik Osterlind
  */
-public class SectionMoteMemory implements MemoryInterface, MoteMemory, AddressMemory {
+public class SectionMoteMemory implements MemoryInterface, AddressMemory {
   private static Logger logger = Logger.getLogger(SectionMoteMemory.class);
 
   private ArrayList<MoteMemorySection> sections = new ArrayList<MoteMemorySection>();
@@ -94,48 +94,48 @@ public class SectionMoteMemory implements MemoryInterface, MoteMemory, AddressMe
     sections.clear();
   }
 
-  @Override
-  public byte[] getMemorySegment(int address, int size) {
-    /* Cooja address space */
-    address -= offset;
-   
-    for (MoteMemorySection section : sections) {
-      if (section.includesAddr(address)
-          && section.includesAddr(address + size - 1)) {
-        return section.getMemorySegment(address, size);
-      }
-    }
-    
-    /* Check if in readonly section */
-    for (MoteMemorySection section : readonlySections) {
-      if (section.includesAddr(address)
-          && section.includesAddr(address + size - 1)) {
-        return section.getMemorySegment(address, size);
-      }
-    }
-    
-    return null;
-  }
+//  @Override
+//  public byte[] getMemorySegment(int address, int size) {
+//    /* Cooja address space */
+//    address -= offset;
+//   
+//    for (MoteMemorySection section : sections) {
+//      if (section.includesAddr(address)
+//          && section.includesAddr(address + size - 1)) {
+//        return section.getMemorySegment(address, size);
+//      }
+//    }
+//    
+//    /* Check if in readonly section */
+//    for (MoteMemorySection section : readonlySections) {
+//      if (section.includesAddr(address)
+//          && section.includesAddr(address + size - 1)) {
+//        return section.getMemorySegment(address, size);
+//      }
+//    }
+//    
+//    return null;
+//  }
 
   public void setMemorySegmentNative(int address, byte[] data) {
     setMemorySegment(address+offset, data);
   }
 
-  @Override
-  public void setMemorySegment(int address, byte[] data) {
-    /* Cooja address space */
-    address -= offset;
-
-    /* TODO XXX Sections may overlap */
-    for (MoteMemorySection section : sections) {
-      if (section.includesAddr(address)
-          && section.includesAddr(address + data.length - 1)) {
-        section.setMemorySegment(address, data);
-        return;
-      }
-    }
-    sections.add(new MoteMemorySection(address, data));
-  }
+//  @Override
+//  public void setMemorySegment(int address, byte[] data) {
+//    /* Cooja address space */
+//    address -= offset;
+//
+//    /* TODO XXX Sections may overlap */
+//    for (MoteMemorySection section : sections) {
+//      if (section.includesAddr(address)
+//          && section.includesAddr(address + data.length - 1)) {
+//        section.setMemorySegment(address, data);
+//        return;
+//      }
+//    }
+//    sections.add(new MoteMemorySection(address, data));
+//  }
 
   public void setReadonlyMemorySegment(int address, byte[] data) {
     /* Cooja address space */
@@ -271,6 +271,11 @@ public class SectionMoteMemory implements MemoryInterface, MoteMemory, AddressMe
     setMemorySegment(varAddr, data);
   }
 
+  @Override
+  public byte[] getMemory() throws MoteMemoryException {
+    throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
+  }
+
   @Override
   public byte[] getMemorySegment(long addr, int size) throws MoteMemoryException {
     throw new UnsupportedOperationException("Not supported yet.");
@@ -430,12 +435,12 @@ public class SectionMoteMemory implements MemoryInterface, MoteMemory, AddressMe
   }
 
   private class PolledMemorySegments {
-    public final MemoryMonitor mm;
+    public final SegmentMonitor mm;
     public final int address;
     public final int size;
     private byte[] oldMem;
 
-    public PolledMemorySegments(MemoryMonitor mm, int address, int size) {
+    public PolledMemorySegments(SegmentMonitor mm, int address, int size) {
       this.mm = mm;
       this.address = address;
       this.size = size;
@@ -449,20 +454,20 @@ public class SectionMoteMemory implements MemoryInterface, MoteMemory, AddressMe
         return;
       }
       
-      mm.memoryChanged(SectionMoteMemory.this, MemoryEventType.WRITE, address);
+      mm.memoryChanged(SectionMoteMemory.this, SegmentMonitor.EventType.WRITE, address);
       oldMem = newMem;
     }
   }
-  
-  @Override
-  public boolean addMemoryMonitor(int address, int size, MemoryMonitor mm) {
+
+//  @Override
+  public boolean addMemoryMonitor(int address, int size, SegmentMonitor mm) {
     PolledMemorySegments t = new PolledMemorySegments(mm, address, size);
     polledMemories.add(t);
     return true;
   }
 
-  @Override
-  public void removeMemoryMonitor(int address, int size, MemoryMonitor mm) {
+//  @Override
+  public void removeMemoryMonitor(int address, int size, SegmentMonitor mm) {
     for (PolledMemorySegments mcm: polledMemories) {
       if (mcm.mm != mm || mcm.address != address || mcm.size != size) {
         continue;
@@ -472,7 +477,7 @@ public class SectionMoteMemory implements MemoryInterface, MoteMemory, AddressMe
     }
   }
 
-  @Override
+//  @Override
   public int parseInt(byte[] memorySegment) {
     int retVal = 0;
     int pos = 0;
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMote.java b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMote.java
index b16b8a95d..e39d5d86e 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMote.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMote.java
@@ -38,7 +38,6 @@ import org.jdom.Element;
 import org.contikios.cooja.Mote;
 import org.contikios.cooja.MoteInterface;
 import org.contikios.cooja.MoteInterfaceHandler;
-import org.contikios.cooja.MoteMemory;
 import org.contikios.cooja.MoteType;
 import org.contikios.cooja.SectionMoteMemory;
 import org.contikios.cooja.Simulation;
@@ -103,8 +102,8 @@ public class ContikiMote extends AbstractWakeupMote implements Mote {
     return myMemory;
   }
 
-  public void setMemory(MoteMemory memory) {
-    myMemory = (SectionMoteMemory) memory;
+  public void setMemory(SectionMoteMemory memory) {
+    myMemory = memory;
   }
 
   @Override
diff --git a/tools/cooja/java/org/contikios/cooja/mote/memory/UnknownVariableException.java b/tools/cooja/java/org/contikios/cooja/mote/memory/UnknownVariableException.java
new file mode 100644
index 000000000..6f32f3698
--- /dev/null
+++ b/tools/cooja/java/org/contikios/cooja/mote/memory/UnknownVariableException.java
@@ -0,0 +1,41 @@
+/*
+ * Copyright (c) 2013, Enrico Joerns
+ * All rights reserved.
+ * 
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ * 3. Neither the name of the Institute nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software
+ *    without specific prior written permission.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE INSTITUTE OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ */
+
+package org.contikios.cooja.mote.memory;
+
+/**
+ * Unknown variable name exception.
+ */
+public class UnknownVariableException extends RuntimeException {
+
+  public UnknownVariableException(String varName) {
+    super("Unknown variable name: " + varName);
+  }
+  
+}
diff --git a/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java b/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
index 11025c183..e4974ac7b 100644
--- a/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
+++ b/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
@@ -39,7 +39,6 @@ import org.jdom.Element;
 import org.contikios.cooja.Mote;
 import org.contikios.cooja.MoteInterface;
 import org.contikios.cooja.MoteInterfaceHandler;
-import org.contikios.cooja.MoteMemory;
 import org.contikios.cooja.MoteType;
 import org.contikios.cooja.RadioPacket;
 import org.contikios.cooja.SectionMoteMemory;
@@ -116,7 +115,7 @@ public abstract class AbstractApplicationMote extends AbstractWakeupMote impleme
     return memory;
   }
 
-  public void setMemory(MoteMemory memory) {
+  public void setMemory(SectionMoteMemory memory) {
     this.memory = (SectionMoteMemory) memory;
   }
 
diff --git a/tools/cooja/java/org/contikios/cooja/plugins/BufferListener.java b/tools/cooja/java/org/contikios/cooja/plugins/BufferListener.java
index 8b2ab1327..aa668b66b 100644
--- a/tools/cooja/java/org/contikios/cooja/plugins/BufferListener.java
+++ b/tools/cooja/java/org/contikios/cooja/plugins/BufferListener.java
@@ -89,8 +89,6 @@ import org.jdom.Element;
 import org.contikios.cooja.ClassDescription;
 import org.contikios.cooja.Cooja;
 import org.contikios.cooja.Mote;
-import org.contikios.cooja.MoteMemory;
-import org.contikios.cooja.MoteMemory.MemoryEventType;
 import org.contikios.cooja.Plugin;
 import org.contikios.cooja.PluginType;
 import org.contikios.cooja.SimEventCentral.MoteCountListener;

From 44767324a53ea1321f3cefd1f9f79480cef6c4e4 Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Wed, 23 Jul 2014 10:48:27 +0200
Subject: [PATCH 10/28] [cooja] memory: Removed AddressMemory class including
 all references

---
 .../cooja/avrmote/AvrMoteMemory.java          | 109 +-------------
 .../cooja/avrmote/interfaces/MicaZID.java     |  36 ++---
 .../cooja/mspmote/MspMoteMemory.java          | 137 +-----------------
 .../mspmote/interfaces/MspDebugOutput.java    |  15 +-
 .../cooja/mspmote/interfaces/MspMoteID.java   |  12 +-
 .../org/contikios/cooja/AddressMemory.java    | 124 ----------------
 .../contikios/cooja/SectionMoteMemory.java    | 128 +---------------
 .../cooja/contikimote/ContikiMoteType.java    |   4 +-
 .../contikimote/interfaces/ContikiBeeper.java |   5 +-
 .../contikimote/interfaces/ContikiButton.java |   5 +-
 .../contikimote/interfaces/ContikiCFS.java    |   5 +-
 .../contikimote/interfaces/ContikiClock.java  |   5 +-
 .../contikimote/interfaces/ContikiEEPROM.java |   5 +-
 .../contikimote/interfaces/ContikiLED.java    |   5 +-
 .../contikimote/interfaces/ContikiMoteID.java |   5 +-
 .../contikimote/interfaces/ContikiPIR.java    |   5 +-
 .../contikimote/interfaces/ContikiRS232.java  |   5 +-
 .../contikimote/interfaces/ContikiRadio.java  |   5 +-
 .../contikimote/interfaces/ContikiVib.java    |   5 +-
 .../cooja/dialogs/ConfigurationWizard.java    |  22 +--
 .../cooja/plugins/VariableWatcher.java        |  18 ++-
 21 files changed, 94 insertions(+), 566 deletions(-)
 delete mode 100644 tools/cooja/java/org/contikios/cooja/AddressMemory.java

diff --git a/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/AvrMoteMemory.java b/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/AvrMoteMemory.java
index 83e5203e0..bd2b719cb 100644
--- a/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/AvrMoteMemory.java
+++ b/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/AvrMoteMemory.java
@@ -28,15 +28,11 @@
 
 package org.contikios.cooja.avrmote;
 
-import java.util.ArrayList;
-import java.util.Iterator;
 
 import org.apache.log4j.Logger;
 
-import org.contikios.cooja.AddressMemory;
 import avrora.arch.avr.AVRProperties;
 import avrora.core.SourceMapping;
-import avrora.core.SourceMapping.Location;
 import avrora.sim.AtmelInterpreter;
 import avrora.sim.Simulator.Watch;
 import java.util.Map;
@@ -45,7 +41,7 @@ import org.contikios.cooja.mote.memory.MemoryLayout;
 /**
  * @author Joakim Eriksson
  */
-public class AvrMoteMemory implements MemoryInterface, AddressMemory {
+public class AvrMoteMemory implements MemoryInterface {
     private static Logger logger = Logger.getLogger(AvrMoteMemory.class);
 
     private SourceMapping memoryMap;
@@ -67,109 +63,6 @@ public class AvrMoteMemory implements MemoryInterface, AddressMemory {
         return 0;
     }
 
-    @Override
-    public byte[] getByteArray(String varName, int length)
-            throws UnknownVariableException {
-        return null;
-    }
-
-    @Override
-    public byte getByteValueOf(String varName) throws UnknownVariableException {
-        return (byte) getValueOf(varName, 1);
-    }
-    
-    private int getValueOf(String varName, int len) throws UnknownVariableException {
-        Location mem = memoryMap.getLocation(varName);
-        if (mem == null) throw new UnknownVariableException("Variable does not exist: " + varName);
-
-        System.out.println("Variable:" + varName + " in section: " + mem.section);
-        System.out.println("LMA: " + Integer.toHexString(mem.lma_addr));
-        System.out.println("VMA: " + Integer.toHexString(mem.vma_addr));
-
-        System.out.println("Data: " + interpreter.getDataByte(mem.lma_addr & 0xfffff));
-        System.out.println("Flash: " + interpreter.getFlashByte(mem.lma_addr & 0xfffff));
-        int data = 0;
-        if (mem.vma_addr > 0xfffff) {
-            for (int i = 0; i < len; i++) {
-                data = (data << 8) + (interpreter.getDataByte((mem.vma_addr & 0xfffff) + len - i - 1) & 0xff);
-                System.out.println("Read byte: " + interpreter.getDataByte((mem.vma_addr & 0xfffff) + i) +
-                        " => " + data);
-            }
-        } else {
-            for (int i = 0; i < len; i++) {
-                data = (data << 8) + interpreter.getFlashByte(mem.vma_addr + len - i - 1) & 0xff;
-            }
-        }
-        return data;
-    }
-
-    private void setValue(String varName, int val, int len) throws UnknownVariableException {
-        Location mem = memoryMap.getLocation(varName);
-        if (mem == null) throw new UnknownVariableException("Variable does not exist: " + varName);
-
-        int data = val;
-        if (mem.vma_addr > 0xfffff) {       
-            // write LSB first.
-            for (int i = 0; i < len; i++) {
-                interpreter.writeDataByte((mem.vma_addr & 0xfffff) + i, (byte) (data & 0xff));
-                System.out.println("Wrote byte: " + (data & 0xff));
-                data = data >> 8;
-            }
-        } else {
-            for (int i = 0; i < len; i++) {
-                interpreter.writeFlashByte(mem.vma_addr + i, (byte) (data & 0xff));
-                data = data >> 8;
-            }
-        }
-    }
-    
-    @Override
-    public int getIntValueOf(String varName) throws UnknownVariableException {
-        return getValueOf(varName, 2);
-    }
-
-    @Override
-    public int getIntegerLength() {
-        return 2;
-    }
-
-    @Override
-    public int getVariableAddress(String varName)
-            throws UnknownVariableException {
-        return 0;
-    }
-
-    @Override
-    public String[] getVariableNames() {
-        ArrayList<String> symbols = new ArrayList<String>();
-        for (Iterator i = memoryMap.getIterator(); i.hasNext();) {
-            symbols.add(((Location) i.next()).name);
-        }
-        return symbols.toArray(new String[0]);
-    }
-
-    @Override
-    public void setByteArray(String varName, byte[] data)
-            throws UnknownVariableException {
-    }
-
-    @Override
-    public void setByteValueOf(String varName, byte newVal)
-            throws UnknownVariableException {
-        setValue(varName, newVal, 1);
-    }
-
-    @Override
-    public void setIntValueOf(String varName, int newVal)
-            throws UnknownVariableException {
-        setValue(varName, newVal, 2);
-    }
-
-    @Override
-    public boolean variableExists(String varName) {
-        return memoryMap.getLocation(varName) != null;
-    }
-
   @Override
   public byte[] getMemory() throws MoteMemoryException {
     throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
diff --git a/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/interfaces/MicaZID.java b/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/interfaces/MicaZID.java
index a9b9e2190..b52e40730 100644
--- a/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/interfaces/MicaZID.java
+++ b/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/interfaces/MicaZID.java
@@ -38,16 +38,15 @@ import javax.swing.JPanel;
 import org.apache.log4j.Logger;
 import org.jdom.Element;
 
-import avrora.sim.State;
-import avrora.sim.Simulator.Watch;
-
 import org.contikios.cooja.Mote;
 import org.contikios.cooja.MoteTimeEvent;
 import org.contikios.cooja.Simulation;
 import org.contikios.cooja.TimeEvent;
-import org.contikios.cooja.avrmote.AvrMoteMemory;
 import org.contikios.cooja.avrmote.MicaZMote;
 import org.contikios.cooja.interfaces.MoteID;
+import org.contikios.cooja.mote.memory.MemoryInterface;
+import org.contikios.cooja.mote.memory.MemoryInterface.SegmentMonitor;
+import org.contikios.cooja.mote.memory.VarMemory;
 
 public class MicaZID extends MoteID {
 
@@ -57,7 +56,7 @@ public class MicaZID extends MoteID {
 
     private int moteID = -1; /* TODO Implement */
 
-    private AvrMoteMemory moteMem;
+    private VarMemory moteMem;
     boolean tosID = false;
     boolean contikiID = false;
     private MicaZMote mote;
@@ -80,23 +79,26 @@ public class MicaZID extends MoteID {
 
     public MicaZID(Mote mote) {
         this.mote = (MicaZMote) mote;
-        this.moteMem = (AvrMoteMemory) mote.getMemory();
+        this.moteMem = new VarMemory(mote.getMemory());
 
         if (moteMem.variableExists("node_id")) {
             contikiID = true;
 
-            int addr = moteMem.getVariableAddress("node_id");
-            moteMem.insertWatch(new Watch() {
-                public void fireAfterRead(State arg0, int arg1, byte arg2) {
-                    System.out.println("Read from node_id: " + arg2);
+            int addr = (int) moteMem.getVariableAddress("node_id");
+            moteMem.addVarMonitor(
+                            SegmentMonitor.EventType.READWRITE, 
+                            "node_id", 
+                            new SegmentMonitor() {
+
+                @Override
+                public void memoryChanged(MemoryInterface memory, SegmentMonitor.EventType type, long address) {
+                    if (type == EventType.READ) {
+                        System.out.println("Read from node_id.");
+                    } else {
+                        System.out.println("Writing to node_id.");
+                    }
                 }
-                public void fireAfterWrite(State arg0, int arg1, byte arg2) {
-                }
-                public void fireBeforeRead(State arg0, int arg1) {
-                }
-                public void fireBeforeWrite(State arg0, int arg1, byte arg2) {
-                    System.out.println("Writing to node_id: " + arg2);
-                }}, addr);
+            });
         }
 
         if (moteMem.variableExists("TOS_NODE_ID")) {
diff --git a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMoteMemory.java b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMoteMemory.java
index 834fb70a6..16b453bf4 100644
--- a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMoteMemory.java
+++ b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMoteMemory.java
@@ -33,14 +33,13 @@ import java.util.Map;
 
 import org.apache.log4j.Logger;
 
-import org.contikios.cooja.AddressMemory;
 import org.contikios.cooja.Mote;
 import org.contikios.cooja.mote.memory.MemoryInterface;
 import org.contikios.cooja.mote.memory.MemoryLayout;
 import se.sics.mspsim.core.MSP430;
 import se.sics.mspsim.util.MapEntry;
 
-public class MspMoteMemory implements MemoryInterface, AddressMemory {
+public class MspMoteMemory implements MemoryInterface {
   private static Logger logger = Logger.getLogger(MspMoteMemory.class);
   private final ArrayList<MapEntry> mapEntries;
 
@@ -58,145 +57,11 @@ public class MspMoteMemory implements MemoryInterface, AddressMemory {
     this.cpu = cpu;
   }
 
-  @Override
-  public String[] getVariableNames() {
-    String[] names = new String[mapEntries.size()];
-    for (int i = 0; i < mapEntries.size(); i++) {
-      names[i] = mapEntries.get(i).getName();
-    }
-    return names;
-  }
-
-  private MapEntry getMapEntry(String varName) throws UnknownVariableException {
-    for (MapEntry entry: mapEntries) {
-      if (entry.getName().equals(varName)) {
-        return entry;
-      }
-    }
-    throw new UnknownVariableException(varName);
-  }
-
-  @Override
-  public int getVariableAddress(String varName) throws UnknownVariableException {
-    MapEntry entry = getMapEntry(varName);
-    return entry.getAddress();
-  }
-
-  @Override
-  public int getIntegerLength() {
-    return 2;
-  }
-
-//  @Override
-//  public byte[] getMemorySegment(int address, int size) {
-//    int[] memInts = new int[size];
-//
-//    System.arraycopy(cpu.memory, address, memInts, 0, size);
-//
-//    /* Convert to byte array */
-//    byte[] memBytes = new byte[size];
-//    for (int i=0; i < size; i++) {
-//      memBytes[i] = (byte) memInts[i];
-//    }
-//
-//    return memBytes;
-//  }
-//
-//  @Override
-//  public void setMemorySegment(int address, byte[] data) {
-//    /* Convert to int array */
-//    int[] memInts = new int[data.length];
-//    for (int i=0; i < data.length; i++) {
-//      memInts[i] = data[i];
-//    }
-//
-//    System.arraycopy(memInts, 0, cpu.memory, address, data.length);
-//  }
-
   @Override
   public int getTotalSize() {
     return cpu.memory.length;
   }
 
-  @Override
-  public boolean variableExists(String varName) {
-    for (MapEntry entry: mapEntries) {
-      if (entry.getName().equals(varName)) {
-        return true;
-      }
-    }
-
-    return false;
-  }
-
-  /* TODO Check correct variable size in below methods */
-
-  @Override
-  public int getIntValueOf(String varName) throws UnknownVariableException {
-    MapEntry entry = getMapEntry(varName);
-
-    int varAddr = entry.getAddress();
-    byte[] varData = getMemorySegment(varAddr, 2);
-    return parseInt(varData);
-  }
-
-  @Override
-  public void setIntValueOf(String varName, int newVal) throws UnknownVariableException {
-    MapEntry entry = getMapEntry(varName);
-    int varAddr = entry.getAddress();
-
-    int newValToSet = Integer.reverseBytes(newVal);
-
-    // Create byte array
-    int pos = 0;
-
-    byte[] varData = new byte[2];
-    varData[pos++] = (byte) ((newValToSet & 0xFF000000) >> 24);
-    varData[pos++] = (byte) ((newValToSet & 0xFF0000) >> 16);
-
-    setMemorySegment(varAddr, varData);
-  }
-
-  @Override
-  public byte getByteValueOf(String varName) throws UnknownVariableException {
-    MapEntry entry = getMapEntry(varName);
-    int varAddr = entry.getAddress();
-
-    byte[] varData = getMemorySegment(varAddr, 1);
-
-    return varData[0];
-  }
-
-  @Override
-  public void setByteValueOf(String varName, byte newVal) throws UnknownVariableException {
-    MapEntry entry = getMapEntry(varName);
-    int varAddr = entry.getAddress();
-
-    byte[] varData = new byte[1];
-
-    varData[0] = newVal;
-
-    setMemorySegment(varAddr, varData);
-  }
-
-  @Override
-  public byte[] getByteArray(String varName, int length) throws UnknownVariableException {
-    MapEntry entry = getMapEntry(varName);
-    int varAddr = entry.getAddress();
-
-    return getMemorySegment(varAddr, length);
-  }
-
-  @Override
-  public void setByteArray(String varName, byte[] data) throws UnknownVariableException {
-    MapEntry entry = getMapEntry(varName);
-    int varAddr = entry.getAddress();
-
-    setMemorySegment(varAddr, data);
-  }
-
-//  private ArrayList<MemoryCPUMonitor> cpuMonitorArray = new ArrayList<MemoryCPUMonitor>();
-
   @Override
   public byte[] getMemory() throws MoteMemoryException {
     throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
diff --git a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/interfaces/MspDebugOutput.java b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/interfaces/MspDebugOutput.java
index 80df3ece4..af72bc63a 100644
--- a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/interfaces/MspDebugOutput.java
+++ b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/interfaces/MspDebugOutput.java
@@ -40,8 +40,9 @@ import org.jdom.Element;
 import org.contikios.cooja.ClassDescription;
 import org.contikios.cooja.Mote;
 import org.contikios.cooja.interfaces.Log;
+import org.contikios.cooja.mote.memory.MemoryInterface;
+import org.contikios.cooja.mote.memory.VarMemory;
 import org.contikios.cooja.mspmote.MspMote;
-import org.contikios.cooja.mspmote.MspMoteMemory;
 import se.sics.mspsim.core.Memory;
 import se.sics.mspsim.core.MemoryMonitor;
 
@@ -64,24 +65,24 @@ public class MspDebugOutput extends Log {
   private final static String CONTIKI_POINTER = "cooja_debug_ptr";
   
   private MspMote mote;
-  private MspMoteMemory mem;
+  private VarMemory mem;
   
   private String lastLog = null;
   private MemoryMonitor memoryMonitor = null;
   
   public MspDebugOutput(Mote mote) {
     this.mote = (MspMote) mote;
-    this.mem = (MspMoteMemory) this.mote.getMemory();
+    this.mem = new VarMemory(this.mote.getMemory());
 
     if (!mem.variableExists(CONTIKI_POINTER)) {
       /* Disabled */
       return;
     }
-    this.mote.getCPU().addWatchPoint(mem.getVariableAddress(CONTIKI_POINTER),
+    this.mote.getCPU().addWatchPoint((int) mem.getVariableAddress(CONTIKI_POINTER),
         memoryMonitor = new MemoryMonitor.Adapter() {
         @Override
         public void notifyWriteAfter(int adr, int data, Memory.AccessMode mode) {
-          String msg = extractString(mem, data);
+          String msg = extractString(MspDebugOutput.this.mote.getMemory(), data);
           if (msg != null && msg.length() > 0) {
             lastLog = "DEBUG: " + msg;
             setChanged();
@@ -91,7 +92,7 @@ public class MspDebugOutput extends Log {
     });
   }
 
-  private String extractString(MspMoteMemory mem, int address) {
+  private String extractString(MemoryInterface mem, int address) {
     StringBuilder sb = new StringBuilder();
     while (true) {
       byte[] data = mem.getMemorySegment(address, 8);
@@ -136,7 +137,7 @@ public class MspDebugOutput extends Log {
     super.removed();
 
     if (memoryMonitor != null) {
-      mote.getCPU().removeWatchPoint(mem.getVariableAddress(CONTIKI_POINTER), memoryMonitor);
+      mote.getCPU().removeWatchPoint((int) mem.getVariableAddress(CONTIKI_POINTER), memoryMonitor);
     }
   }
 }
diff --git a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/interfaces/MspMoteID.java b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/interfaces/MspMoteID.java
index 0c71ca208..a7ced648b 100644
--- a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/interfaces/MspMoteID.java
+++ b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/interfaces/MspMoteID.java
@@ -39,8 +39,8 @@ import org.apache.log4j.Logger;
 
 import org.contikios.cooja.Mote;
 import org.contikios.cooja.interfaces.MoteID;
+import org.contikios.cooja.mote.memory.VarMemory;
 import org.contikios.cooja.mspmote.MspMote;
-import org.contikios.cooja.mspmote.MspMoteMemory;
 import se.sics.mspsim.core.Memory;
 import se.sics.mspsim.core.MemoryMonitor;
 
@@ -53,7 +53,7 @@ public class MspMoteID extends MoteID {
 	private static Logger logger = Logger.getLogger(MspMoteID.class);
 
 	private MspMote mote;
-	private MspMoteMemory moteMem = null;
+	private VarMemory moteMem = null;
 
 	private boolean writeFlashHeader = true;
 	private int moteID = -1;
@@ -69,7 +69,7 @@ public class MspMoteID extends MoteID {
 	 */
 	public MspMoteID(Mote m) {
 		this.mote = (MspMote) m;
-		this.moteMem = (MspMoteMemory) mote.getMemory();
+		this.moteMem = new VarMemory(mote.getMemory());
 	}
 
 	public int getMoteID() {
@@ -144,7 +144,7 @@ public class MspMoteID extends MoteID {
 		            byte[] id = new byte[2];
 		            id[0] = (byte) (moteID & 0xff);
 		            id[1] = (byte) ((moteID >> 8) & 0xff);
-		            moteMem.setMemorySegment(dstAddress & ~1, id);
+		            mote.getMemory().setMemorySegment(dstAddress & ~1, id);
 		        }
 
 		    };
@@ -201,7 +201,7 @@ public class MspMoteID extends MoteID {
 
 	private void addMonitor(String variable, MemoryMonitor monitor) {
 	    if (moteMem.variableExists(variable)) {
-	        int address = moteMem.getVariableAddress(variable);
+	        int address = (int) moteMem.getVariableAddress(variable);
 	        if ((address & 1) != 0) {
 	            // Variable can not be a word - must be a byte
 	        } else {
@@ -213,7 +213,7 @@ public class MspMoteID extends MoteID {
 
         private void removeMonitor(String variable, MemoryMonitor monitor) {
             if (moteMem.variableExists(variable)) {
-                int address = moteMem.getVariableAddress(variable);
+                int address = (int) moteMem.getVariableAddress(variable);
                 mote.getCPU().removeWatchPoint(address, monitor);
                 mote.getCPU().removeWatchPoint(address + 1, monitor);
             }
diff --git a/tools/cooja/java/org/contikios/cooja/AddressMemory.java b/tools/cooja/java/org/contikios/cooja/AddressMemory.java
deleted file mode 100644
index 4f126ab7e..000000000
--- a/tools/cooja/java/org/contikios/cooja/AddressMemory.java
+++ /dev/null
@@ -1,124 +0,0 @@
-/*
- * Copyright (c) 2006, Swedish Institute of Computer Science. All rights
- * reserved.
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- * 1. Redistributions of source code must retain the above copyright notice,
- * this list of conditions and the following disclaimer. 2. Redistributions in
- * binary form must reproduce the above copyright notice, this list of
- * conditions and the following disclaimer in the documentation and/or other
- * materials provided with the distribution. 3. Neither the name of the
- * Institute nor the names of its contributors may be used to endorse or promote
- * products derived from this software without specific prior written
- * permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND ANY
- * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- * DISCLAIMED. IN NO EVENT SHALL THE INSTITUTE OR CONTRIBUTORS BE LIABLE FOR ANY
- * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
- * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- *
- */
-
-package org.contikios.cooja;
-
-public interface AddressMemory {
-
-  /**
-   * @return All variable names known and residing in this memory
-   */
-  public String[] getVariableNames();
-
-  /**
-   * Checks if given variable exists in memory.
-   *
-   * @param varName Variable name
-   * @return True if variable exists, false otherwise
-   */
-  public boolean variableExists(String varName);
-
-  /**
-   * Returns address of variable with given name.
-   *
-   * @param varName Variable name
-   * @return Variable address
-   * @throws UnknownVariableException Variable does not exist
-   */
-  public int getVariableAddress(String varName) throws UnknownVariableException;
-
-  /**
-   * Returns a value of the byte variable with the given name.
-   *
-   * @param varName Name of byte variable
-   * @return Value of byte variable
-   * @throws UnknownVariableException Variable does not exist
-   */
-  public byte getByteValueOf(String varName) throws UnknownVariableException;
-
-  /**
-   * Set byte value of variable with given name.
-   *
-   * @param varName Name of byte variable
-   * @param newVal New value of byte
-   * @throws UnknownVariableException Variable does not exist
-   */
-  public void setByteValueOf(String varName, byte newVal) throws UnknownVariableException;
-
-  /**
-   * Returns byte array of given length and with the given name.
-   *
-   * @param varName Name of array
-   * @param length Length of array
-   * @return Data of array
-   * @throws UnknownVariableException Variable does not exist
-   */
-  public byte[] getByteArray(String varName, int length) throws UnknownVariableException;
-
-  /**
-   * Set byte array of the variable with the given name.
-   *
-   * @param varName Name of array
-   * @param data New data of array
-   * @throws UnknownVariableException Variable does not exist
-   */
-  public void setByteArray(String varName, byte[] data) throws UnknownVariableException;
-
-  /**
-   * @return Number of bytes in an integer
-   */
-  public int getIntegerLength();
-
-  /**
-   * Returns a value of the integer variable with the given name.
-   *
-   * @param varName Name of integer variable
-   * @return Value of integer variable
-   * @throws UnknownVariableException Variable does not exist
-   */
-  public int getIntValueOf(String varName) throws UnknownVariableException;
-
-  /**
-   * Set integer value of variable with given name.
-   *
-   * @param varName Name of integer variable
-   * @param newVal New integer value
-   * @throws UnknownVariableException Variable does not exist
-   */
-  public void setIntValueOf(String varName, int newVal) throws UnknownVariableException;
-
-  /**
-   * Unknown variable name exception.
-   */
-  public class UnknownVariableException extends RuntimeException {
-    public UnknownVariableException(String varName) {
-      super("Unknown variable name: " + varName);
-    }
-  }
-
-}
diff --git a/tools/cooja/java/org/contikios/cooja/SectionMoteMemory.java b/tools/cooja/java/org/contikios/cooja/SectionMoteMemory.java
index e772f9f7c..73f246eb2 100644
--- a/tools/cooja/java/org/contikios/cooja/SectionMoteMemory.java
+++ b/tools/cooja/java/org/contikios/cooja/SectionMoteMemory.java
@@ -46,7 +46,7 @@ import org.contikios.cooja.mote.memory.MemoryLayout;
  *
  * @author Fredrik Osterlind
  */
-public class SectionMoteMemory implements MemoryInterface, AddressMemory {
+public class SectionMoteMemory implements MemoryInterface {
   private static Logger logger = Logger.getLogger(SectionMoteMemory.class);
 
   private ArrayList<MoteMemorySection> sections = new ArrayList<MoteMemorySection>();
@@ -69,73 +69,16 @@ public class SectionMoteMemory implements MemoryInterface, AddressMemory {
     this.offset = offset;
   }
 
-  @Override
-  public String[] getVariableNames() {
-    return addresses.keySet().toArray(new String[0]);
-  }
-
-  @Override
-  public int getVariableAddress(String varName) throws UnknownVariableException {
-    /* Cooja address space */
-    if (!addresses.containsKey(varName)) {
-      throw new UnknownVariableException(varName);
-    }
-    
-    return addresses.get(varName).intValue() + offset;
-  }
-
-  @Override
-  public int getIntegerLength() {
-    return 4;
-  }
 
   @Override
   public void clearMemory() {
     sections.clear();
   }
 
-//  @Override
-//  public byte[] getMemorySegment(int address, int size) {
-//    /* Cooja address space */
-//    address -= offset;
-//   
-//    for (MoteMemorySection section : sections) {
-//      if (section.includesAddr(address)
-//          && section.includesAddr(address + size - 1)) {
-//        return section.getMemorySegment(address, size);
-//      }
-//    }
-//    
-//    /* Check if in readonly section */
-//    for (MoteMemorySection section : readonlySections) {
-//      if (section.includesAddr(address)
-//          && section.includesAddr(address + size - 1)) {
-//        return section.getMemorySegment(address, size);
-//      }
-//    }
-//    
-//    return null;
-//  }
-
   public void setMemorySegmentNative(int address, byte[] data) {
     setMemorySegment(address+offset, data);
   }
 
-//  @Override
-//  public void setMemorySegment(int address, byte[] data) {
-//    /* Cooja address space */
-//    address -= offset;
-//
-//    /* TODO XXX Sections may overlap */
-//    for (MoteMemorySection section : sections) {
-//      if (section.includesAddr(address)
-//          && section.includesAddr(address + data.length - 1)) {
-//        section.setMemorySegment(address, data);
-//        return;
-//      }
-//    }
-//    sections.add(new MoteMemorySection(address, data));
-//  }
 
   public void setReadonlyMemorySegment(int address, byte[] data) {
     /* Cooja address space */
@@ -202,75 +145,6 @@ public class SectionMoteMemory implements MemoryInterface, AddressMemory {
     return sections.get(sectionNr).getData();
   }
 
-  @Override
-  public boolean variableExists(String varName) {
-    return addresses.containsKey(varName);
-  }
-
-  @Override
-  public int getIntValueOf(String varName) throws UnknownVariableException {
-    int varAddr = getVariableAddress(varName);
-    byte[] varData = getMemorySegment(varAddr, 4);
-
-    if (varData == null) {
-      throw new UnknownVariableException(varName);
-    }
-
-    return parseInt(varData);
-  }
-
-  @Override
-  public void setIntValueOf(String varName, int newVal) throws UnknownVariableException {
-    int varAddr = getVariableAddress(varName);
-
-    /* TODO Correct for all platforms? */
-    int newValToSet = Integer.reverseBytes(newVal);
-
-    int pos = 0;
-
-    byte[] varData = new byte[4];
-    varData[pos++] = (byte) ((newValToSet & 0xFF000000) >> 24);
-    varData[pos++] = (byte) ((newValToSet & 0xFF0000) >> 16);
-    varData[pos++] = (byte) ((newValToSet & 0xFF00) >> 8);
-    varData[pos++] = (byte) ((newValToSet & 0xFF) >> 0);
-
-    setMemorySegment(varAddr, varData);
-  }
-
-  @Override
-  public byte getByteValueOf(String varName) throws UnknownVariableException {
-    int varAddr = getVariableAddress(varName);
-    byte[] varData = getMemorySegment(varAddr, 1);
-
-    if (varData == null) {
-      throw new UnknownVariableException(varName);
-    }
-
-    return varData[0];
-  }
-
-  @Override
-  public void setByteValueOf(String varName, byte newVal) throws UnknownVariableException {
-    int varAddr = getVariableAddress(varName);
-    byte[] varData = new byte[1];
-
-    varData[0] = newVal;
-
-    setMemorySegment(varAddr, varData);
-  }
-
-  @Override
-  public byte[] getByteArray(String varName, int length) throws UnknownVariableException {
-    int varAddr = getVariableAddress(varName);
-    return getMemorySegment(varAddr, length);
-  }
-
-  @Override
-  public void setByteArray(String varName, byte[] data) throws UnknownVariableException {
-    int varAddr = getVariableAddress(varName);
-    setMemorySegment(varAddr, data);
-  }
-
   @Override
   public byte[] getMemory() throws MoteMemoryException {
     throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
index f3ff8f4c4..8ca58f6c1 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
@@ -68,6 +68,7 @@ import org.contikios.cooja.dialogs.CompileContiki;
 import org.contikios.cooja.dialogs.ContikiMoteCompileDialog;
 import org.contikios.cooja.dialogs.MessageList;
 import org.contikios.cooja.dialogs.MessageList.MessageContainer;
+import org.contikios.cooja.mote.memory.VarMemory;
 import org.contikios.cooja.util.StringUtils;
 
 /**
@@ -505,6 +506,7 @@ public class ContikiMoteType implements MoteType {
     int offset;
     {
       SectionMoteMemory tmp = new SectionMoteMemory(addresses, 0);
+      VarMemory varMem = new VarMemory(tmp);
       byte[] data = new byte[dataSectionSize];
       getCoreMemory(dataSectionAddr, dataSectionSize, data);
       tmp.setMemorySegment(dataSectionAddr, data);
@@ -512,7 +514,7 @@ public class ContikiMoteType implements MoteType {
       getCoreMemory(bssSectionAddr, bssSectionSize, bss);
       tmp.setMemorySegment(bssSectionAddr, bss);
 
-      offset = tmp.getIntValueOf("referenceVar");
+      offset = varMem.getIntValueOf("referenceVar");
       logger.info(getContikiFirmwareFile().getName() +
           ": offsetting Cooja mote address space: " + offset);
     }
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiBeeper.java b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiBeeper.java
index c9ef326a9..5fce4e931 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiBeeper.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiBeeper.java
@@ -48,6 +48,7 @@ import org.contikios.cooja.SectionMoteMemory;
 import org.contikios.cooja.contikimote.ContikiMoteInterface;
 import org.contikios.cooja.interfaces.Beeper;
 import org.contikios.cooja.interfaces.PolledAfterActiveTicks;
+import org.contikios.cooja.mote.memory.VarMemory;
 
 /**
  * Beeper mote interface.
@@ -70,7 +71,7 @@ import org.contikios.cooja.interfaces.PolledAfterActiveTicks;
  */
 public class ContikiBeeper extends Beeper implements ContikiMoteInterface, PolledAfterActiveTicks {
   private Mote mote = null;
-  private SectionMoteMemory moteMem = null;
+  private VarMemory moteMem = null;
   private static Logger logger = Logger.getLogger(ContikiBeeper.class);
 
   /**
@@ -83,7 +84,7 @@ public class ContikiBeeper extends Beeper implements ContikiMoteInterface, Polle
    */
   public ContikiBeeper(Mote mote) {
     this.mote = mote;
-    this.moteMem = (SectionMoteMemory) mote.getMemory();
+    this.moteMem = new VarMemory(mote.getMemory());
   }
 
   public boolean isBeeping() {
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiButton.java b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiButton.java
index 57f7b7fd6..852383a09 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiButton.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiButton.java
@@ -40,6 +40,7 @@ import org.contikios.cooja.*;
 import org.contikios.cooja.contikimote.ContikiMote;
 import org.contikios.cooja.contikimote.ContikiMoteInterface;
 import org.contikios.cooja.interfaces.Button;
+import org.contikios.cooja.mote.memory.VarMemory;
 
 /**
  * Button mote interface.
@@ -62,7 +63,7 @@ import org.contikios.cooja.interfaces.Button;
  * @author Fredrik Osterlind
  */
 public class ContikiButton extends Button implements ContikiMoteInterface {
-  private SectionMoteMemory moteMem;
+  private VarMemory moteMem;
   private ContikiMote mote;
 
   private static Logger logger = Logger.getLogger(ContikiButton.class);
@@ -76,7 +77,7 @@ public class ContikiButton extends Button implements ContikiMoteInterface {
    */
   public ContikiButton(Mote mote) {
     this.mote = (ContikiMote) mote;
-    this.moteMem = (SectionMoteMemory) mote.getMemory();
+    this.moteMem = new VarMemory(mote.getMemory());
   }
 
   public static String[] getCoreInterfaceDependencies() {
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiCFS.java b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiCFS.java
index e831a1607..5a8dbb41e 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiCFS.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiCFS.java
@@ -43,6 +43,7 @@ import org.jdom.Element;
 import org.contikios.cooja.*;
 import org.contikios.cooja.contikimote.ContikiMoteInterface;
 import org.contikios.cooja.interfaces.PolledAfterActiveTicks;
+import org.contikios.cooja.mote.memory.VarMemory;
 
 /**
  * Contiki FileSystem (CFS) interface (such as external flash).
@@ -71,7 +72,7 @@ public class ContikiCFS extends MoteInterface implements ContikiMoteInterface, P
 
   public int FILESYSTEM_SIZE = 4000; /* Configure CFS size here and in cfs-cooja.c */
   private Mote mote = null;
-  private SectionMoteMemory moteMem = null;
+  private VarMemory moteMem = null;
 
   private int lastRead = 0;
   private int lastWritten = 0;
@@ -85,7 +86,7 @@ public class ContikiCFS extends MoteInterface implements ContikiMoteInterface, P
    */
   public ContikiCFS(Mote mote) {
     this.mote = mote;
-    this.moteMem = (SectionMoteMemory) mote.getMemory();
+    this.moteMem = new VarMemory(mote.getMemory());
   }
 
   public static String[] getCoreInterfaceDependencies() {
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiClock.java b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiClock.java
index 3864c4724..dce0063cb 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiClock.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiClock.java
@@ -44,6 +44,7 @@ import org.contikios.cooja.contikimote.ContikiMoteInterface;
 import org.contikios.cooja.interfaces.Clock;
 import org.contikios.cooja.interfaces.PolledAfterAllTicks;
 import org.contikios.cooja.interfaces.PolledBeforeActiveTicks;
+import org.contikios.cooja.mote.memory.VarMemory;
 
 /**
  * Clock mote interface. Controls Contiki time.
@@ -71,7 +72,7 @@ public class ContikiClock extends Clock implements ContikiMoteInterface, PolledB
 
   private Simulation simulation;
   private ContikiMote mote;
-  private SectionMoteMemory moteMem;
+  private VarMemory moteMem;
 
   private long moteTime; /* Microseconds */
   private long timeDrift; /* Microseconds */
@@ -85,7 +86,7 @@ public class ContikiClock extends Clock implements ContikiMoteInterface, PolledB
   public ContikiClock(Mote mote) {
     this.simulation = mote.getSimulation();
     this.mote = (ContikiMote) mote;
-    this.moteMem = (SectionMoteMemory) mote.getMemory();
+    this.moteMem = new VarMemory(mote.getMemory());
     timeDrift = 0;
     moteTime = 0;
   }
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiEEPROM.java b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiEEPROM.java
index a1b1d5e56..aeca322d1 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiEEPROM.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiEEPROM.java
@@ -45,6 +45,7 @@ import org.jdom.Element;
 import org.contikios.cooja.*;
 import org.contikios.cooja.contikimote.ContikiMoteInterface;
 import org.contikios.cooja.interfaces.PolledAfterActiveTicks;
+import org.contikios.cooja.mote.memory.VarMemory;
 
 /**
  * Contiki EEPROM interface
@@ -73,7 +74,7 @@ public class ContikiEEPROM extends MoteInterface implements ContikiMoteInterface
 
   public int EEPROM_SIZE = 1024; /* Configure EEPROM size here and in eeprom.c. Should really be multiple of 16 */
   private Mote mote = null;
-  private SectionMoteMemory moteMem = null;
+  private VarMemory moteMem = null;
 
   private int lastRead = 0;
   private int lastWritten = 0;
@@ -87,7 +88,7 @@ public class ContikiEEPROM extends MoteInterface implements ContikiMoteInterface
    */
   public ContikiEEPROM(Mote mote) {
     this.mote = mote;
-    this.moteMem = (SectionMoteMemory) mote.getMemory();
+    this.moteMem = new VarMemory(mote.getMemory());
   }
 
   public static String[] getCoreInterfaceDependencies() {
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiLED.java b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiLED.java
index b6372751d..cc549e142 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiLED.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiLED.java
@@ -40,6 +40,7 @@ import org.contikios.cooja.*;
 import org.contikios.cooja.contikimote.ContikiMoteInterface;
 import org.contikios.cooja.interfaces.LED;
 import org.contikios.cooja.interfaces.PolledAfterActiveTicks;
+import org.contikios.cooja.mote.memory.VarMemory;
 
 /**
  * LEDs mote interface.
@@ -64,7 +65,7 @@ public class ContikiLED extends LED implements ContikiMoteInterface, PolledAfter
   private static Logger logger = Logger.getLogger(ContikiLED.class);
 
   private Mote mote = null;
-  private SectionMoteMemory moteMem = null;
+  private VarMemory moteMem = null;
   private byte currentLedValue = 0;
 
   private static final byte LEDS_GREEN = 1;
@@ -91,7 +92,7 @@ public class ContikiLED extends LED implements ContikiMoteInterface, PolledAfter
    */
   public ContikiLED(Mote mote) {
     this.mote = mote;
-    this.moteMem = (SectionMoteMemory) mote.getMemory();
+    this.moteMem = new VarMemory(mote.getMemory());
   }
 
   public static String[] getCoreInterfaceDependencies() {
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiMoteID.java b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiMoteID.java
index 8a9887638..e83d0c2fa 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiMoteID.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiMoteID.java
@@ -38,6 +38,7 @@ import org.jdom.Element;
 import org.contikios.cooja.*;
 import org.contikios.cooja.contikimote.ContikiMoteInterface;
 import org.contikios.cooja.interfaces.MoteID;
+import org.contikios.cooja.mote.memory.VarMemory;
 
 /**
  * Mote ID interface: 'node_id'.
@@ -60,7 +61,7 @@ import org.contikios.cooja.interfaces.MoteID;
  * @author Fredrik Osterlind
  */
 public class ContikiMoteID extends MoteID implements ContikiMoteInterface {
-  private SectionMoteMemory moteMem = null;
+  private VarMemory moteMem = null;
   private static Logger logger = Logger.getLogger(ContikiMoteID.class);
 
   private int moteID = 0;
@@ -77,7 +78,7 @@ public class ContikiMoteID extends MoteID implements ContikiMoteInterface {
    */
   public ContikiMoteID(Mote mote) {
     this.mote = mote;
-    this.moteMem = (SectionMoteMemory) mote.getMemory();
+    this.moteMem = new VarMemory(mote.getMemory());
   }
 
   public static String[] getCoreInterfaceDependencies() {
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiPIR.java b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiPIR.java
index 0dbb90f03..c56233d25 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiPIR.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiPIR.java
@@ -41,6 +41,7 @@ import org.contikios.cooja.SectionMoteMemory;
 import org.contikios.cooja.contikimote.ContikiMote;
 import org.contikios.cooja.contikimote.ContikiMoteInterface;
 import org.contikios.cooja.interfaces.PIR;
+import org.contikios.cooja.mote.memory.VarMemory;
 
 /**
  * Passive IR sensor mote interface.
@@ -65,7 +66,7 @@ import org.contikios.cooja.interfaces.PIR;
 public class ContikiPIR extends PIR implements ContikiMoteInterface {
 
   private ContikiMote mote;
-  private SectionMoteMemory moteMem;
+  private VarMemory moteMem;
 
   /**
    * Creates an interface to the PIR at mote.
@@ -77,7 +78,7 @@ public class ContikiPIR extends PIR implements ContikiMoteInterface {
    */
   public ContikiPIR(Mote mote) {
     this.mote = (ContikiMote) mote;
-    this.moteMem = (SectionMoteMemory) mote.getMemory();
+    this.moteMem = new VarMemory(mote.getMemory());
   }
 
   public static String[] getCoreInterfaceDependencies() {
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiRS232.java b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiRS232.java
index 304ffa5ae..2607bc1ea 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiRS232.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiRS232.java
@@ -38,6 +38,7 @@ import org.contikios.cooja.contikimote.ContikiMote;
 import org.contikios.cooja.contikimote.ContikiMoteInterface;
 import org.contikios.cooja.dialogs.SerialUI;
 import org.contikios.cooja.interfaces.PolledAfterActiveTicks;
+import org.contikios.cooja.mote.memory.VarMemory;
 
 /**
  * Contiki mote serial port and log interfaces.
@@ -68,7 +69,7 @@ public class ContikiRS232 extends SerialUI implements ContikiMoteInterface, Poll
   private static Logger logger = Logger.getLogger(ContikiRS232.class);
 
   private ContikiMote mote = null;
-  private SectionMoteMemory moteMem = null;
+  private VarMemory moteMem = null;
 
   static final int SERIAL_BUF_SIZE = 1024; /* rs232.c:40 */
   
@@ -82,7 +83,7 @@ public class ContikiRS232 extends SerialUI implements ContikiMoteInterface, Poll
    */
   public ContikiRS232(Mote mote) {
     this.mote = (ContikiMote) mote;
-    this.moteMem = (SectionMoteMemory) mote.getMemory();
+    this.moteMem = new VarMemory(mote.getMemory());
   }
 
   public static String[] getCoreInterfaceDependencies() {
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiRadio.java b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiRadio.java
index ebe24e52a..be239338b 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiRadio.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiRadio.java
@@ -46,6 +46,7 @@ import org.contikios.cooja.contikimote.ContikiMoteInterface;
 import org.contikios.cooja.interfaces.PolledAfterActiveTicks;
 import org.contikios.cooja.interfaces.Position;
 import org.contikios.cooja.interfaces.Radio;
+import org.contikios.cooja.mote.memory.VarMemory;
 import org.contikios.cooja.radiomediums.UDGM;
 
 /**
@@ -89,7 +90,7 @@ import org.contikios.cooja.radiomediums.UDGM;
 public class ContikiRadio extends Radio implements ContikiMoteInterface, PolledAfterActiveTicks {
   private ContikiMote mote;
 
-  private SectionMoteMemory myMoteMemory;
+  private VarMemory myMoteMemory;
 
   private static Logger logger = Logger.getLogger(ContikiRadio.class);
 
@@ -132,7 +133,7 @@ public class ContikiRadio extends Radio implements ContikiMoteInterface, PolledA
         ContikiRadio.class, "RADIO_TRANSMISSION_RATE_kbps");
 
     this.mote = (ContikiMote) mote;
-    this.myMoteMemory = (SectionMoteMemory) mote.getMemory();
+    this.myMoteMemory = new VarMemory(mote.getMemory());
 
     radioOn = myMoteMemory.getByteValueOf("simRadioHWOn") == 1;
   }
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiVib.java b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiVib.java
index 9584674ac..f80a1bc63 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiVib.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiVib.java
@@ -42,6 +42,7 @@ import org.contikios.cooja.MoteInterface;
 import org.contikios.cooja.SectionMoteMemory;
 import org.contikios.cooja.contikimote.ContikiMote;
 import org.contikios.cooja.contikimote.ContikiMoteInterface;
+import org.contikios.cooja.mote.memory.VarMemory;
 
 /**
  * Vibration sensor mote interface.
@@ -67,7 +68,7 @@ import org.contikios.cooja.contikimote.ContikiMoteInterface;
 public class ContikiVib extends MoteInterface implements ContikiMoteInterface {
 
   private ContikiMote mote;
-  private SectionMoteMemory moteMem;
+  private VarMemory moteMem;
 
   /**
    * Creates an interface to the vibration sensor at mote.
@@ -79,7 +80,7 @@ public class ContikiVib extends MoteInterface implements ContikiMoteInterface {
    */
   public ContikiVib(Mote mote) {
     this.mote = (ContikiMote) mote;
-    this.moteMem = (SectionMoteMemory) mote.getMemory();
+    this.moteMem = new VarMemory(mote.getMemory());
   }
 
   public static String[] getCoreInterfaceDependencies() {
diff --git a/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java b/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
index 3010625e4..82726f266 100644
--- a/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
+++ b/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
@@ -68,6 +68,7 @@ import org.contikios.cooja.Cooja;
 import org.contikios.cooja.MoteType.MoteTypeCreationException;
 import org.contikios.cooja.SectionMoteMemory;
 import org.contikios.cooja.contikimote.ContikiMoteType;
+import org.contikios.cooja.mote.memory.VarMemory;
 
 /* TODO Test common section */
 /* TODO Test readonly section */
@@ -944,14 +945,15 @@ public class ConfigurationWizard extends JDialog {
     javaLibrary.getMemory(relDataSectionAddr, dataSectionSize, initialDataSection);
     javaLibrary.getMemory(relBssSectionAddr, bssSectionSize, initialBssSection);
     SectionMoteMemory memory = new SectionMoteMemory(addresses, 0);
+    VarMemory varMem = new VarMemory(memory);
     memory.setMemorySegment(relDataSectionAddr, initialDataSection);
     memory.setMemorySegment(relBssSectionAddr, initialBssSection);
 
     int contikiDataCounter, contikiBSSCounter;
 
     testOutput.addMessage("### Checking initial variable values: 1,0");
-    contikiDataCounter = memory.getIntValueOf("var1");
-    contikiBSSCounter = memory.getIntValueOf("uvar1");
+    contikiDataCounter = varMem.getIntValueOf("var1");
+    contikiBSSCounter = varMem.getIntValueOf("uvar1");
     int javaDataCounter = 1;
     int javaBSSCounter = 0;
     if (contikiDataCounter != javaDataCounter) {
@@ -975,8 +977,8 @@ public class ConfigurationWizard extends JDialog {
     javaLibrary.getMemory(relBssSectionAddr, bssSectionSize, initialBssSection);
     memory.setMemorySegment(relDataSectionAddr, initialDataSection);
     memory.setMemorySegment(relBssSectionAddr, initialBssSection);
-    contikiDataCounter = memory.getIntValueOf("var1");
-    contikiBSSCounter = memory.getIntValueOf("uvar1");
+    contikiDataCounter = varMem.getIntValueOf("var1");
+    contikiBSSCounter = varMem.getIntValueOf("uvar1");
     if (contikiDataCounter != javaDataCounter) {
       testOutput.addMessage("### Data section mismatch (" + contikiDataCounter + " != " + javaDataCounter + ")", MessageList.ERROR);
       return false;
@@ -1004,8 +1006,8 @@ public class ConfigurationWizard extends JDialog {
     javaLibrary.getMemory(relBssSectionAddr, bssSectionSize, initialBssSection);
     memory.setMemorySegment(relDataSectionAddr, initialDataSection);
     memory.setMemorySegment(relBssSectionAddr, initialBssSection);
-    contikiDataCounter = memory.getIntValueOf("var1");
-    contikiBSSCounter = memory.getIntValueOf("uvar1");
+    contikiDataCounter = varMem.getIntValueOf("var1");
+    contikiBSSCounter = varMem.getIntValueOf("uvar1");
     if (contikiDataCounter != javaDataCounter) {
       testOutput.addMessage("### Data section mismatch (" + contikiDataCounter + " != " + javaDataCounter + ")", MessageList.ERROR);
       return false;
@@ -1029,8 +1031,8 @@ public class ConfigurationWizard extends JDialog {
     javaLibrary.getMemory(relBssSectionAddr, bssSectionSize, initialBssSection);
     memory.setMemorySegment(relDataSectionAddr, initialDataSection);
     memory.setMemorySegment(relBssSectionAddr, initialBssSection);
-    contikiDataCounter = memory.getIntValueOf("var1");
-    contikiBSSCounter = memory.getIntValueOf("uvar1");
+    contikiDataCounter = varMem.getIntValueOf("var1");
+    contikiBSSCounter = varMem.getIntValueOf("uvar1");
     if (contikiDataCounter != javaDataCounter) {
       testOutput.addMessage("### Data section mismatch (" + contikiDataCounter + " != " + javaDataCounter + ")", MessageList.ERROR);
       return false;
@@ -1049,8 +1051,8 @@ public class ConfigurationWizard extends JDialog {
     javaLibrary.getMemory(relBssSectionAddr, bssSectionSize, initialBssSection);
     memory.setMemorySegment(relDataSectionAddr, initialDataSection);
     memory.setMemorySegment(relBssSectionAddr, initialBssSection);
-    contikiDataCounter = memory.getIntValueOf("var1");
-    contikiBSSCounter = memory.getIntValueOf("uvar1");
+    contikiDataCounter = varMem.getIntValueOf("var1");
+    contikiBSSCounter = varMem.getIntValueOf("uvar1");
     if (contikiDataCounter != javaDataCounter) {
       testOutput.addMessage("### Data section mismatch (" + contikiDataCounter + " != " + javaDataCounter + ")", MessageList.ERROR);
       return false;
diff --git a/tools/cooja/java/org/contikios/cooja/plugins/VariableWatcher.java b/tools/cooja/java/org/contikios/cooja/plugins/VariableWatcher.java
index b6dc2061c..6c8c82ea9 100644
--- a/tools/cooja/java/org/contikios/cooja/plugins/VariableWatcher.java
+++ b/tools/cooja/java/org/contikios/cooja/plugins/VariableWatcher.java
@@ -44,8 +44,10 @@ import java.awt.event.KeyListener;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
 import java.text.NumberFormat;
-import java.util.Arrays;
+import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
 import java.util.Vector;
 
 import javax.swing.BorderFactory;
@@ -64,7 +66,6 @@ import javax.swing.text.PlainDocument;
 
 import org.jdom.Element;
 
-import org.contikios.cooja.AddressMemory;
 import org.contikios.cooja.ClassDescription;
 import org.contikios.cooja.Cooja;
 import org.contikios.cooja.Mote;
@@ -72,7 +73,8 @@ import org.contikios.cooja.MotePlugin;
 import org.contikios.cooja.PluginType;
 import org.contikios.cooja.Simulation;
 import org.contikios.cooja.VisPlugin;
-import org.contikios.cooja.AddressMemory.UnknownVariableException;
+import org.contikios.cooja.mote.memory.UnknownVariableException;
+import org.contikios.cooja.mote.memory.VarMemory;
 
 /**
  * Variable Watcher enables a user to watch mote variables during a simulation.
@@ -87,7 +89,7 @@ import org.contikios.cooja.AddressMemory.UnknownVariableException;
 public class VariableWatcher extends VisPlugin implements MotePlugin {
   private static final long serialVersionUID = 1L;
 
-  private AddressMemory moteMemory;
+  private VarMemory moteMemory;
 
   private final static int LABEL_WIDTH = 170;
   private final static int LABEL_HEIGHT = 15;
@@ -124,7 +126,7 @@ public class VariableWatcher extends VisPlugin implements MotePlugin {
   public VariableWatcher(Mote moteToView, Simulation simulation, Cooja gui) {
     super("Variable Watcher (" + moteToView + ")", gui);
     this.mote = moteToView;
-    moteMemory = (AddressMemory) moteToView.getMemory();
+    moteMemory = new VarMemory(moteToView.getMemory());
 
     JLabel label;
     integerFormat = NumberFormat.getIntegerInstance();
@@ -143,8 +145,8 @@ public class VariableWatcher extends VisPlugin implements MotePlugin {
     varName.setEditable(true);
     varName.setSelectedItem("[enter or pick name]");
 
-    String[] allPotentialVarNames = moteMemory.getVariableNames();
-    Arrays.sort(allPotentialVarNames);
+    List<String> allPotentialVarNames = new ArrayList<>(moteMemory.getVariableNames());
+    Collections.sort(allPotentialVarNames);
     for (String aVarName: allPotentialVarNames) {
       varName.addItem(aVarName);
     }
@@ -172,7 +174,7 @@ public class VariableWatcher extends VisPlugin implements MotePlugin {
 
     varType = new JComboBox();
     varType.addItem("Byte (1 byte)"); // BYTE_INDEX = 0
-    varType.addItem("Integer (" + moteMemory.getIntegerLength() + " bytes)"); // INT_INDEX = 1
+    varType.addItem("Integer (" + moteToView.getMemory().getLayout().intSize + " bytes)"); // INT_INDEX = 1
     varType.addItem("Byte array (x bytes)"); // ARRAY_INDEX = 2
     varType.addItem("Char array (x bytes)"); // CHAR_ARRAY_INDEX = 3
 

From 186240821f1f6bb5d458ec91c1e28f47305d2e96 Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Wed, 23 Jul 2014 10:52:25 +0200
Subject: [PATCH 11/28] [cooja] memory: Moved SectionMoteMemory to package
 memory

---
 .../cooja/java/org/contikios/cooja/contikimote/ContikiMote.java | 2 +-
 .../java/org/contikios/cooja/contikimote/ContikiMoteType.java   | 2 +-
 .../contikios/cooja/contikimote/interfaces/ContikiBeeper.java   | 2 +-
 .../contikios/cooja/contikimote/interfaces/ContikiClock.java    | 2 +-
 .../org/contikios/cooja/contikimote/interfaces/ContikiPIR.java  | 2 +-
 .../contikios/cooja/contikimote/interfaces/ContikiRadio.java    | 2 +-
 .../org/contikios/cooja/contikimote/interfaces/ContikiVib.java  | 2 +-
 .../java/org/contikios/cooja/dialogs/ConfigurationWizard.java   | 2 +-
 .../contikios/cooja/{ => mote/memory}/SectionMoteMemory.java    | 2 +-
 .../java/org/contikios/cooja/motes/AbstractApplicationMote.java | 2 +-
 10 files changed, 10 insertions(+), 10 deletions(-)
 rename tools/cooja/java/org/contikios/cooja/{ => mote/memory}/SectionMoteMemory.java (99%)

diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMote.java b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMote.java
index e39d5d86e..de033aaa4 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMote.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMote.java
@@ -39,7 +39,7 @@ import org.contikios.cooja.Mote;
 import org.contikios.cooja.MoteInterface;
 import org.contikios.cooja.MoteInterfaceHandler;
 import org.contikios.cooja.MoteType;
-import org.contikios.cooja.SectionMoteMemory;
+import org.contikios.cooja.mote.memory.SectionMoteMemory;
 import org.contikios.cooja.Simulation;
 import org.contikios.cooja.mote.memory.MemoryInterface;
 import org.contikios.cooja.motes.AbstractWakeupMote;
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
index 8ca58f6c1..6d58d2d6a 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
@@ -62,7 +62,7 @@ import org.contikios.cooja.Mote;
 import org.contikios.cooja.MoteInterface;
 import org.contikios.cooja.MoteType;
 import org.contikios.cooja.ProjectConfig;
-import org.contikios.cooja.SectionMoteMemory;
+import org.contikios.cooja.mote.memory.SectionMoteMemory;
 import org.contikios.cooja.Simulation;
 import org.contikios.cooja.dialogs.CompileContiki;
 import org.contikios.cooja.dialogs.ContikiMoteCompileDialog;
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiBeeper.java b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiBeeper.java
index 5fce4e931..01f9c757e 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiBeeper.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiBeeper.java
@@ -44,7 +44,7 @@ import org.apache.log4j.Logger;
 import org.jdom.Element;
 
 import org.contikios.cooja.Mote;
-import org.contikios.cooja.SectionMoteMemory;
+import org.contikios.cooja.mote.memory.SectionMoteMemory;
 import org.contikios.cooja.contikimote.ContikiMoteInterface;
 import org.contikios.cooja.interfaces.Beeper;
 import org.contikios.cooja.interfaces.PolledAfterActiveTicks;
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiClock.java b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiClock.java
index dce0063cb..127a7a3a7 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiClock.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiClock.java
@@ -37,7 +37,7 @@ import org.apache.log4j.Logger;
 import org.jdom.Element;
 
 import org.contikios.cooja.Mote;
-import org.contikios.cooja.SectionMoteMemory;
+import org.contikios.cooja.mote.memory.SectionMoteMemory;
 import org.contikios.cooja.Simulation;
 import org.contikios.cooja.contikimote.ContikiMote;
 import org.contikios.cooja.contikimote.ContikiMoteInterface;
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiPIR.java b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiPIR.java
index c56233d25..cbfb7d66c 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiPIR.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiPIR.java
@@ -37,7 +37,7 @@ import javax.swing.JButton;
 import javax.swing.JPanel;
 import org.jdom.Element;
 import org.contikios.cooja.Mote;
-import org.contikios.cooja.SectionMoteMemory;
+import org.contikios.cooja.mote.memory.SectionMoteMemory;
 import org.contikios.cooja.contikimote.ContikiMote;
 import org.contikios.cooja.contikimote.ContikiMoteInterface;
 import org.contikios.cooja.interfaces.PIR;
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiRadio.java b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiRadio.java
index be239338b..5502b9a8a 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiRadio.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiRadio.java
@@ -39,7 +39,7 @@ import org.jdom.Element;
 import org.contikios.cooja.COOJARadioPacket;
 import org.contikios.cooja.Mote;
 import org.contikios.cooja.RadioPacket;
-import org.contikios.cooja.SectionMoteMemory;
+import org.contikios.cooja.mote.memory.SectionMoteMemory;
 import org.contikios.cooja.Simulation;
 import org.contikios.cooja.contikimote.ContikiMote;
 import org.contikios.cooja.contikimote.ContikiMoteInterface;
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiVib.java b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiVib.java
index f80a1bc63..ba1920715 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiVib.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/interfaces/ContikiVib.java
@@ -39,7 +39,7 @@ import org.jdom.Element;
 import org.contikios.cooja.ClassDescription;
 import org.contikios.cooja.Mote;
 import org.contikios.cooja.MoteInterface;
-import org.contikios.cooja.SectionMoteMemory;
+import org.contikios.cooja.mote.memory.SectionMoteMemory;
 import org.contikios.cooja.contikimote.ContikiMote;
 import org.contikios.cooja.contikimote.ContikiMoteInterface;
 import org.contikios.cooja.mote.memory.VarMemory;
diff --git a/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java b/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
index 82726f266..0fa575be9 100644
--- a/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
+++ b/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
@@ -66,7 +66,7 @@ import javax.swing.JScrollPane;
 import org.contikios.cooja.CoreComm;
 import org.contikios.cooja.Cooja;
 import org.contikios.cooja.MoteType.MoteTypeCreationException;
-import org.contikios.cooja.SectionMoteMemory;
+import org.contikios.cooja.mote.memory.SectionMoteMemory;
 import org.contikios.cooja.contikimote.ContikiMoteType;
 import org.contikios.cooja.mote.memory.VarMemory;
 
diff --git a/tools/cooja/java/org/contikios/cooja/SectionMoteMemory.java b/tools/cooja/java/org/contikios/cooja/mote/memory/SectionMoteMemory.java
similarity index 99%
rename from tools/cooja/java/org/contikios/cooja/SectionMoteMemory.java
rename to tools/cooja/java/org/contikios/cooja/mote/memory/SectionMoteMemory.java
index 73f246eb2..75c8d4dfa 100644
--- a/tools/cooja/java/org/contikios/cooja/SectionMoteMemory.java
+++ b/tools/cooja/java/org/contikios/cooja/mote/memory/SectionMoteMemory.java
@@ -25,7 +25,7 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.contikios.cooja;
+package org.contikios.cooja.mote.memory;
 
 import java.util.ArrayList;
 import java.util.Arrays;
diff --git a/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java b/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
index e4974ac7b..b8bccaf63 100644
--- a/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
+++ b/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
@@ -41,7 +41,7 @@ import org.contikios.cooja.MoteInterface;
 import org.contikios.cooja.MoteInterfaceHandler;
 import org.contikios.cooja.MoteType;
 import org.contikios.cooja.RadioPacket;
-import org.contikios.cooja.SectionMoteMemory;
+import org.contikios.cooja.mote.memory.SectionMoteMemory;
 import org.contikios.cooja.Simulation;
 import org.contikios.cooja.interfaces.ApplicationRadio;
 import org.contikios.cooja.interfaces.ApplicationSerialPort;

From e5a35821c3481ce7d8bcb29fdc0946f0705bb8b9 Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Wed, 23 Jul 2014 11:18:35 +0200
Subject: [PATCH 12/28] [cooja] Implementation of former AvrMoteMemory dummy
 functions

---
 .../cooja/avrmote/AvrMoteMemory.java          | 165 +++++++++++++++---
 .../contikios/cooja/avrmote/MicaZMote.java    |   3 -
 2 files changed, 139 insertions(+), 29 deletions(-)

diff --git a/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/AvrMoteMemory.java b/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/AvrMoteMemory.java
index bd2b719cb..61cd12b8c 100644
--- a/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/AvrMoteMemory.java
+++ b/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/AvrMoteMemory.java
@@ -1,4 +1,5 @@
 /*
+ * Copyright (c) 2014, TU Braunschweig. All rights reserved.
  * Copyright (c) 2009, Swedish Institute of Computer Science. All rights
  * reserved.
  *
@@ -33,35 +34,43 @@ import org.apache.log4j.Logger;
 
 import avrora.arch.avr.AVRProperties;
 import avrora.core.SourceMapping;
+import avrora.core.SourceMapping.Location;
 import avrora.sim.AtmelInterpreter;
 import avrora.sim.Simulator.Watch;
+import avrora.sim.State;
+import java.nio.ByteOrder;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
 import java.util.Map;
 import org.contikios.cooja.mote.memory.MemoryInterface;
+import org.contikios.cooja.mote.memory.MemoryInterface.SegmentMonitor.EventType;
 import org.contikios.cooja.mote.memory.MemoryLayout;
 /**
- * @author Joakim Eriksson
+ * @author Joakim Eriksson, Fredrik Osterlind, David Kopf, Enrico Jorns
  */
 public class AvrMoteMemory implements MemoryInterface {
-    private static Logger logger = Logger.getLogger(AvrMoteMemory.class);
+  private static Logger logger = Logger.getLogger(AvrMoteMemory.class);
+  private static final boolean DEBUG = logger.isDebugEnabled();
+
+  private final SourceMapping memoryMap;
+  private final AVRProperties avrProperties;
+  private final AtmelInterpreter interpreter;
+  private final ArrayList<AvrByteMonitor> memoryMonitors = new ArrayList<>();
+  private final MemoryLayout memLayout = new MemoryLayout(ByteOrder.LITTLE_ENDIAN, MemoryLayout.ARCH_8BIT, 2);
+
+  private boolean coojaIsAccessingMemory;
 
-    private SourceMapping memoryMap;
-    private AtmelInterpreter interpreter;
-    private AVRProperties avrProperties;
-    
     public AvrMoteMemory(SourceMapping map, AVRProperties avrProperties, AtmelInterpreter interpreter) {
         memoryMap = map;
         this.interpreter = interpreter;
         this.avrProperties = avrProperties;
     }
 
-    public void insertWatch(Watch w, int address) {
-        interpreter.getSimulator().insertWatch(w, address);
-    }
-
-    @Override
-    public int getTotalSize() {
-        return 0;
-    }
+  @Override
+  public int getTotalSize() {
+    return avrProperties.sram_size;
+  }
 
   @Override
   public byte[] getMemory() throws MoteMemoryException {
@@ -69,43 +78,147 @@ public class AvrMoteMemory implements MemoryInterface {
   }
 
   @Override
-  public byte[] getMemorySegment(long addr, int size) throws MoteMemoryException {
-    throw new UnsupportedOperationException("Not supported yet.");
+  public byte[] getMemorySegment(long address, int size) throws MoteMemoryException {
+    /*logger.info("getMemorySegment(" + String.format("0x%04x", address) +
+     ", " + size + ")");*/
+    if (!accessInRange(address, size)) {
+      throw new MoteMemoryException(
+              "Getting memory segment [0x%x,0x%x] failed: Out of range",
+              address, address + size - 1);
+    }
+
+    /* XXX Unsure whether this is the appropriate method to use, as it
+     * triggers memoryRead monitor. Right now I'm using a flag to indicate
+     * that Cooja (as opposed to Contiki) read the memory, to avoid infinite
+     * recursion. */
+    coojaIsAccessingMemory = true;
+    byte[] data = new byte[(int) size];
+    for (int i = 0; i < size; i++) {
+      data[i] = (byte) (interpreter.getDataByte((int) address + i) & 0xff);
+    }
+    coojaIsAccessingMemory = false;
+    return data;
   }
 
   @Override
-  public void setMemorySegment(long addr, byte[] data) throws MoteMemoryException {
-    throw new UnsupportedOperationException("Not supported yet.");
+  public void setMemorySegment(long address, byte[] data) throws MoteMemoryException {
+    if (!accessInRange(address, data.length)) {
+      throw new MoteMemoryException(
+              "Writing memory segment [0x%x,0x%x] failed: Out of range",
+              address, address + data.length - 1);
+    }
+
+    /* XXX See comment in getMemorySegment. */
+    coojaIsAccessingMemory = true;
+    for (int i = 0; i < data.length; i++) {
+      interpreter.writeDataByte((int) address + i, data[i]);
+    }
+    coojaIsAccessingMemory = false;
+    if (DEBUG) {
+      logger.debug(String.format(
+              "Wrote memory segment [0x%x,0x%x]",
+              address, address + data.length - 1));
+    }
   }
 
   @Override
   public void clearMemory() {
-    throw new UnsupportedOperationException("Not supported yet.");
+    setMemorySegment(0L, new byte[avrProperties.sram_size]);
+  }
+  
+  private boolean accessInRange(long address, int size) {
+    return (address >= 0) && (address + size <= avrProperties.sram_size);
   }
 
   @Override
   public long getStartAddr() {
-    throw new UnsupportedOperationException("Not supported yet.");
+    return 0;// XXX
   }
 
   @Override
   public Map<String, Symbol> getSymbolMap() {
-    throw new UnsupportedOperationException("Not supported yet.");
+    // XXX do not fetch in function!
+    Map<String, Symbol> symbols = new HashMap<>();
+    for (Iterator<Location> iter = memoryMap.getIterator(); iter.hasNext();) {
+      Location loc = iter.next();
+      if (loc == null || (loc.section.equals(".text"))) {
+        continue;
+      }
+      symbols.put(loc.name, new Symbol(Symbol.Type.VARIABLE, loc.name, loc.section, loc.vma_addr & 0x7fffff, -1));
+    }
+    return symbols;
   }
 
+
   @Override
   public MemoryLayout getLayout() {
-    throw new UnsupportedOperationException("Not supported yet.");
+    return memLayout;
+  }
+
+  class AvrByteMonitor extends Watch.Empty {
+
+    /** start address to monitor */
+    final long address;
+    /** size to monitor */
+    final int size;
+    /** Segment monitor to notify */
+    final SegmentMonitor mm;
+    /** MonitorType we are listening to */
+    final EventType flag;
+
+    public AvrByteMonitor(long address, int size, SegmentMonitor mm, EventType flag) {
+      this.address = address;
+      this.size = size;
+      this.mm = mm;
+      this.flag = flag;
+    }
+
+    @Override
+    public void fireAfterRead(State state, int data_addr, byte value) {
+      if (flag == EventType.WRITE || coojaIsAccessingMemory) {
+        return;
+      }
+      mm.memoryChanged(AvrMoteMemory.this, EventType.READ, data_addr);
+    }
+
+    @Override
+    public void fireAfterWrite(State state, int data_addr, byte value) {
+      if (flag == EventType.READ || coojaIsAccessingMemory) {
+        return;
+      }
+      mm.memoryChanged(AvrMoteMemory.this, EventType.WRITE, data_addr);
+    }
   }
 
   @Override
-  public boolean addSegmentMonitor(SegmentMonitor.EventType flag, long address, int size, SegmentMonitor monitor) {
-    throw new UnsupportedOperationException("Not supported yet.");
+  public boolean addSegmentMonitor(EventType flag, long address, int size, SegmentMonitor mm) {
+    AvrByteMonitor mon = new AvrByteMonitor(address, size, mm, flag);
+
+    memoryMonitors.add(mon);
+    /* logger.debug("Added AvrByteMonitor " + Integer.toString(mon.hashCode()) + " for addr " + mon.address + " size " + mon.size + " with watch" + mon.watch); */
+
+    /* Add byte monitor (watch) for every byte in range */
+    for (int idx = 0; idx < mon.size; idx++) {
+      interpreter.getSimulator().insertWatch(mon, (int) mon.address + idx);
+      /* logger.debug("Inserted watch " + Integer.toString(mon.watch.hashCode()) + " for " + (mon.address + idx)); */
+    }
+    return true;
   }
 
   @Override
-  public boolean removeSegmentMonitor(long address, int size, SegmentMonitor monitor) {
-    throw new UnsupportedOperationException("Not supported yet.");
+  public boolean removeSegmentMonitor(long address, int size, SegmentMonitor mm) {
+    for (AvrByteMonitor mcm : memoryMonitors) {
+      if (mcm.mm != mm || mcm.address != address || mcm.size != size) {
+        continue;
+      }
+      for (int idx = 0; idx < mcm.size; idx++) {
+        interpreter.getSimulator().removeWatch(mcm, (int) mcm.address + idx);
+        /* logger.debug("Removed watch " + Integer.toString(mcm.watch.hashCode()) + " for " + (mcm.address + idx)); */
+      }
+      memoryMonitors.remove(mcm);
+      return true;
+    }
+    return false;
   }
 
 }
diff --git a/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/MicaZMote.java b/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/MicaZMote.java
index 1c45e12ef..0819b616e 100644
--- a/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/MicaZMote.java
+++ b/tools/cooja/apps/avrora/src/org/contikios/cooja/avrmote/MicaZMote.java
@@ -43,7 +43,6 @@ import org.contikios.cooja.MoteInterfaceHandler;
 import org.contikios.cooja.MoteType;
 import org.contikios.cooja.Simulation;
 import org.contikios.cooja.mote.memory.MemoryInterface;
-import org.contikios.cooja.mote.memory.MemoryLayout;
 import org.contikios.cooja.motes.AbstractEmulatedMote;
 import avrora.arch.avr.AVRProperties;
 import avrora.core.LoadableProgram;
@@ -54,7 +53,6 @@ import avrora.sim.mcu.AtmelMicrocontroller;
 import avrora.sim.mcu.EEPROM;
 import avrora.sim.platform.MicaZ;
 import avrora.sim.platform.PlatformFactory;
-import java.nio.ByteOrder;
 
 /**
  * @author Joakim Eriksson, Fredrik Osterlind
@@ -145,7 +143,6 @@ public class MicaZMote extends AbstractEmulatedMote implements Mote {
     avrProperties = (AVRProperties) myCpu.getProperties();
     Simulator sim = myCpu.getSimulator();
     interpreter = (AtmelInterpreter) sim.getInterpreter();
-    new MemoryLayout(ByteOrder.LITTLE_ENDIAN, MemoryLayout.ARCH_8BIT, 2);
 //     State state = interpreter.getState();
     myMemory = new AvrMoteMemory(program.getProgram().getSourceMapping(), avrProperties, interpreter);
   }

From 434c4db1a24893437bc4234915108ceeb010a24e Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Wed, 23 Jul 2014 11:30:44 +0200
Subject: [PATCH 13/28] [cooja] Implementation of former MspMoteMemory dummy
 functions

---
 .../org/contikios/cooja/mspmote/MspMote.java  |   3 -
 .../cooja/mspmote/MspMoteMemory.java          | 115 ++++++++++++++----
 2 files changed, 90 insertions(+), 28 deletions(-)

diff --git a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMote.java b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMote.java
index 1b0d5be11..403376583 100644
--- a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMote.java
+++ b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMote.java
@@ -34,7 +34,6 @@ import java.awt.Component;
 import java.io.File;
 import java.io.IOException;
 import java.io.PrintStream;
-import java.nio.ByteOrder;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Hashtable;
@@ -52,7 +51,6 @@ import org.contikios.cooja.Watchpoint;
 import org.contikios.cooja.WatchpointMote;
 import org.contikios.cooja.interfaces.IPAddress;
 import org.contikios.cooja.mote.memory.MemoryInterface;
-import org.contikios.cooja.mote.memory.MemoryLayout;
 import org.contikios.cooja.motes.AbstractEmulatedMote;
 import org.contikios.cooja.mspmote.interfaces.Msp802154Radio;
 import org.contikios.cooja.mspmote.interfaces.MspSerial;
@@ -107,7 +105,6 @@ public abstract class MspMote extends AbstractEmulatedMote implements Mote, Watc
   public MspMote(MspMoteType moteType, Simulation simulation) {
     this.simulation = simulation;
     myMoteType = moteType;
-    new MemoryLayout(ByteOrder.LITTLE_ENDIAN, MemoryLayout.ARCH_16BIT, 2);
 
     /* Schedule us immediately */
     requestImmediateWakeup();
diff --git a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMoteMemory.java b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMoteMemory.java
index 16b453bf4..6e2e58c36 100644
--- a/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMoteMemory.java
+++ b/tools/cooja/apps/mspsim/src/org/contikios/cooja/mspmote/MspMoteMemory.java
@@ -1,4 +1,5 @@
 /*
+ * Copyright (c) 2014, TU Braunschweig. All rights reserved.
  * Copyright (c) 2007, Swedish Institute of Computer Science. All rights
  * reserved.
  *
@@ -28,20 +29,27 @@
 
 package org.contikios.cooja.mspmote;
 
+import java.nio.ByteOrder;
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
 import java.util.Map;
 
 import org.apache.log4j.Logger;
 
 import org.contikios.cooja.Mote;
 import org.contikios.cooja.mote.memory.MemoryInterface;
+import org.contikios.cooja.mote.memory.MemoryInterface.SegmentMonitor.EventType;
 import org.contikios.cooja.mote.memory.MemoryLayout;
 import se.sics.mspsim.core.MSP430;
+import se.sics.mspsim.core.Memory.AccessMode;
+import se.sics.mspsim.core.Memory.AccessType;
 import se.sics.mspsim.util.MapEntry;
 
 public class MspMoteMemory implements MemoryInterface {
   private static Logger logger = Logger.getLogger(MspMoteMemory.class);
   private final ArrayList<MapEntry> mapEntries;
+  private final MemoryLayout memLayout;
 
   private final MSP430 cpu;
 
@@ -55,6 +63,7 @@ public class MspMoteMemory implements MemoryInterface {
     }
 
     this.cpu = cpu;
+    memLayout = new MemoryLayout(ByteOrder.LITTLE_ENDIAN, MemoryLayout.ARCH_16BIT, 2);
   }
 
   @Override
@@ -68,55 +77,111 @@ public class MspMoteMemory implements MemoryInterface {
   }
 
   @Override
-  public byte[] getMemorySegment(long addr, int size) throws MoteMemoryException {
-    throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
+  public byte[] getMemorySegment(long address, int size) {
+    int[] memInts = new int[size];
+
+    System.arraycopy(cpu.memory, (int) address, memInts, 0, size);
+
+    /* Convert to byte array */
+    byte[] memBytes = new byte[size];
+    for (int i = 0; i < size; i++) {
+      memBytes[i] = (byte) memInts[i];
+    }
+
+    return memBytes;
   }
 
   @Override
-  public void setMemorySegment(long addr, byte[] data) throws MoteMemoryException {
-    throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
+  public void setMemorySegment(long address, byte[] data) {
+    /* Convert to int array */
+    int[] memInts = new int[data.length];
+    for (int i = 0; i < data.length; i++) {
+      memInts[i] = data[i];
+    }
+
+    System.arraycopy(memInts, 0, cpu.memory, (int) address, data.length);
   }
 
   @Override
   public void clearMemory() {
-    throw new UnsupportedOperationException("Not supported yet.");
+    Arrays.fill(cpu.memory, 0);
   }
 
   @Override
   public long getStartAddr() {
-    throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
+    return 0;// XXXX
   }
 
   @Override
   public Map<String, Symbol> getSymbolMap() {
-    throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
+    Map<String, Symbol> vars = new HashMap<>();
+    for (MapEntry entry : mapEntries) {
+      if (entry.getType() != MapEntry.TYPE.variable) {
+        continue;
+      }
+      vars.put(entry.getName(), new Symbol(
+              Symbol.Type.VARIABLE,
+              entry.getName(), 
+              entry.getAddress(), 
+              entry.getSize()));
+    }
+    return vars;
   }
 
   @Override
   public MemoryLayout getLayout() {
-    throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
+    return memLayout;
   }
 
-  @Override
-  public boolean addSegmentMonitor(SegmentMonitor.EventType flag, long address, int size, SegmentMonitor monitor) {
-    throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
-  }
+  private final ArrayList<MemoryCPUMonitor> cpuMonitorArray = new ArrayList<>();
 
-  @Override
-  public boolean removeSegmentMonitor(long address, int size, SegmentMonitor monitor) {
-    throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
-  }
+  class MemoryCPUMonitor extends se.sics.mspsim.core.MemoryMonitor.Adapter {
 
-  public int parseInt(byte[] memorySegment) {
-    if (memorySegment.length < 2) {
-      return -1;
+    public final SegmentMonitor mm;
+    public final int address;
+    public final int size;
+
+    public MemoryCPUMonitor(SegmentMonitor mm, int address, int size) {
+      this.mm = mm;
+      this.address = address;
+      this.size = size;
     }
-    
-    int retVal = 0;
-    int pos = 0;
-    retVal += ((memorySegment[pos++] & 0xFF)) << 8;
-    retVal += ((memorySegment[pos++] & 0xFF)) << 0;
 
-    return Integer.reverseBytes(retVal) >> 16;
+    @Override
+    public void notifyReadAfter(int address, AccessMode mode, AccessType type) {
+      mm.memoryChanged(MspMoteMemory.this, EventType.READ, address);
+    }
+
+    @Override
+    public void notifyWriteAfter(int dstAddress, int data, AccessMode mode) {
+      mm.memoryChanged(MspMoteMemory.this, EventType.WRITE, dstAddress);
+    }
+  }
+
+  @Override
+  public boolean addSegmentMonitor(EventType type, long address, int size, SegmentMonitor mm) {
+    MemoryCPUMonitor t = new MemoryCPUMonitor(mm, (int) address, size);
+    cpuMonitorArray.add(t);
+
+    for (int a = (int) address; a < address + size; a++) {
+      cpu.addWatchPoint(a, t);
+    }
+
+    return true;
+  }
+
+  @Override
+  public boolean removeSegmentMonitor(long address, int size, SegmentMonitor mm) {
+    for (MemoryCPUMonitor mcm : cpuMonitorArray) {
+      if (mcm.mm != mm || mcm.address != address || mcm.size != size) {
+        continue;
+      }
+      for (int a = (int) address; a < (int) address + size; a++) {
+        cpu.removeWatchPoint(a, mcm);
+      }
+      cpuMonitorArray.remove(mcm);
+      return true;
+    }
+    return false;
   }
 }

From dae92d93bbfad6e79b7f748c4a4665469d83a7e8 Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Wed, 23 Jul 2014 11:46:09 +0200
Subject: [PATCH 14/28] [cooja] ContikiMoteType: Non-functional indention and
 code style updates

---
 .../cooja/contikimote/ContikiMoteType.java    | 465 +++++++++---------
 1 file changed, 235 insertions(+), 230 deletions(-)

diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
index 6d58d2d6a..6ad0b9da5 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
@@ -27,7 +27,6 @@
  * SUCH DAMAGE.
  *
  */
-
 package org.contikios.cooja.contikimote;
 
 import java.awt.Container;
@@ -41,6 +40,7 @@ import java.lang.reflect.Method;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.Random;
@@ -93,7 +93,8 @@ import org.contikios.cooja.util.StringUtils;
 @ClassDescription("Cooja mote")
 @AbstractionLevelDescription("OS level")
 public class ContikiMoteType implements MoteType {
-  private static Logger logger = Logger.getLogger(ContikiMoteType.class);
+
+  private static final Logger logger = Logger.getLogger(ContikiMoteType.class);
 
   public static final String ID_PREFIX = "mtype";
 
@@ -121,6 +122,7 @@ public class ContikiMoteType implements MoteType {
    * Communication stacks in Contiki.
    */
   public enum NetworkStack {
+
     DEFAULT, MANUAL;
     public String manualHeader = "netstack-conf-example.h";
 
@@ -167,7 +169,7 @@ public class ContikiMoteType implements MoteType {
     }
   }
 
-  private final String[] sensors = { "button_sensor", "pir_sensor", "vib_sensor" };
+  private final String[] sensors = {"button_sensor", "pir_sensor", "vib_sensor"};
 
   private String identifier = null;
   private String description = null;
@@ -177,10 +179,15 @@ public class ContikiMoteType implements MoteType {
 
   /* For internal use only: using during Contiki compilation. */
   private File contikiApp = null; /* Contiki application: hello-world.c */
+
   public File libSource = null; /* JNI library: obj_cooja/mtype1.c */
+
   public File libFile = null; /* JNI library: obj_cooja/mtype1.lib */
+
   public File archiveFile = null; /* Contiki archive: obj_cooja/mtype1.a */
+
   public File mapFile = null; /* Contiki map: obj_cooja/mtype1.map */
+
   public String javaClassName = null; /* Loading Java class name: Lib1 */
 
   private String[] coreInterfaces = null;
@@ -213,18 +220,18 @@ public class ContikiMoteType implements MoteType {
 
   @Override
   public boolean configureAndInit(Container parentContainer, Simulation simulation,
-      boolean visAvailable) throws MoteTypeCreationException {
+                                  boolean visAvailable) throws MoteTypeCreationException {
     myConfig = simulation.getCooja().getProjectConfig().clone();
 
     if (visAvailable) {
 
       if (getDescription() == null) {
-        setDescription("Cooja Mote Type #" + (simulation.getMoteTypes().length+1));
+        setDescription("Cooja Mote Type #" + (simulation.getMoteTypes().length + 1));
       }
 
       /* Compile Contiki from dialog */
-      boolean compileOK =
-        ContikiMoteCompileDialog.showDialog(parentContainer, simulation, this);
+      boolean compileOK
+              = ContikiMoteCompileDialog.showDialog(parentContainer, simulation, this);
       if (!compileOK) {
         return false;
       }
@@ -240,17 +247,17 @@ public class ContikiMoteType implements MoteType {
       /* Create variables used for compiling Contiki */
       contikiApp = getContikiSourceFile();
       libSource = new File(
-          contikiApp.getParentFile(),
-          "obj_cooja/" + getIdentifier() + ".c");
+              contikiApp.getParentFile(),
+              "obj_cooja/" + getIdentifier() + ".c");
       libFile = new File(
-          contikiApp.getParentFile(),
-          "obj_cooja/" + getIdentifier() + librarySuffix);
+              contikiApp.getParentFile(),
+              "obj_cooja/" + getIdentifier() + librarySuffix);
       archiveFile = new File(
-          contikiApp.getParentFile(),
-          "obj_cooja/" + getIdentifier() + dependSuffix);
+              contikiApp.getParentFile(),
+              "obj_cooja/" + getIdentifier() + dependSuffix);
       mapFile = new File(
-          contikiApp.getParentFile(),
-          "obj_cooja/" + getIdentifier() + mapSuffix);
+              contikiApp.getParentFile(),
+              "obj_cooja/" + getIdentifier() + mapSuffix);
       javaClassName = CoreComm.getAvailableClassName();
 
       if (javaClassName == null) {
@@ -265,37 +272,36 @@ public class ContikiMoteType implements MoteType {
 
       /* Generate Contiki main source */
       /*try {
-        CompileContiki.generateSourceFile(
-            libSource,
-            javaClassName,
-            getSensors(),
-            getCoreInterfaces()
-        );
-      } catch (Exception e) {
-        throw (MoteTypeCreationException) new MoteTypeCreationException(
-        "Error when generating Contiki main source").initCause(e);
-      }*/
+       CompileContiki.generateSourceFile(
+       libSource,
+       javaClassName,
+       getSensors(),
+       getCoreInterfaces()
+       );
+       } catch (Exception e) {
+       throw (MoteTypeCreationException) new MoteTypeCreationException(
+       "Error when generating Contiki main source").initCause(e);
+       }*/
 
       /* Prepare compiler environment */
       String[][] env;
       try {
         env = CompileContiki.createCompilationEnvironment(
-            getIdentifier(),
-            contikiApp,
-            mapFile,
-            libFile,
-            archiveFile,
-            javaClassName);
+                getIdentifier(),
+                contikiApp,
+                mapFile,
+                libFile,
+                archiveFile,
+                javaClassName);
         CompileContiki.redefineCOOJASources(
-        		this,
-        		env
+                this,
+                env
         );
       } catch (Exception e) {
-        throw (MoteTypeCreationException) new MoteTypeCreationException(
-            "Error when creating environment: " + e.getMessage()).initCause(e);
+        throw new MoteTypeCreationException("Error when creating environment: " + e.getMessage(), e);
       }
       String[] envOneDimension = new String[env.length];
-      for (int i=0; i < env.length; i++) {
+      for (int i = 0; i < env.length; i++) {
         envOneDimension[i] = env[i][0] + "=" + env[i][1];
       }
 
@@ -305,31 +311,31 @@ public class ContikiMoteType implements MoteType {
       }
       final MessageList compilationOutput = new MessageList();
       String[] arr = getCompileCommands().split("\n");
-      for (String cmd: arr) {
+      for (String cmd : arr) {
         if (cmd.trim().isEmpty()) {
           continue;
         }
 
         try {
           CompileContiki.compile(
-              cmd,
-              envOneDimension,
-              null /* Do not observe output firmware file */,
-              getContikiSourceFile().getParentFile(),
-              null,
-              null,
-              compilationOutput,
-              true
+                  cmd,
+                  envOneDimension,
+                  null /* Do not observe output firmware file */,
+                  getContikiSourceFile().getParentFile(),
+                  null,
+                  null,
+                  compilationOutput,
+                  true
           );
         } catch (Exception e) {
-          MoteTypeCreationException newException =
-            new MoteTypeCreationException("Mote type creation failed: " + e.getMessage());
+          MoteTypeCreationException newException
+                  = new MoteTypeCreationException("Mote type creation failed: " + e.getMessage());
           newException = (MoteTypeCreationException) newException.initCause(e);
           newException.setCompilationOutput(compilationOutput);
 
           /* Print last 10 compilation errors to console */
           MessageContainer[] messages = compilationOutput.getMessages();
-          for (int i=messages.length-10; i < messages.length; i++) {
+          for (int i = messages.length - 10; i < messages.length; i++) {
             if (i < 0) {
               continue;
             }
@@ -342,8 +348,8 @@ public class ContikiMoteType implements MoteType {
       }
 
       /* Make sure compiled firmware exists */
-      if (getContikiFirmwareFile() == null ||
-          !getContikiFirmwareFile().exists()) {
+      if (getContikiFirmwareFile() == null
+              || !getContikiFirmwareFile().exists()) {
         throw new MoteTypeCreationException("Contiki firmware file does not exist: " + getContikiFirmwareFile());
       }
     }
@@ -355,7 +361,7 @@ public class ContikiMoteType implements MoteType {
 
   public static File getExpectedFirmwareFile(File source) {
     File parentDir = source.getParentFile();
-    String sourceNoExtension = source.getName().substring(0, source.getName().length()-2);
+    String sourceNoExtension = source.getName().substring(0, source.getName().length() - 2);
 
     return new File(parentDir, sourceNoExtension + librarySuffix);
   }
@@ -363,8 +369,10 @@ public class ContikiMoteType implements MoteType {
   /**
    * For internal use.
    *
-   * This method creates a core communicator linking a Contiki library and a Java class.
-   * It furthermore parses library Contiki memory addresses and creates the initial memory.
+   * This method creates a core communicator linking a Contiki library and a
+   * Java class.
+   * It furthermore parses library Contiki memory addresses and creates the
+   * initial memory.
    *
    * @throws MoteTypeCreationException
    */
@@ -372,11 +380,11 @@ public class ContikiMoteType implements MoteType {
 
     if (myCoreComm != null) {
       throw new MoteTypeCreationException(
-          "Core communicator already used: " + myCoreComm.getClass().getName());
+              "Core communicator already used: " + myCoreComm.getClass().getName());
     }
 
-    if (getContikiFirmwareFile() == null ||
-        !getContikiFirmwareFile().exists()) {
+    if (getContikiFirmwareFile() == null
+            || !getContikiFirmwareFile().exists()) {
       throw new MoteTypeCreationException("Library file could not be found: " + getContikiFirmwareFile());
     }
 
@@ -426,8 +434,8 @@ public class ContikiMoteType implements MoteType {
 
     } else {
       /* Parse command output */
-      if (mapFile == null ||
-          !mapFile.exists()) {
+      if (mapFile == null
+              || !mapFile.exists()) {
         throw new MoteTypeCreationException("Map file " + mapFile + " could not be found");
       }
       String[] mapData = loadMapFile(mapFile);
@@ -453,38 +461,38 @@ public class ContikiMoteType implements MoteType {
     }
 
     if (dataSectionAddr >= 0) {
-      logger.info(getContikiFirmwareFile().getName() +
-          ": data section at 0x" + Integer.toHexString(dataSectionAddr) +
-          " (" + dataSectionSize + " == 0x" + Integer.toHexString(dataSectionSize) + " bytes)");
+      logger.info(getContikiFirmwareFile().getName()
+              + ": data section at 0x" + Integer.toHexString(dataSectionAddr)
+              + " (" + dataSectionSize + " == 0x" + Integer.toHexString(dataSectionSize) + " bytes)");
     } else {
       logger.fatal(getContikiFirmwareFile().getName() + ": no data section found");
     }
     if (bssSectionAddr >= 0) {
-      logger.info(getContikiFirmwareFile().getName() +
-          ": BSS section at 0x" + Integer.toHexString(bssSectionAddr) +
-          " (" + bssSectionSize + " == 0x" + Integer.toHexString(bssSectionSize) + " bytes)");
+      logger.info(getContikiFirmwareFile().getName()
+              + ": BSS section at 0x" + Integer.toHexString(bssSectionAddr)
+              + " (" + bssSectionSize + " == 0x" + Integer.toHexString(bssSectionSize) + " bytes)");
     } else {
       logger.fatal(getContikiFirmwareFile().getName() + ": no BSS section found");
     }
     if (commonSectionAddr >= 0) {
-      logger.info(getContikiFirmwareFile().getName() +
-          ": common section at 0x" + Integer.toHexString(commonSectionAddr) +
-          " (" + commonSectionSize + " == 0x" + Integer.toHexString(commonSectionSize) + " bytes)");
+      logger.info(getContikiFirmwareFile().getName()
+              + ": common section at 0x" + Integer.toHexString(commonSectionAddr)
+              + " (" + commonSectionSize + " == 0x" + Integer.toHexString(commonSectionSize) + " bytes)");
     } else {
       logger.info(getContikiFirmwareFile().getName() + ": no common section found");
     }
     if (readonlySectionAddr >= 0) {
-      logger.info(getContikiFirmwareFile().getName() +
-          ": readonly section at 0x" + Integer.toHexString(readonlySectionAddr) +
-          " (" + readonlySectionSize + " == 0x" + Integer.toHexString(readonlySectionSize) + " bytes)");
+      logger.info(getContikiFirmwareFile().getName()
+              + ": readonly section at 0x" + Integer.toHexString(readonlySectionAddr)
+              + " (" + readonlySectionSize + " == 0x" + Integer.toHexString(readonlySectionSize) + " bytes)");
     } else {
       logger.warn(getContikiFirmwareFile().getName() + ": no readonly section found");
     }
-    if (addresses.size() == 0) {
+    if (addresses.isEmpty()) {
       throw new MoteTypeCreationException("Library variables parsing failed");
     }
     if (dataSectionAddr <= 0 || dataSectionSize <= 0
-        || bssSectionAddr <= 0 || bssSectionSize <= 0) {
+            || bssSectionAddr <= 0 || bssSectionSize <= 0) {
       throw new MoteTypeCreationException("Library section addresses parsing failed");
     }
 
@@ -493,8 +501,7 @@ public class ContikiMoteType implements MoteType {
       int referenceVar = addresses.get("referenceVar");
       myCoreComm.setReferenceAddress(referenceVar);
     } catch (Exception e) {
-      throw (MoteTypeCreationException) new MoteTypeCreationException(
-          "JNI call error: " + e.getMessage()).initCause(e);
+      throw new MoteTypeCreationException("JNI call error: " + e.getMessage(), e);
     }
 
     /* We first need the value of Contiki's referenceVar, which tells us the
@@ -515,8 +522,8 @@ public class ContikiMoteType implements MoteType {
       tmp.setMemorySegment(bssSectionAddr, bss);
 
       offset = varMem.getIntValueOf("referenceVar");
-      logger.info(getContikiFirmwareFile().getName() +
-          ": offsetting Cooja mote address space: " + offset);
+      logger.info(getContikiFirmwareFile().getName()
+              + ": offsetting Cooja mote address space: " + offset);
     }
 
     /* Create initial memory: data+bss+optional common */
@@ -540,7 +547,7 @@ public class ContikiMoteType implements MoteType {
     if (readonlySectionAddr >= 0 && readonlySectionSize > 0) {
       byte[] readonlySection = new byte[readonlySectionSize];
       getCoreMemory(readonlySectionAddr, readonlySectionSize, readonlySection);
-      initialMemory.setReadonlyMemorySegment(readonlySectionAddr+offset, readonlySection);
+      initialMemory.setReadonlyMemorySegment(readonlySectionAddr + offset, readonlySection);
     }
   }
 
@@ -568,13 +575,13 @@ public class ContikiMoteType implements MoteType {
    * but instead via ContikiMote.setMemory().
    *
    * @param mem
-   *          New memory
+   * New memory
    */
   public void setCoreMemory(SectionMoteMemory mem) {
     for (int i = 0; i < mem.getNumberOfSections(); i++) {
       setCoreMemory(
-          mem.getSectionNativeAddress(i) /* native address space */,
-          mem.getSizeOfSection(i), mem.getDataOfSection(i));
+              mem.getSectionNativeAddress(i) /* native address space */,
+              mem.getSizeOfSection(i), mem.getDataOfSection(i));
     }
   }
 
@@ -583,9 +590,9 @@ public class ContikiMoteType implements MoteType {
    * mappings are added to the given properties object.
    *
    * @param mapFileData
-   *          Contents of entire map file
+   * Contents of entire map file
    * @param varAddresses
-   *          Properties that should contain the name to addresses mappings.
+   * Properties that should contain the name to addresses mappings.
    */
   public static boolean parseMapFileData(String[] mapFileData, HashMap<String, Integer> varAddresses) {
     String[] varNames = getMapFileVarNames(mapFileData);
@@ -599,7 +606,7 @@ public class ContikiMoteType implements MoteType {
         varAddresses.put(varName, new Integer(varAddress));
       } else {
         logger.warn("Parsed Contiki variable '" + varName
-            + "' but could not find address");
+                + "' but could not find address");
       }
     }
 
@@ -616,8 +623,8 @@ public class ContikiMoteType implements MoteType {
   public static boolean parseCommandData(String[] output, HashMap<String, Integer> addresses) {
     int nrNew = 0, nrOld = 0, nrMismatch = 0;
 
-    Pattern pattern =
-      Pattern.compile(Cooja.getExternalToolsSetting("COMMAND_VAR_NAME_ADDRESS"));
+    Pattern pattern
+            = Pattern.compile(Cooja.getExternalToolsSetting("COMMAND_VAR_NAME_ADDRESS"));
 
     for (String line : output) {
       Matcher matcher = pattern.matcher(line);
@@ -634,7 +641,7 @@ public class ContikiMoteType implements MoteType {
           int oldAddress = addresses.get(symbol);
           if (oldAddress != address) {
             /*logger.warn("Warning, command response not matching previous entry of: "
-                + varName);*/
+             + varName);*/
             nrMismatch++;
           }
           nrOld++;
@@ -643,14 +650,13 @@ public class ContikiMoteType implements MoteType {
     }
 
     /*if (nrMismatch > 0) {
-      logger.debug("Command response parsing summary: Added " + nrNew
-          + " variables. Found " + nrOld
-          + " old variables. Mismatching addresses: " + nrMismatch);
-    } else {
-      logger.debug("Command response parsing summary: Added " + nrNew
-          + " variables. Found " + nrOld + " old variables");
-    }*/
-
+     logger.debug("Command response parsing summary: Added " + nrNew
+     + " variables. Found " + nrOld
+     + " old variables. Mismatching addresses: " + nrMismatch);
+     } else {
+     logger.debug("Command response parsing summary: Added " + nrNew
+     + " variables. Found " + nrOld + " old variables");
+     }*/
     return (nrNew + nrOld) > 0;
   }
 
@@ -659,11 +665,12 @@ public class ContikiMoteType implements MoteType {
    * instead via ContikiMote.getMemory().
    *
    * @param mem
-   *          Memory to set
+   * Memory to set
    */
   public void getCoreMemory(SectionMoteMemory mem) {
     for (int i = 0; i < mem.getNumberOfSections(); i++) {
       int startAddr = mem.getSectionNativeAddress(i); /* native address space */
+
       int size = mem.getSizeOfSection(i);
       byte[] data = mem.getDataOfSection(i);
       getCoreMemory(startAddr, size, data);
@@ -750,10 +757,10 @@ public class ContikiMoteType implements MoteType {
       return varAddrInteger.intValue();
     }
 
-    String regExp =
-      Cooja.getExternalToolsSetting("MAPFILE_VAR_ADDRESS_1") +
-      varName +
-      Cooja.getExternalToolsSetting("MAPFILE_VAR_ADDRESS_2");
+    String regExp
+            = Cooja.getExternalToolsSetting("MAPFILE_VAR_ADDRESS_1")
+            + varName
+            + Cooja.getExternalToolsSetting("MAPFILE_VAR_ADDRESS_2");
     String retString = getFirstMatchGroup(mapFileData, regExp, 1);
 
     if (retString != null) {
@@ -792,37 +799,35 @@ public class ContikiMoteType implements MoteType {
    * @return Variable names found in the data and bss section
    */
   public static String[] getMapFileVarNames(String[] mapFileData) {
-    ArrayList<String> varNames = new ArrayList<String>();
+    ArrayList<String> varNames = new ArrayList<>();
 
     String[] dataVariables = getAllVariableNames(
-        mapFileData,
-        parseMapDataSectionAddr(mapFileData),
-        parseMapDataSectionAddr(mapFileData) + parseMapDataSectionSize(mapFileData));
-    for (String v: dataVariables) {
+            mapFileData,
+            parseMapDataSectionAddr(mapFileData),
+            parseMapDataSectionAddr(mapFileData) + parseMapDataSectionSize(mapFileData));
+    for (String v : dataVariables) {
       varNames.add(v);
     }
 
     String[] bssVariables = getAllVariableNames(
-        mapFileData,
-        parseMapBssSectionAddr(mapFileData),
-        parseMapBssSectionAddr(mapFileData) + parseMapBssSectionSize(mapFileData));
-    for (String v: bssVariables) {
-      varNames.add(v);
-    }
+            mapFileData,
+            parseMapBssSectionAddr(mapFileData),
+            parseMapBssSectionAddr(mapFileData) + parseMapBssSectionSize(mapFileData));
+    varNames.addAll(Arrays.asList(bssVariables));
 
     return varNames.toArray(new String[0]);
   }
 
   private static String[] getAllVariableNames(String[] lines,
-      int startAddress, int endAddress) {
-    ArrayList<String> varNames = new ArrayList<String>();
+                                              int startAddress, int endAddress) {
+    ArrayList<String> varNames = new ArrayList<>();
 
     Pattern pattern = Pattern.compile(Cooja.getExternalToolsSetting("MAPFILE_VAR_NAME"));
     for (String line : lines) {
       Matcher matcher = pattern.matcher(line);
       if (matcher.find()) {
         if (Integer.decode(matcher.group(1)).intValue() >= startAddress
-            && Integer.decode(matcher.group(1)).intValue() <= endAddress) {
+                && Integer.decode(matcher.group(1)).intValue() <= endAddress) {
           varNames.add(matcher.group(2));
         }
       }
@@ -832,9 +837,9 @@ public class ContikiMoteType implements MoteType {
 
   protected int getVariableSize(Vector<String> lines, String varName) {
     Pattern pattern = Pattern.compile(
-        Cooja.getExternalToolsSetting("MAPFILE_VAR_SIZE_1") +
-        varName +
-        Cooja.getExternalToolsSetting("MAPFILE_VAR_SIZE_2"));
+            Cooja.getExternalToolsSetting("MAPFILE_VAR_SIZE_1")
+            + varName
+            + Cooja.getExternalToolsSetting("MAPFILE_VAR_SIZE_2"));
     for (int i = 0; i < lines.size(); i++) {
       Matcher matcher = pattern.matcher(lines.get(i));
       if (matcher.find()) {
@@ -845,8 +850,8 @@ public class ContikiMoteType implements MoteType {
   }
 
   private static int parseFirstHexInt(String regexp, String[] data) {
-    String retString =
-      getFirstMatchGroup(data, regexp, 1);
+    String retString
+            = getFirstMatchGroup(data, regexp, 1);
 
     if (retString != null) {
       return Integer.parseInt(retString.trim(), 16);
@@ -862,6 +867,7 @@ public class ContikiMoteType implements MoteType {
     }
     return parseFirstHexInt(regexp, mapFileData);
   }
+
   public static int parseMapDataSectionSize(String[] mapFileData) {
     String regexp = Cooja.getExternalToolsSetting("MAPFILE_DATA_SIZE", "");
     if (regexp.equals("")) {
@@ -869,6 +875,7 @@ public class ContikiMoteType implements MoteType {
     }
     return parseFirstHexInt(regexp, mapFileData);
   }
+
   public static int parseMapBssSectionAddr(String[] mapFileData) {
     String regexp = Cooja.getExternalToolsSetting("MAPFILE_BSS_START", "");
     if (regexp.equals("")) {
@@ -876,6 +883,7 @@ public class ContikiMoteType implements MoteType {
     }
     return parseFirstHexInt(regexp, mapFileData);
   }
+
   public static int parseMapBssSectionSize(String[] mapFileData) {
     String regexp = Cooja.getExternalToolsSetting("MAPFILE_BSS_SIZE", "");
     if (regexp.equals("")) {
@@ -883,6 +891,7 @@ public class ContikiMoteType implements MoteType {
     }
     return parseFirstHexInt(regexp, mapFileData);
   }
+
   public static int parseMapCommonSectionAddr(String[] mapFileData) {
     String regexp = Cooja.getExternalToolsSetting("MAPFILE_COMMON_START", "");
     if (regexp.equals("")) {
@@ -890,6 +899,7 @@ public class ContikiMoteType implements MoteType {
     }
     return parseFirstHexInt(regexp, mapFileData);
   }
+
   public static int parseMapCommonSectionSize(String[] mapFileData) {
     String regexp = Cooja.getExternalToolsSetting("MAPFILE_COMMON_SIZE", "");
     if (regexp.equals("")) {
@@ -905,6 +915,7 @@ public class ContikiMoteType implements MoteType {
     }
     return parseFirstHexInt(regexp, output);
   }
+
   public static int parseCommandDataSectionSize(String[] output) {
     String regexp = Cooja.getExternalToolsSetting("COMMAND_DATA_END", "");
     if (regexp.equals("")) {
@@ -921,6 +932,7 @@ public class ContikiMoteType implements MoteType {
     }
     return end - start;
   }
+
   public static int parseCommandBssSectionAddr(String[] output) {
     String regexp = Cooja.getExternalToolsSetting("COMMAND_BSS_START", "");
     if (regexp.equals("")) {
@@ -928,6 +940,7 @@ public class ContikiMoteType implements MoteType {
     }
     return parseFirstHexInt(regexp, output);
   }
+
   public static int parseCommandBssSectionSize(String[] output) {
     String regexp = Cooja.getExternalToolsSetting("COMMAND_BSS_END", "");
     if (regexp.equals("")) {
@@ -944,6 +957,7 @@ public class ContikiMoteType implements MoteType {
     }
     return end - start;
   }
+
   public static int parseCommandCommonSectionAddr(String[] output) {
     String regexp = Cooja.getExternalToolsSetting("COMMAND_COMMON_START", "");
     if (regexp.equals("")) {
@@ -951,6 +965,7 @@ public class ContikiMoteType implements MoteType {
     }
     return parseFirstHexInt(regexp, output);
   }
+
   public static int parseCommandCommonSectionSize(String[] output) {
     String regexp = Cooja.getExternalToolsSetting("COMMAND_COMMON_END", "");
     if (regexp.equals("")) {
@@ -971,6 +986,7 @@ public class ContikiMoteType implements MoteType {
   private static int parseCommandReadonlySectionAddr(String[] output) {
     return parseFirstHexInt("^([0-9A-Fa-f]*)[ \t]t[ \t].text$", output);
   }
+
   private static int parseCommandReadonlySectionSize(String[] output) {
     int start = parseCommandReadonlySectionAddr(output);
     if (start < 0) {
@@ -978,16 +994,16 @@ public class ContikiMoteType implements MoteType {
     }
 
     /* Extract the last specified address, assuming that the interval covers all the memory */
-    String last  = output[output.length-1];
-    int lastAddress = Integer.parseInt(last.split("[ \t]")[0],16);
+    String last = output[output.length - 1];
+    int lastAddress = Integer.parseInt(last.split("[ \t]")[0], 16);
     return lastAddress - start;
   }
 
   private static int getRelVarAddr(String mapFileData[], String varName) {
-    String regExp =
-      Cooja.getExternalToolsSetting("MAPFILE_VAR_ADDRESS_1") +
-      varName +
-      Cooja.getExternalToolsSetting("MAPFILE_VAR_ADDRESS_2");
+    String regExp
+            = Cooja.getExternalToolsSetting("MAPFILE_VAR_ADDRESS_1")
+            + varName
+            + Cooja.getExternalToolsSetting("MAPFILE_VAR_ADDRESS_2");
     String retString = getFirstMatchGroup(mapFileData, regExp, 1);
 
     if (retString != null) {
@@ -1012,7 +1028,7 @@ public class ContikiMoteType implements MoteType {
    * @return Execution response, or null at failure
    */
   public static String[] loadCommandData(File libraryFile) {
-    ArrayList<String> output = new ArrayList<String>();
+    ArrayList<String> output = new ArrayList<>();
 
     try {
       String command = Cooja.getExternalToolsSetting("PARSE_COMMAND");
@@ -1022,17 +1038,17 @@ public class ContikiMoteType implements MoteType {
 
       /* Prepare command */
       command = command.replace("$(LIBFILE)",
-          libraryFile.getName().replace(File.separatorChar, '/'));
+                                libraryFile.getName().replace(File.separatorChar, '/'));
 
       /* Execute command, read response */
       String line;
       Process p = Runtime.getRuntime().exec(
-          command.split(" "),
-          null,
-          libraryFile.getParentFile()
+              command.split(" "),
+              null,
+              libraryFile.getParentFile()
       );
       BufferedReader input = new BufferedReader(
-          new InputStreamReader(p.getInputStream())
+              new InputStreamReader(p.getInputStream())
       );
       p.getErrorStream().close();
       while ((line = input.readLine()) != null) {
@@ -1040,11 +1056,11 @@ public class ContikiMoteType implements MoteType {
       }
       input.close();
 
-      if (output == null || output.size() == 0) {
+      if (output == null || output.isEmpty()) {
         return null;
       }
       return output.toArray(new String[0]);
-    } catch (Exception err) {
+    } catch (IOException err) {
       logger.fatal("Command error: " + err.getMessage(), err);
       return null;
     }
@@ -1070,7 +1086,7 @@ public class ContikiMoteType implements MoteType {
    * simulator project configuration.
    *
    * @param moteTypeConfig
-   *          Project configuration
+   * Project configuration
    */
   public void setConfig(ProjectConfig moteTypeConfig) {
     myConfig = moteTypeConfig;
@@ -1098,7 +1114,7 @@ public class ContikiMoteType implements MoteType {
    * Set core interfaces
    *
    * @param coreInterfaces
-   *          New core interfaces
+   * New core interfaces
    */
   public void setCoreInterfaces(String[] coreInterfaces) {
     this.coreInterfaces = coreInterfaces;
@@ -1116,10 +1132,8 @@ public class ContikiMoteType implements MoteType {
 
   @Override
   public void setMoteInterfaceClasses(Class<? extends MoteInterface>[] moteInterfaces) {
-    this.moteInterfacesClasses = new ArrayList<Class<? extends MoteInterface>>();
-    for (Class<? extends MoteInterface> intf: moteInterfaces) {
-      this.moteInterfacesClasses.add(intf);
-    }
+    this.moteInterfacesClasses = new ArrayList<>();
+    this.moteInterfacesClasses.addAll(Arrays.asList(moteInterfaces));
   }
 
   /**
@@ -1127,7 +1141,7 @@ public class ContikiMoteType implements MoteType {
    * when loading a saved simulation.
    *
    * @param file
-   *          File containg data to checksum
+   * File containg data to checksum
    * @return Checksum
    */
   protected byte[] createChecksum(File file) {
@@ -1146,9 +1160,7 @@ public class ContikiMoteType implements MoteType {
         }
       }
       fileInputStream.close();
-    } catch (NoSuchAlgorithmException e) {
-      return null;
-    } catch (IOException e) {
+    } catch (NoSuchAlgorithmException | IOException e) {
       return null;
     }
     return messageDigest.digest();
@@ -1195,8 +1207,8 @@ public class ContikiMoteType implements MoteType {
       // Check if identifier library has been loaded
       /* XXX Currently only checks the build directory! */
       File libraryFile = new File(
-          ContikiMoteType.tempOutputDirectory,
-          testID + ContikiMoteType.librarySuffix);
+              ContikiMoteType.tempOutputDirectory,
+              testID + ContikiMoteType.librarySuffix);
       if (libraryFile.exists() || CoreComm.hasLibraryFileBeenLoaded(libraryFile)) {
         okID = false;
       }
@@ -1215,41 +1227,41 @@ public class ContikiMoteType implements MoteType {
     StringBuilder sb = new StringBuilder();
     // Identifier
     sb.append("<html><table><tr><td>Identifier</td><td>")
-    .append(getIdentifier()).append("</td></tr>");
+            .append(getIdentifier()).append("</td></tr>");
 
     // Description
     sb.append("<tr><td>Description</td><td>")
-    .append(getDescription()).append("</td></tr>");
+            .append(getDescription()).append("</td></tr>");
 
     /* Contiki application */
     sb.append("<tr><td>Contiki application</td><td>")
-    .append(getContikiSourceFile().getAbsolutePath()).append("</td></tr>");
+            .append(getContikiSourceFile().getAbsolutePath()).append("</td></tr>");
 
     /* Contiki firmware */
     sb.append("<tr><td>Contiki firmware</td><td>")
-    .append(getContikiFirmwareFile().getAbsolutePath()).append("</td></tr>");
+            .append(getContikiFirmwareFile().getAbsolutePath()).append("</td></tr>");
 
     /* JNI class */
     sb.append("<tr><td>JNI library</td><td>")
-    .append(this.javaClassName).append("</td></tr>");
+            .append(this.javaClassName).append("</td></tr>");
 
     /* Contiki sensors */
     sb.append("<tr><td valign=\"top\">Contiki sensors</td><td>");
-    for (String sensor: sensors) {
+    for (String sensor : sensors) {
       sb.append(sensor).append("<br>");
     }
     sb.append("</td></tr>");
 
     /* Mote interfaces */
     sb.append("<tr><td valign=\"top\">Mote interface</td><td>");
-    for (Class<? extends MoteInterface> moteInterface: moteInterfacesClasses) {
+    for (Class<? extends MoteInterface> moteInterface : moteInterfacesClasses) {
       sb.append(moteInterface.getSimpleName()).append("<br>");
     }
     sb.append("</td></tr>");
 
     /* Contiki core mote interfaces */
     sb.append("<tr><td valign=\"top\">Contiki's mote interface</td><td>");
-    for (String coreInterface: getCoreInterfaces()) {
+    for (String coreInterface : getCoreInterfaces()) {
       sb.append(coreInterface).append("<br>");
     }
     sb.append("</td></tr>");
@@ -1261,7 +1273,7 @@ public class ContikiMoteType implements MoteType {
 
   @Override
   public Collection<Element> getConfigXML(Simulation simulation) {
-    ArrayList<Element> config = new ArrayList<Element>();
+    ArrayList<Element> config = new ArrayList<>();
     Element element;
 
     element = new Element("identifier");
@@ -1302,8 +1314,8 @@ public class ContikiMoteType implements MoteType {
 
   @Override
   public boolean setConfigXML(Simulation simulation,
-      Collection<Element> configXML, boolean visAvailable)
-  throws MoteTypeCreationException {
+                              Collection<Element> configXML, boolean visAvailable)
+          throws MoteTypeCreationException {
     boolean warnedOldVersion = false;
     File oldVersionSource = null;
 
@@ -1311,91 +1323,87 @@ public class ContikiMoteType implements MoteType {
 
     for (Element element : configXML) {
       String name = element.getName();
-
-      if (name.equals("identifier")) {
-        identifier = element.getText();
-      } else if (name.equals("description")) {
-        description = element.getText();
-      } else if (name.equals("contikiapp") || name.equals("source")) {
-        File file = new File(element.getText());
-        if (!file.exists()) {
-          file = simulation.getCooja().restorePortablePath(file);
-        }
-
-        setContikiSourceFile(file);
-
-        /* XXX Do not load the generated firmware. Instead, load the unique library file directly */
+      switch (name) {
+        case "identifier":
+          identifier = element.getText();
+          break;
+        case "description":
+          description = element.getText();
+          break;
+        case "contikiapp":
+        case "source":
+          File file = new File(element.getText());
+          if (!file.exists()) {
+            file = simulation.getCooja().restorePortablePath(file);
+          } setContikiSourceFile(file);
+          /* XXX Do not load the generated firmware. Instead, load the unique library file directly */
         File contikiFirmware = new File(
-            getContikiSourceFile().getParentFile(),
-            "obj_cooja/" + getIdentifier() + librarySuffix);
-        setContikiFirmwareFile(contikiFirmware);
-
-      } else if (name.equals("commands")) {
-        compileCommands = element.getText();
-      } else if (name.equals("symbols")) {
-        hasSystemSymbols = Boolean.parseBoolean(element.getText());
-      } else if (name.equals("commstack")) {
-        logger.warn("The Cooja communication stack config was removed: " + element.getText());
-        logger.warn("Instead assuming default network stack.");
-        netStack = NetworkStack.DEFAULT;
-      } else if (name.equals("netstack")) {
-        netStack = NetworkStack.parseConfig(element.getText());
-      } else if (name.equals("moteinterface")) {
-        String intfClass = element.getText().trim();
-
-        /* Backwards compatibility: se.sics -> org.contikios */
-        if (intfClass.startsWith("se.sics")) {
-          intfClass = intfClass.replaceFirst("se\\.sics", "org.contikios");
-        }
-
-        Class<? extends MoteInterface> moteInterfaceClass =
-          simulation.getCooja().tryLoadClass(
-              this, MoteInterface.class, intfClass);
-
+                getContikiSourceFile().getParentFile(),
+                "obj_cooja/" + getIdentifier() + librarySuffix);
+          setContikiFirmwareFile(contikiFirmware);
+          break;
+        case "commands":
+          compileCommands = element.getText();
+          break;
+        case "symbols":
+          hasSystemSymbols = Boolean.parseBoolean(element.getText());
+          break;
+        case "commstack":
+          logger.warn("The Cooja communication stack config was removed: " + element.getText());
+          logger.warn("Instead assuming default network stack.");
+          netStack = NetworkStack.DEFAULT;
+          break;
+        case "netstack":
+          netStack = NetworkStack.parseConfig(element.getText());
+          break;
+        case "moteinterface":
+          String intfClass = element.getText().trim();
+          /* Backwards compatibility: se.sics -> org.contikios */
+          if (intfClass.startsWith("se.sics")) {
+            intfClass = intfClass.replaceFirst("se\\.sics", "org.contikios");
+          } Class<? extends MoteInterface> moteInterfaceClass
+                = simulation.getCooja().tryLoadClass(
+                        this, MoteInterface.class, intfClass);
         if (moteInterfaceClass == null) {
           logger.warn("Can't find mote interface class: " + intfClass);
         } else {
           moteInterfacesClasses.add(moteInterfaceClass);
-        }
-      } else if (
-          name.equals("contikibasedir") ||
-          name.equals("contikicoredir") ||
-          name.equals("projectdir") ||
-          name.equals("compilefile") ||
-          name.equals("process") ||
-          name.equals("sensor") ||
-          name.equals("coreinterface")) {
-        /* Backwards compatibility: old cooja mote type is being loaded */
-        if (!warnedOldVersion) {
-          warnedOldVersion = true;
-          logger.warn("Old simulation config detected: Cooja mote types may not load correctly");
-        }
-
-        if (name.equals("compilefile")) {
+        } break;
+        case "contikibasedir":
+        case "contikicoredir":
+        case "projectdir":
+        case "compilefile":
+        case "process":
+        case "sensor":
+        case "coreinterface":
+          /* Backwards compatibility: old cooja mote type is being loaded */
+          if (!warnedOldVersion) {
+            warnedOldVersion = true;
+            logger.warn("Old simulation config detected: Cooja mote types may not load correctly");
+          } if (name.equals("compilefile")) {
           if (element.getText().endsWith(".c")) {
             File potentialFile = new File(element.getText());
             if (potentialFile.exists()) {
               oldVersionSource = potentialFile;
             }
           }
-        }
-
-      } else {
-        logger.fatal("Unrecognized entry in loaded configuration: " + name);
+        } break;
+        default:
+          logger.fatal("Unrecognized entry in loaded configuration: " + name);
+          break;
       }
     }
 
     /* Create initial core interface dependencies */
-    Class<? extends MoteInterface>[] arr =
-      new Class[moteInterfacesClasses.size()];
+    Class<? extends MoteInterface>[] arr
+            = new Class[moteInterfacesClasses.size()];
     moteInterfacesClasses.toArray(arr);
     setCoreInterfaces(ContikiMoteType.getRequiredCoreInterfaces(arr));
 
     /* Backwards compatibility: old cooja mote type is being loaded */
-    if (getContikiSourceFile() == null &&
-        warnedOldVersion &&
-        oldVersionSource != null)
-    {
+    if (getContikiSourceFile() == null
+            && warnedOldVersion
+            && oldVersionSource != null) {
       /* Guess Contiki source */
       setContikiSourceFile(oldVersionSource);
       logger.info("Guessing Contiki source: " + oldVersionSource.getAbsolutePath());
@@ -1404,8 +1412,8 @@ public class ContikiMoteType implements MoteType {
       logger.info("Guessing Contiki firmware: " + getContikiFirmwareFile().getAbsolutePath());
 
       /* Guess compile commands */
-      String compileCommands =
-        "make " + getExpectedFirmwareFile(oldVersionSource).getName() + " TARGET=cooja";
+      String compileCommands
+              = "make " + getExpectedFirmwareFile(oldVersionSource).getName() + " TARGET=cooja";
       logger.info("Guessing compile commands: " + compileCommands);
       setCompileCommands(compileCommands);
     }
@@ -1415,10 +1423,10 @@ public class ContikiMoteType implements MoteType {
   }
 
   public static String[] getRequiredCoreInterfaces(
-      Class<? extends MoteInterface>[] moteInterfaces) {
+          Class<? extends MoteInterface>[] moteInterfaces) {
     /* Extract Contiki dependencies from currently selected mote interfaces */
-    ArrayList<String> coreInterfacesList = new ArrayList<String>();
-    for (Class<? extends MoteInterface> intf: moteInterfaces) {
+    ArrayList<String> coreInterfacesList = new ArrayList<>();
+    for (Class<? extends MoteInterface> intf : moteInterfaces) {
       if (!ContikiMoteInterface.class.isAssignableFrom(intf)) {
         continue;
       }
@@ -1437,10 +1445,7 @@ public class ContikiMoteType implements MoteType {
       if (deps == null || deps.length == 0) {
         continue;
       }
-
-      for (String dep: deps) {
-        coreInterfacesList.add(dep);
-      }
+      coreInterfacesList.addAll(Arrays.asList(deps));
     }
 
     String[] coreInterfaces = new String[coreInterfacesList.size()];

From f6a0f54424d9db86509320981086013afbfcf6de Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Wed, 23 Jul 2014 14:18:16 +0200
Subject: [PATCH 15/28] [cooja] ContikiMoteType: Some renames and function
 reordering

---
 .../cooja/contikimote/ContikiMoteType.java    | 198 +++++++++---------
 1 file changed, 99 insertions(+), 99 deletions(-)

diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
index 6ad0b9da5..c1065e951 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
@@ -396,13 +396,15 @@ public class ContikiMoteType implements MoteType {
     logger.info("Creating core communicator between Java class '" + javaClassName + "' and Contiki library '" + getContikiFirmwareFile().getName() + "'");
     myCoreComm = CoreComm.createCoreComm(this.javaClassName, getContikiFirmwareFile());
 
-    /* Parse addresses using map file or command */
+    /* Parse addresses using map file
+     * or output of command specified in external tools settings (e.g. nm -a )
+     */
     boolean useCommand = Boolean.parseBoolean(Cooja.getExternalToolsSetting("PARSE_WITH_COMMAND", "false"));
 
-    int dataSectionAddr = -1, dataSectionSize = -1;
-    int bssSectionAddr = -1, bssSectionSize = -1;
-    int commonSectionAddr = -1, commonSectionSize = -1;
-    int readonlySectionAddr = -1, readonlySectionSize = -1;
+    int dataSectionRelAddr = -1, dataSectionSize = -1;
+    int bssSectionRelAddr = -1, bssSectionSize = -1;
+    int commonSectionRelAddr = -1, commonSectionSize = -1;
+    int readonlySectionRelAddr = -1, readonlySectionSize = -1;
 
     HashMap<String, Integer> addresses = new HashMap<String, Integer>();
     if (useCommand) {
@@ -417,23 +419,23 @@ public class ContikiMoteType implements MoteType {
         throw new MoteTypeCreationException("Command output parsing failed");
       }
 
-      dataSectionAddr = parseCommandDataSectionAddr(output);
+      dataSectionRelAddr = parseCommandDataSectionAddr(output);
       dataSectionSize = parseCommandDataSectionSize(output);
-      bssSectionAddr = parseCommandBssSectionAddr(output);
+      bssSectionRelAddr = parseCommandBssSectionAddr(output);
       bssSectionSize = parseCommandBssSectionSize(output);
-      commonSectionAddr = parseCommandCommonSectionAddr(output);
+      commonSectionRelAddr = parseCommandCommonSectionAddr(output);
       commonSectionSize = parseCommandCommonSectionSize(output);
 
       try {
-        readonlySectionAddr = parseCommandReadonlySectionAddr(output);
+        readonlySectionRelAddr = parseCommandReadonlySectionAddr(output);
         readonlySectionSize = parseCommandReadonlySectionSize(output);
       } catch (Exception e) {
-        readonlySectionAddr = -1;
+        readonlySectionRelAddr = -1;
         readonlySectionSize = -1;
       }
 
     } else {
-      /* Parse command output */
+      /* Parse map file */
       if (mapFile == null
               || !mapFile.exists()) {
         throw new MoteTypeCreationException("Map file " + mapFile + " could not be found");
@@ -449,41 +451,41 @@ public class ContikiMoteType implements MoteType {
         throw new MoteTypeCreationException("Map data parsing failed: " + mapFile);
       }
 
-      dataSectionAddr = parseMapDataSectionAddr(mapData);
+      dataSectionRelAddr = parseMapDataSectionAddr(mapData);
       dataSectionSize = parseMapDataSectionSize(mapData);
-      bssSectionAddr = parseMapBssSectionAddr(mapData);
+      bssSectionRelAddr = parseMapBssSectionAddr(mapData);
       bssSectionSize = parseMapBssSectionSize(mapData);
-      commonSectionAddr = parseMapCommonSectionAddr(mapData);
+      commonSectionRelAddr = parseMapCommonSectionAddr(mapData);
       commonSectionSize = parseMapCommonSectionSize(mapData);
-      readonlySectionAddr = -1;
+      readonlySectionRelAddr = -1;
       readonlySectionSize = -1;
 
     }
 
-    if (dataSectionAddr >= 0) {
+    if (dataSectionRelAddr >= 0) {
       logger.info(getContikiFirmwareFile().getName()
-              + ": data section at 0x" + Integer.toHexString(dataSectionAddr)
+              + ": data section at 0x" + Integer.toHexString(dataSectionRelAddr)
               + " (" + dataSectionSize + " == 0x" + Integer.toHexString(dataSectionSize) + " bytes)");
     } else {
       logger.fatal(getContikiFirmwareFile().getName() + ": no data section found");
     }
-    if (bssSectionAddr >= 0) {
+    if (bssSectionRelAddr >= 0) {
       logger.info(getContikiFirmwareFile().getName()
-              + ": BSS section at 0x" + Integer.toHexString(bssSectionAddr)
+              + ": BSS section at 0x" + Integer.toHexString(bssSectionRelAddr)
               + " (" + bssSectionSize + " == 0x" + Integer.toHexString(bssSectionSize) + " bytes)");
     } else {
       logger.fatal(getContikiFirmwareFile().getName() + ": no BSS section found");
     }
-    if (commonSectionAddr >= 0) {
+    if (commonSectionRelAddr >= 0) {
       logger.info(getContikiFirmwareFile().getName()
-              + ": common section at 0x" + Integer.toHexString(commonSectionAddr)
+              + ": common section at 0x" + Integer.toHexString(commonSectionRelAddr)
               + " (" + commonSectionSize + " == 0x" + Integer.toHexString(commonSectionSize) + " bytes)");
     } else {
       logger.info(getContikiFirmwareFile().getName() + ": no common section found");
     }
-    if (readonlySectionAddr >= 0) {
+    if (readonlySectionRelAddr >= 0) {
       logger.info(getContikiFirmwareFile().getName()
-              + ": readonly section at 0x" + Integer.toHexString(readonlySectionAddr)
+              + ": readonly section at 0x" + Integer.toHexString(readonlySectionRelAddr)
               + " (" + readonlySectionSize + " == 0x" + Integer.toHexString(readonlySectionSize) + " bytes)");
     } else {
       logger.warn(getContikiFirmwareFile().getName() + ": no readonly section found");
@@ -491,8 +493,8 @@ public class ContikiMoteType implements MoteType {
     if (addresses.isEmpty()) {
       throw new MoteTypeCreationException("Library variables parsing failed");
     }
-    if (dataSectionAddr <= 0 || dataSectionSize <= 0
-            || bssSectionAddr <= 0 || bssSectionSize <= 0) {
+    if (dataSectionRelAddr <= 0 || dataSectionSize <= 0
+        || bssSectionRelAddr <= 0 || bssSectionSize <= 0) {
       throw new MoteTypeCreationException("Library section addresses parsing failed");
     }
 
@@ -515,11 +517,11 @@ public class ContikiMoteType implements MoteType {
       SectionMoteMemory tmp = new SectionMoteMemory(addresses, 0);
       VarMemory varMem = new VarMemory(tmp);
       byte[] data = new byte[dataSectionSize];
-      getCoreMemory(dataSectionAddr, dataSectionSize, data);
-      tmp.setMemorySegment(dataSectionAddr, data);
+      getCoreMemory(dataSectionRelAddr, dataSectionSize, data);
+      tmp.setMemorySegment(dataSectionRelAddr, data);
       byte[] bss = new byte[bssSectionSize];
-      getCoreMemory(bssSectionAddr, bssSectionSize, bss);
-      tmp.setMemorySegment(bssSectionAddr, bss);
+      getCoreMemory(bssSectionRelAddr, bssSectionSize, bss);
+      tmp.setMemorySegment(bssSectionRelAddr, bss);
 
       offset = varMem.getIntValueOf("referenceVar");
       logger.info(getContikiFirmwareFile().getName()
@@ -530,24 +532,24 @@ public class ContikiMoteType implements MoteType {
     initialMemory = new SectionMoteMemory(addresses, offset);
 
     byte[] initialDataSection = new byte[dataSectionSize];
-    getCoreMemory(dataSectionAddr, dataSectionSize, initialDataSection);
-    initialMemory.setMemorySegmentNative(dataSectionAddr, initialDataSection);
+    getCoreMemory(dataSectionRelAddr, dataSectionSize, initialDataSection);
+    initialMemory.setMemorySegmentNative(dataSectionRelAddr, initialDataSection);
 
     byte[] initialBssSection = new byte[bssSectionSize];
-    getCoreMemory(bssSectionAddr, bssSectionSize, initialBssSection);
-    initialMemory.setMemorySegmentNative(bssSectionAddr, initialBssSection);
+    getCoreMemory(bssSectionRelAddr, bssSectionSize, initialBssSection);
+    initialMemory.setMemorySegmentNative(bssSectionRelAddr, initialBssSection);
 
-    if (commonSectionAddr >= 0 && commonSectionSize > 0) {
+    if (commonSectionRelAddr >= 0 && commonSectionSize > 0) {
       byte[] initialCommonSection = new byte[commonSectionSize];
-      getCoreMemory(commonSectionAddr, commonSectionSize, initialCommonSection);
-      initialMemory.setMemorySegmentNative(commonSectionAddr, initialCommonSection);
+      getCoreMemory(commonSectionRelAddr, commonSectionSize, initialCommonSection);
+      initialMemory.setMemorySegmentNative(commonSectionRelAddr, initialCommonSection);
     }
 
     /* Read "read-only" memory */
-    if (readonlySectionAddr >= 0 && readonlySectionSize > 0) {
+    if (readonlySectionRelAddr >= 0 && readonlySectionSize > 0) {
       byte[] readonlySection = new byte[readonlySectionSize];
-      getCoreMemory(readonlySectionAddr, readonlySectionSize, readonlySection);
-      initialMemory.setReadonlyMemorySegment(readonlySectionAddr + offset, readonlySection);
+      getCoreMemory(readonlySectionRelAddr, readonlySectionSize, readonlySection);
+      initialMemory.setReadonlyMemorySegment(readonlySectionRelAddr+offset, readonlySection);
     }
   }
 
@@ -570,6 +572,26 @@ public class ContikiMoteType implements MoteType {
     return initialMemory.clone();
   }
 
+  /**
+   * Copy core memory to given memory. This should not be used directly, but
+   * instead via ContikiMote.getMemory().
+   *
+   * @param mem
+   *          Memory to set
+   */
+  public void getCoreMemory(SectionMoteMemory mem) {
+    for (int i = 0; i < mem.getNumberOfSections(); i++) {
+      getCoreMemory(
+              (int) mem.getSectionNativeAddress(i) /* native address space */,
+              mem.getSizeOfSection(i),
+              mem.getDataOfSection(i));
+    }
+  }
+
+  private void getCoreMemory(int relAddr, int length, byte[] data) {
+    myCoreComm.getMemory(relAddr, length, data);
+  }
+
   /**
    * Copy given memory to the Contiki system. This should not be used directly,
    * but instead via ContikiMote.setMemory().
@@ -580,11 +602,16 @@ public class ContikiMoteType implements MoteType {
   public void setCoreMemory(SectionMoteMemory mem) {
     for (int i = 0; i < mem.getNumberOfSections(); i++) {
       setCoreMemory(
-              mem.getSectionNativeAddress(i) /* native address space */,
-              mem.getSizeOfSection(i), mem.getDataOfSection(i));
+              (int) mem.getSectionNativeAddress(i) /* native address space */,
+              mem.getSizeOfSection(i),
+              mem.getDataOfSection(i));
     }
   }
 
+  private void setCoreMemory(int relAddr, int length, byte[] mem) {
+    myCoreComm.setMemory(relAddr, length, mem);
+  }
+
   /**
    * Parses specified map file data for variable name to addresses mappings. The
    * mappings are added to the given properties object.
@@ -660,23 +687,6 @@ public class ContikiMoteType implements MoteType {
     return (nrNew + nrOld) > 0;
   }
 
-  /**
-   * Copy core memory to given memory. This should not be used directly, but
-   * instead via ContikiMote.getMemory().
-   *
-   * @param mem
-   * Memory to set
-   */
-  public void getCoreMemory(SectionMoteMemory mem) {
-    for (int i = 0; i < mem.getNumberOfSections(); i++) {
-      int startAddr = mem.getSectionNativeAddress(i); /* native address space */
-
-      int size = mem.getSizeOfSection(i);
-      byte[] data = mem.getDataOfSection(i);
-      getCoreMemory(startAddr, size, data);
-    }
-  }
-
   @Override
   public String getIdentifier() {
     return identifier;
@@ -745,41 +755,6 @@ public class ContikiMoteType implements MoteType {
     return netStack;
   }
 
-  /**
-   * Get relative address of variable with given name.
-   *
-   * @param varName Name of variable
-   * @return Relative memory address of variable or -1 if not found
-   */
-  private static int getMapFileVarAddress(String[] mapFileData, String varName, HashMap<String, Integer> varAddresses) {
-    Integer varAddrInteger;
-    if ((varAddrInteger = varAddresses.get(varName)) != null) {
-      return varAddrInteger.intValue();
-    }
-
-    String regExp
-            = Cooja.getExternalToolsSetting("MAPFILE_VAR_ADDRESS_1")
-            + varName
-            + Cooja.getExternalToolsSetting("MAPFILE_VAR_ADDRESS_2");
-    String retString = getFirstMatchGroup(mapFileData, regExp, 1);
-
-    if (retString != null) {
-      varAddrInteger = Integer.parseInt(retString.trim(), 16);
-      varAddresses.put(varName, varAddrInteger);
-      return varAddrInteger.intValue();
-    } else {
-      return -1;
-    }
-  }
-
-  private void getCoreMemory(int relAddr, int length, byte[] data) {
-    myCoreComm.getMemory(relAddr, length, data);
-  }
-
-  private void setCoreMemory(int relAddr, int length, byte[] mem) {
-    myCoreComm.setMemory(relAddr, length, mem);
-  }
-
   private static String getFirstMatchGroup(String[] lines, String regexp, int groupNr) {
     Pattern pattern = Pattern.compile(regexp);
     for (String line : lines) {
@@ -805,9 +780,7 @@ public class ContikiMoteType implements MoteType {
             mapFileData,
             parseMapDataSectionAddr(mapFileData),
             parseMapDataSectionAddr(mapFileData) + parseMapDataSectionSize(mapFileData));
-    for (String v : dataVariables) {
-      varNames.add(v);
-    }
+    varNames.addAll(Arrays.asList(dataVariables));
 
     String[] bssVariables = getAllVariableNames(
             mapFileData,
@@ -835,13 +808,40 @@ public class ContikiMoteType implements MoteType {
     return varNames.toArray(new String[0]);
   }
 
-  protected int getVariableSize(Vector<String> lines, String varName) {
+  /**
+   * Get relative address of variable with given name.
+   *
+   * @param varName Name of variable
+   * @return Relative memory address of variable or -1 if not found
+   */
+  private static int getMapFileVarAddress(String[] mapFileData, String varName, HashMap<String, Integer> varAddresses) {
+    Integer varAddrInteger;
+    if ((varAddrInteger = varAddresses.get(varName)) != null) {
+      return varAddrInteger.intValue();
+    }
+
+    String regExp = Cooja.getExternalToolsSetting("MAPFILE_VAR_ADDRESS_1")
+            + varName
+            + Cooja.getExternalToolsSetting("MAPFILE_VAR_ADDRESS_2");
+    String retString = getFirstMatchGroup(mapFileData, regExp, 1);
+
+    if (retString != null) {
+      varAddrInteger = Integer.parseInt(retString.trim(), 16);
+      varAddresses.put(varName, varAddrInteger);
+      return varAddrInteger.intValue();
+    }
+    else {
+      return -1;
+    }
+  }
+
+  protected static int getMapFileVarSize(String[] mapFileData, String varName) {
     Pattern pattern = Pattern.compile(
             Cooja.getExternalToolsSetting("MAPFILE_VAR_SIZE_1")
             + varName
             + Cooja.getExternalToolsSetting("MAPFILE_VAR_SIZE_2"));
-    for (int i = 0; i < lines.size(); i++) {
-      Matcher matcher = pattern.matcher(lines.get(i));
+    for (String line : mapFileData) {
+      Matcher matcher = pattern.matcher(line);
       if (matcher.find()) {
         return Integer.decode(matcher.group(1));
       }

From 070e0ba0fc8a958329c7c811a3c4026ca91272dd Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Tue, 29 Jul 2014 13:50:14 +0200
Subject: [PATCH 16/28] [cooja] memory: Implementation of simple array-backed
 memory class 'ArrayMamory'

---
 .../cooja/mote/memory/ArrayMemory.java        | 126 ++++++++++++++++++
 1 file changed, 126 insertions(+)
 create mode 100644 tools/cooja/java/org/contikios/cooja/mote/memory/ArrayMemory.java

diff --git a/tools/cooja/java/org/contikios/cooja/mote/memory/ArrayMemory.java b/tools/cooja/java/org/contikios/cooja/mote/memory/ArrayMemory.java
new file mode 100644
index 000000000..95966e01b
--- /dev/null
+++ b/tools/cooja/java/org/contikios/cooja/mote/memory/ArrayMemory.java
@@ -0,0 +1,126 @@
+/*
+ * Copyright (c) 2013, Enrico Joerns
+ * All rights reserved.
+ * 
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ * 3. Neither the name of the Institute nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software
+ *    without specific prior written permission.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE INSTITUTE OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ */
+
+package org.contikios.cooja.mote.memory;
+
+import java.util.Arrays;
+import java.util.Map;
+
+/**
+ * A memory that is backed by an array.
+ *
+ * @author Enrico Joerns
+ */
+public class ArrayMemory implements MemoryInterface {
+
+  private final byte memory[];
+  private final long startAddress;
+  private final MemoryLayout layout;
+  private final boolean readonly;
+  private final Map<String, Symbol> symbols;// XXX Allow to set symbols
+
+  public ArrayMemory(long address, int size, MemoryLayout layout, Map<String, Symbol> symbols) {
+    this(address, layout, new byte[size], symbols);
+  }
+
+  public ArrayMemory(long address, MemoryLayout layout, byte[] memory, Map<String, Symbol> symbols) {
+    this(address, layout, memory, false, symbols);
+  }
+
+  public ArrayMemory(long address, MemoryLayout layout, byte[] memory, boolean readonly, Map<String, Symbol> symbols) {
+    this.startAddress = address;
+    this.layout = layout;
+    this.memory = memory;
+    this.readonly = readonly;
+    this.symbols = symbols;
+  }
+
+  @Override
+  public byte[] getMemory() {
+    return memory;
+  }
+
+  /**
+   * XXX Should addr be the relative or the absolute address of this section?
+   * @param addr
+   * @param size
+   * @return
+   * @throws org.contikios.cooja.mote.memory.MemoryInterface.MoteMemoryException 
+   */
+  @Override
+  public byte[] getMemorySegment(long addr, int size) throws MoteMemoryException {
+    byte[] ret = new byte[size];
+    System.arraycopy(memory, (int) (addr - startAddress), ret, 0, size);
+    return ret;
+  }
+
+  @Override
+  public void setMemorySegment(long addr, byte[] data) throws MoteMemoryException {
+    if (readonly) {
+      throw new MoteMemoryException("Invalid write access for readonly memory");
+    }
+    System.arraycopy(data, 0, memory, (int) (addr - startAddress), data.length);
+  }
+
+  @Override
+  public void clearMemory() {
+    Arrays.fill(memory, (byte) 0x00);
+  }
+
+  @Override
+  public long getStartAddr() {
+    return startAddress;
+  }
+
+  @Override
+  public int getTotalSize() {
+    return memory.length;
+  }
+
+  @Override
+  public Map<String, Symbol> getSymbolMap() {
+    return symbols;
+  }
+
+  @Override
+  public MemoryLayout getLayout() {
+    return layout;
+  }
+
+  @Override
+  public boolean addSegmentMonitor(SegmentMonitor.EventType flag, long address, int size, SegmentMonitor monitor) {
+    throw new UnsupportedOperationException("Not supported yet.");
+  }
+
+  @Override
+  public boolean removeSegmentMonitor(long address, int size, SegmentMonitor monitor) {
+    throw new UnsupportedOperationException("Not supported yet.");
+  }
+  
+}

From f4979ffeeb091265fae8a053c1562b820ac846e6 Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Tue, 29 Jul 2014 17:50:11 +0200
Subject: [PATCH 17/28] [cooja] memory: SectionMoteMemory implementation of
 MemoryInterface functions as forwarding to encapsulated memory sections

Requires to make use of Symbol class for cooja motes, too
---
 .../cooja/contikimote/ContikiMoteType.java    |  56 ++-
 .../cooja/dialogs/ConfigurationWizard.java    |   9 +-
 .../cooja/mote/memory/SectionMoteMemory.java  | 387 ++++++++----------
 .../cooja/motes/AbstractApplicationMote.java  |   5 +-
 4 files changed, 212 insertions(+), 245 deletions(-)

diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
index c1065e951..4049cb85c 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
@@ -68,6 +68,10 @@ import org.contikios.cooja.dialogs.CompileContiki;
 import org.contikios.cooja.dialogs.ContikiMoteCompileDialog;
 import org.contikios.cooja.dialogs.MessageList;
 import org.contikios.cooja.dialogs.MessageList.MessageContainer;
+import org.contikios.cooja.mote.memory.ArrayMemory;
+import org.contikios.cooja.mote.memory.MemoryInterface;
+import org.contikios.cooja.mote.memory.MemoryInterface.Symbol;
+import org.contikios.cooja.mote.memory.MemoryLayout;
 import org.contikios.cooja.mote.memory.VarMemory;
 import org.contikios.cooja.util.StringUtils;
 
@@ -406,7 +410,7 @@ public class ContikiMoteType implements MoteType {
     int commonSectionRelAddr = -1, commonSectionSize = -1;
     int readonlySectionRelAddr = -1, readonlySectionSize = -1;
 
-    HashMap<String, Integer> addresses = new HashMap<String, Integer>();
+    HashMap<String, Symbol> addresses = new HashMap<String, Symbol>();
     if (useCommand) {
       /* Parse command output */
       String[] output = loadCommandData(getContikiFirmwareFile());
@@ -500,7 +504,7 @@ public class ContikiMoteType implements MoteType {
 
     try {
       /* Relative <-> absolute addresses offset */
-      int referenceVar = addresses.get("referenceVar");
+      int referenceVar = (int) addresses.get("referenceVar").addr;
       myCoreComm.setReferenceAddress(referenceVar);
     } catch (Exception e) {
       throw new MoteTypeCreationException("JNI call error: " + e.getMessage(), e);
@@ -518,10 +522,10 @@ public class ContikiMoteType implements MoteType {
       VarMemory varMem = new VarMemory(tmp);
       byte[] data = new byte[dataSectionSize];
       getCoreMemory(dataSectionRelAddr, dataSectionSize, data);
-      tmp.setMemorySegment(dataSectionRelAddr, data);
+      tmp.addMemorySection("data", new ArrayMemory(dataSectionRelAddr, MemoryLayout.getNative(), data, null));
       byte[] bss = new byte[bssSectionSize];
       getCoreMemory(bssSectionRelAddr, bssSectionSize, bss);
-      tmp.setMemorySegment(bssSectionRelAddr, bss);
+      tmp.addMemorySection("bss", new ArrayMemory(bssSectionRelAddr, MemoryLayout.getNative(), bss, null));
 
       offset = varMem.getIntValueOf("referenceVar");
       logger.info(getContikiFirmwareFile().getName()
@@ -533,23 +537,23 @@ public class ContikiMoteType implements MoteType {
 
     byte[] initialDataSection = new byte[dataSectionSize];
     getCoreMemory(dataSectionRelAddr, dataSectionSize, initialDataSection);
-    initialMemory.setMemorySegmentNative(dataSectionRelAddr, initialDataSection);
+    initialMemory.addMemorySection("data", new ArrayMemory(dataSectionRelAddr, MemoryLayout.getNative(), initialDataSection, null));
 
     byte[] initialBssSection = new byte[bssSectionSize];
     getCoreMemory(bssSectionRelAddr, bssSectionSize, initialBssSection);
-    initialMemory.setMemorySegmentNative(bssSectionRelAddr, initialBssSection);
+    initialMemory.addMemorySection("bss", new ArrayMemory(bssSectionRelAddr, MemoryLayout.getNative(), initialBssSection, null));
 
     if (commonSectionRelAddr >= 0 && commonSectionSize > 0) {
       byte[] initialCommonSection = new byte[commonSectionSize];
       getCoreMemory(commonSectionRelAddr, commonSectionSize, initialCommonSection);
-      initialMemory.setMemorySegmentNative(commonSectionRelAddr, initialCommonSection);
+      initialMemory.addMemorySection("common", new ArrayMemory(commonSectionRelAddr, MemoryLayout.getNative(), initialCommonSection, null));
     }
 
     /* Read "read-only" memory */
     if (readonlySectionRelAddr >= 0 && readonlySectionSize > 0) {
       byte[] readonlySection = new byte[readonlySectionSize];
       getCoreMemory(readonlySectionRelAddr, readonlySectionSize, readonlySection);
-      initialMemory.setReadonlyMemorySegment(readonlySectionRelAddr+offset, readonlySection);
+      initialMemory.addMemorySection("readonly", new ArrayMemory(readonlySectionRelAddr, MemoryLayout.getNative(), readonlySection, true, null));
     }
   }
 
@@ -580,11 +584,8 @@ public class ContikiMoteType implements MoteType {
    *          Memory to set
    */
   public void getCoreMemory(SectionMoteMemory mem) {
-    for (int i = 0; i < mem.getNumberOfSections(); i++) {
-      getCoreMemory(
-              (int) mem.getSectionNativeAddress(i) /* native address space */,
-              mem.getSizeOfSection(i),
-              mem.getDataOfSection(i));
+    for (MemoryInterface section : mem.getSections().values()) {
+      getCoreMemory((int) section.getStartAddr(), section.getTotalSize(), section.getMemory());
     }
   }
 
@@ -600,11 +601,8 @@ public class ContikiMoteType implements MoteType {
    * New memory
    */
   public void setCoreMemory(SectionMoteMemory mem) {
-    for (int i = 0; i < mem.getNumberOfSections(); i++) {
-      setCoreMemory(
-              (int) mem.getSectionNativeAddress(i) /* native address space */,
-              mem.getSizeOfSection(i),
-              mem.getDataOfSection(i));
+    for (MemoryInterface section : mem.getSections().values()) {
+      setCoreMemory((int) section.getStartAddr(), section.getTotalSize(), section.getMemory());
     }
   }
 
@@ -621,16 +619,16 @@ public class ContikiMoteType implements MoteType {
    * @param varAddresses
    * Properties that should contain the name to addresses mappings.
    */
-  public static boolean parseMapFileData(String[] mapFileData, HashMap<String, Integer> varAddresses) {
+  public static boolean parseMapFileData(String[] mapFileData, HashMap<String, Symbol> varAddresses) {
     String[] varNames = getMapFileVarNames(mapFileData);
     if (varNames == null || varNames.length == 0) {
       return false;
     }
 
     for (String varName : varNames) {
-      int varAddress = getMapFileVarAddress(mapFileData, varName, varAddresses);
+      int varAddress = getMapFileVarAddress(mapFileData, varName);
       if (varAddress > 0) {
-        varAddresses.put(varName, new Integer(varAddress));
+        varAddresses.put(varName, new Symbol(Symbol.Type.VARIABLE, varName, varAddress, 1));
       } else {
         logger.warn("Parsed Contiki variable '" + varName
                 + "' but could not find address");
@@ -647,7 +645,7 @@ public class ContikiMoteType implements MoteType {
    * @param output Command output
    * @param addresses Variable addresses mappings
    */
-  public static boolean parseCommandData(String[] output, HashMap<String, Integer> addresses) {
+  public static boolean parseCommandData(String[] output, HashMap<String, Symbol> addresses) {
     int nrNew = 0, nrOld = 0, nrMismatch = 0;
 
     Pattern pattern
@@ -663,9 +661,9 @@ public class ContikiMoteType implements MoteType {
 
         if (!addresses.containsKey(symbol)) {
           nrNew++;
-          addresses.put(symbol, new Integer(address));
+          addresses.put(symbol, new Symbol(Symbol.Type.VARIABLE, symbol, address, 1));
         } else {
-          int oldAddress = addresses.get(symbol);
+          int oldAddress = (int) addresses.get(symbol).addr;
           if (oldAddress != address) {
             /*logger.warn("Warning, command response not matching previous entry of: "
              + varName);*/
@@ -814,11 +812,7 @@ public class ContikiMoteType implements MoteType {
    * @param varName Name of variable
    * @return Relative memory address of variable or -1 if not found
    */
-  private static int getMapFileVarAddress(String[] mapFileData, String varName, HashMap<String, Integer> varAddresses) {
-    Integer varAddrInteger;
-    if ((varAddrInteger = varAddresses.get(varName)) != null) {
-      return varAddrInteger.intValue();
-    }
+  private static int getMapFileVarAddress(String[] mapFileData, String varName) {
 
     String regExp = Cooja.getExternalToolsSetting("MAPFILE_VAR_ADDRESS_1")
             + varName
@@ -826,9 +820,7 @@ public class ContikiMoteType implements MoteType {
     String retString = getFirstMatchGroup(mapFileData, regExp, 1);
 
     if (retString != null) {
-      varAddrInteger = Integer.parseInt(retString.trim(), 16);
-      varAddresses.put(varName, varAddrInteger);
-      return varAddrInteger.intValue();
+      return Integer.parseInt(retString.trim(), 16);
     }
     else {
       return -1;
diff --git a/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java b/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
index 0fa575be9..946d0f88c 100644
--- a/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
+++ b/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
@@ -68,6 +68,7 @@ import org.contikios.cooja.Cooja;
 import org.contikios.cooja.MoteType.MoteTypeCreationException;
 import org.contikios.cooja.mote.memory.SectionMoteMemory;
 import org.contikios.cooja.contikimote.ContikiMoteType;
+import org.contikios.cooja.mote.memory.MemoryInterface.Symbol;
 import org.contikios.cooja.mote.memory.VarMemory;
 
 /* TODO Test common section */
@@ -142,7 +143,7 @@ public class ConfigurationWizard extends JDialog {
   private static File cLibraryFile;
   private static String javaLibraryName;
   private static CoreComm javaLibrary;
-  private static HashMap<String, Integer> addresses;
+  private static HashMap<String, Symbol> addresses;
   private static int relDataSectionAddr;
   private static int dataSectionSize;
   private static int relBssSectionAddr;
@@ -758,7 +759,7 @@ public class ConfigurationWizard extends JDialog {
     }
 
     testOutput.addMessage("### Parsing map file data for addresses");
-    addresses = new HashMap<String, Integer>();
+    addresses = new HashMap<String, Symbol>();
     boolean parseOK = ContikiMoteType.parseMapFileData(mapData, addresses);
     if (!parseOK) {
       testOutput.addMessage("### Error: Failed parsing map file data", MessageList.ERROR);
@@ -838,7 +839,7 @@ public class ConfigurationWizard extends JDialog {
     }
 
     testOutput.addMessage("### Parsing command output for addresses");
-    addresses = new HashMap<String, Integer>();
+    addresses = new HashMap<String, Symbol>();
     boolean parseOK = ContikiMoteType.parseCommandData(commandData, addresses);
     if (!parseOK) {
       testOutput.addMessage("### Error: Failed parsing command output", MessageList.ERROR);
@@ -936,7 +937,7 @@ public class ConfigurationWizard extends JDialog {
       testOutput.addMessage("Could not find address of referenceVar", MessageList.ERROR);
       return false;
     }
-    int relRefAddress = addresses.get("referenceVar");
+    int relRefAddress = (int) addresses.get("referenceVar").addr;
     javaLibrary.setReferenceAddress(relRefAddress);
 
     testOutput.addMessage("### Creating data and BSS memory sections");
diff --git a/tools/cooja/java/org/contikios/cooja/mote/memory/SectionMoteMemory.java b/tools/cooja/java/org/contikios/cooja/mote/memory/SectionMoteMemory.java
index 75c8d4dfa..f1a43cebe 100644
--- a/tools/cooja/java/org/contikios/cooja/mote/memory/SectionMoteMemory.java
+++ b/tools/cooja/java/org/contikios/cooja/mote/memory/SectionMoteMemory.java
@@ -1,4 +1,5 @@
 /*
+ * Copyright (c) 2014, TU Braunschweig. All rights reserved.
  * Copyright (c) 2006, Swedish Institute of Computer Science. All rights
  * reserved.
  *
@@ -33,66 +34,90 @@ import java.util.HashMap;
 import java.util.Map;
 
 import org.apache.log4j.Logger;
-import org.contikios.cooja.mote.memory.MemoryInterface;
-import org.contikios.cooja.mote.memory.MemoryLayout;
 
 /**
  * Represents a mote memory consisting of non-overlapping memory sections with
  * symbol addresses.
  * <p>
- * When an non-existing memory segment is written, a new section is automatically
- * created for this segment.
+ * Every section must implement MemoyInterface.
  * <p>
+ * Implements MemoryInterface by forwarding calls to available sections or returning
+ * an error if no section is available.
  *
  * @author Fredrik Osterlind
+ * @author Enrico Jorns
  */
 public class SectionMoteMemory implements MemoryInterface {
   private static Logger logger = Logger.getLogger(SectionMoteMemory.class);
+  private static final boolean DEBUG = logger.isDebugEnabled();
 
-  private ArrayList<MoteMemorySection> sections = new ArrayList<MoteMemorySection>();
- 
-  /* readonly memory is never written to Contiki core, and is used to provide 
-   * access to, for instance, strings */
-  private ArrayList<MoteMemorySection> readonlySections = new ArrayList<MoteMemorySection>();
+  private Map<String, MemoryInterface> sections = new HashMap<>();
 
-  private final HashMap<String, Integer> addresses;
+  private final Map<String, Symbol> symbols;
+  private MemoryLayout memLayout;
+  private long startAddr = Long.MAX_VALUE;
 
   /* used to map Cooja's address space to native (Contiki's) addresses */
   private final int offset;
   
   /**
-   * @param addresses Symbol addresses
+   * @param symbols Symbol addresses
    * @param offset Offset for internally used addresses
    */
-  public SectionMoteMemory(HashMap<String, Integer> addresses, int offset) {
-    this.addresses = addresses;
+  public SectionMoteMemory(Map<String, Symbol> symbols, int offset) {
+    this.symbols = symbols;
     this.offset = offset;
   }
 
+  /**
+   * Adds a section to this memory.
+   * 
+   * A new section will be checked for address overlap with existing sections.
+   *
+   * @param name
+   * @param section
+   * @return true if adding succeeded, false otherwise
+   */
+  public boolean addMemorySection(String name ,MemoryInterface section) {
 
-  @Override
-  public void clearMemory() {
-    sections.clear();
-  }
-
-  public void setMemorySegmentNative(int address, byte[] data) {
-    setMemorySegment(address+offset, data);
-  }
-
-
-  public void setReadonlyMemorySegment(int address, byte[] data) {
-    /* Cooja address space */
-    address -= offset;
-
-    readonlySections.add(new MoteMemorySection(address, data));
-  }
-
-  public int getTotalSize() {
-    int totalSize = 0;
-    for (MoteMemorySection section : sections) {
-      totalSize += section.getSize();
+    if (section == null) {
+      return false;
     }
-    return totalSize;
+
+    /* Cooja address space */
+    for (MemoryInterface sec : sections.values()) {
+      /* check for overlap with existing region */
+      if ((section.getStartAddr() <= sec.getStartAddr() + sec.getTotalSize() - 1)
+              && (section.getStartAddr() + section.getTotalSize() - 1 >= sec.getStartAddr())) {
+        logger.error(String.format(
+                "Failed adding section '%s' of size %d @0x%x",
+                name,
+                section.getTotalSize(),
+                section.getStartAddr()));
+        return false;
+      }
+      /* Min start address is main start address */
+      startAddr = sec.getStartAddr() < startAddr ? sec.getStartAddr() : startAddr;
+      /* Layout is last layout. XXX Check layout consistency? */
+      memLayout = section.getLayout();
+    }
+
+    sections.put(name, section);
+    if (section.getSymbolMap() != null) {
+      for (String s : section.getSymbolMap().keySet()) {
+        // XXX how to handle double names here?
+        symbols.put(s, section.getSymbolMap().get(s));
+      }
+    }
+
+    if (DEBUG) {
+      logger.debug(String.format(
+              "Added section '%s' of size %d @0x%x",
+              name,
+              section.getTotalSize(),
+              section.getStartAddr()));
+    }
+    return true;
   }
 
   /**
@@ -105,44 +130,69 @@ public class SectionMoteMemory implements MemoryInterface {
   }
 
   /**
-   * Get start address of given section in native address space.
-   *
-   * @param sectionNr Section position
-   * @return Start address of section
+   * Returns memory section of this memory.
+   * @param name Name of section
+   * @return memory section
    */
-  public int getSectionNativeAddress(int sectionNr) {
-    if (sectionNr >= sections.size()) {
-      return -1;
+  public MemoryInterface getSection(String name) {
+    for (String memsec : sections.keySet()) {
+      if (memsec.equals(name)) {
+        return sections.get(name);
+      }
     }
-    return sections.get(sectionNr).getStartAddr();
+
+    logger.warn("Section '" + name + "' not found");
+    return null;
   }
 
   /**
-   * Get size of section at given position.
-   *
-   * @param sectionNr Section position
-   * @return Size of section
+   * Return all sections of this memory.
+   * @return All memory sections
    */
-  public int getSizeOfSection(int sectionNr) {
-    if (sectionNr >= sections.size()) {
-      return -1;
-    }
-
-    return sections.get(sectionNr).getSize();
+  public Map<String, MemoryInterface> getSections() {
+    return sections;
   }
 
   /**
-   * Get data of section at given position.
+   * True if given address is part of this memory section.
    *
-   * @param sectionNr Section position
-   * @return Data at section
+   * @param intf
+   * @param addr
+   * Address
+   * @return True if given address is part of this memory section, false
+   * otherwise
    */
-  public byte[] getDataOfSection(int sectionNr) {
-    if (sectionNr >= sections.size()) {
-      return null;
-    }
+  public static boolean includesAddr(MemoryInterface intf, long addr) {
+    return addr >= intf.getStartAddr() && addr < (intf.getStartAddr() + intf.getTotalSize());
+  }
 
-    return sections.get(sectionNr).getData();
+  /**
+   * True if the whole address range specified by address and size
+   * lies inside this memory section.
+   *
+   * @param intf
+   * @param addr Start address of segment to check
+   * @param size Size of segment to check
+   *
+   * @return True if given address range lies inside address range of this
+   * section
+   */
+  public static boolean inSection(MemoryInterface intf, long addr, int size) {
+    return addr >= intf.getStartAddr() && addr + size <= intf.getStartAddr() + intf.getTotalSize();
+  }
+
+  @Override
+  public void clearMemory() {
+    sections.clear();
+  }
+
+  @Override
+  public int getTotalSize() {
+    int totalSize = 0;
+    for (MemoryInterface section : sections.values()) {
+      totalSize += section.getTotalSize();
+    }
+    return totalSize;
   }
 
   @Override
@@ -150,153 +200,106 @@ public class SectionMoteMemory implements MemoryInterface {
     throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
   }
 
+
+  /**
+   * Returns memory segment from section matching segment given by address and size
+   * @param address start address of segment to get
+   * @param size size of segmetn to get
+   * @return Array containing data of segment
+   * @throws MoteMemoryException if no single section containing the given address range was found
+   */
   @Override
-  public byte[] getMemorySegment(long addr, int size) throws MoteMemoryException {
-    throw new UnsupportedOperationException("Not supported yet.");
+  public byte[] getMemorySegment(long address, int size) throws MoteMemoryException {
+
+    for (MemoryInterface section : sections.values()) {
+      if (includesAddr(section, address) && includesAddr(section, address + size - 1)) {
+        return section.getMemorySegment(address, size);
+      }
+    }
+
+    throw new MoteMemoryException(
+            "Getting memory segment [0x%x,0x%x] failed: No section available",
+            address, address + size - 1);
   }
 
+  /**
+   * Sets memory segment of section matching segment given by address and size.
+   * @param address start address of segment to set
+   * @param data data to set
+   * @throws MoteMemoryException if no single section containing the given address range was found
+   * or memory is readonly.
+   */
   @Override
-  public void setMemorySegment(long addr, byte[] data) throws MoteMemoryException {
-    throw new UnsupportedOperationException("Not supported yet.");
+  public void setMemorySegment(long address, byte[] data) throws MoteMemoryException {
+
+    for (MemoryInterface section : sections.values()) {
+      if (inSection(section, address, data.length)) {
+        section.setMemorySegment(address, data);
+        if (DEBUG) {
+          logger.debug(String.format(
+                  "Wrote memory segment [0x%x,0x%x]",
+                  address, address + data.length - 1));
+        }
+        return;
+      }
+    }
+    throw new MoteMemoryException(
+            "Writing memory segment [0x%x,0x%x] failed: No section available",
+            address, address + data.length - 1);
+  }
+
+  public void setMemorySegmentNative(long address, byte[] data) throws MoteMemoryException {
+    setMemorySegment(address + offset, data);
   }
 
   @Override
   public long getStartAddr() {
-    throw new UnsupportedOperationException("Not supported yet.");
+    return startAddr;
   }
 
   @Override
   public Map<String, Symbol> getSymbolMap() {
-    throw new UnsupportedOperationException("Not supported yet.");
+    return symbols;
   }
 
   @Override
   public MemoryLayout getLayout() {
-    throw new UnsupportedOperationException("Not supported yet.");
+    return memLayout;
   }
 
   @Override
   public boolean addSegmentMonitor(SegmentMonitor.EventType flag, long address, int size, SegmentMonitor monitor) {
-    throw new UnsupportedOperationException("Not supported yet.");
+    PolledMemorySegments t = new PolledMemorySegments(monitor, (int) address, size);
+    polledMemories.add(t);
+    return true;
   }
 
   @Override
   public boolean removeSegmentMonitor(long address, int size, SegmentMonitor monitor) {
-    throw new UnsupportedOperationException("Not supported yet.");
-  }
-
-  /**
-   * A memory section contains a byte array and a start address.
-   *
-   * @author Fredrik Osterlind
-   */
-  private static class MoteMemorySection {
-    private byte[] data = null;
-    private final int startAddr;
-
-    /**
-     * Create a new memory section.
-     *
-     * @param startAddr
-     *          Start address of section
-     * @param data
-     *          Data of section
-     */
-    public MoteMemorySection(int startAddr, byte[] data) {
-      this.startAddr = startAddr;
-      this.data = data;
-    }
-
-    /**
-     * Returns start address of this memory section.
-     *
-     * @return Start address
-     */
-    public int getStartAddr() {
-      return startAddr;
-    }
-
-    /**
-     * Returns size of this memory section.
-     *
-     * @return Size
-     */
-    public int getSize() {
-      return data.length;
-    }
-
-    /**
-     * Returns the entire byte array which defines this section.
-     *
-     * @return Byte array
-     */
-    public byte[] getData() {
-      return data;
-    }
-
-    /**
-     * True if given address is part of this memory section.
-     *
-     * @param addr
-     *          Address
-     * @return True if given address is part of this memory section, false
-     *         otherwise
-     */
-    public boolean includesAddr(int addr) {
-      if (data == null) {
-        return false;
+    for (PolledMemorySegments mcm: polledMemories) {
+      if (mcm.mm != monitor || mcm.address != address || mcm.size != size) {
+        continue;
       }
-
-      return (addr >= startAddr && addr < (startAddr + data.length));
-    }
-
-    /**
-     * Returns memory segment.
-     *
-     * @param addr
-     *          Start address of memory segment
-     * @param size
-     *          Size of memory segment
-     * @return Memory segment
-     */
-    public byte[] getMemorySegment(int addr, int size) {
-      byte[] ret = new byte[size];
-      System.arraycopy(data, addr - startAddr, ret, 0, size);
-      return ret;
-    }
-
-    /**
-     * Sets a memory segment.
-     *
-     * @param addr
-     *          Start of memory segment
-     * @param data
-     *          Data of memory segment
-     */
-    public void setMemorySegment(int addr, byte[] data) {
-      System.arraycopy(data, 0, this.data, addr - startAddr, data.length);
-    }
-
-    @Override
-    public MoteMemorySection clone() {
-      byte[] dataClone = new byte[data.length];
-      System.arraycopy(data, 0, dataClone, 0, data.length);
-
-      MoteMemorySection clone = new MoteMemorySection(startAddr, dataClone);
-      return clone;
+      polledMemories.remove(mcm);
+      return true;
     }
+    return false;
   }
 
+  /** Copies seciton memory to new (array backed) one
+   * @return Cloned memory
+   */
   @Override
   public SectionMoteMemory clone() {
-    ArrayList<MoteMemorySection> sectionsClone = new ArrayList<MoteMemorySection>();
-    for (MoteMemorySection section : sections) {
-      sectionsClone.add(section.clone());
-    }
 
-    SectionMoteMemory clone = new SectionMoteMemory(addresses, offset);
-    clone.sections = sectionsClone;
-    clone.readonlySections = readonlySections;
+    SectionMoteMemory clone = new SectionMoteMemory(symbols, offset);
+
+    for (String secname : sections.keySet()) {
+      // Copy section memory to new ArrayMemory
+      MemoryInterface section = sections.get(secname);
+      MemoryInterface cpmem = new ArrayMemory(section.getStartAddr(), section.getLayout(), section.getMemory().clone(), section.getSymbolMap());
+      clone.addMemorySection(secname, cpmem);
+    }
 
     return clone;
   }
@@ -333,34 +336,4 @@ public class SectionMoteMemory implements MemoryInterface {
     }
   }
 
-//  @Override
-  public boolean addMemoryMonitor(int address, int size, SegmentMonitor mm) {
-    PolledMemorySegments t = new PolledMemorySegments(mm, address, size);
-    polledMemories.add(t);
-    return true;
-  }
-
-//  @Override
-  public void removeMemoryMonitor(int address, int size, SegmentMonitor mm) {
-    for (PolledMemorySegments mcm: polledMemories) {
-      if (mcm.mm != mm || mcm.address != address || mcm.size != size) {
-        continue;
-      }
-      polledMemories.remove(mcm);
-      break;
-    }
-  }
-
-//  @Override
-  public int parseInt(byte[] memorySegment) {
-    int retVal = 0;
-    int pos = 0;
-    retVal += ((memorySegment[pos++] & 0xFF)) << 24;
-    retVal += ((memorySegment[pos++] & 0xFF)) << 16;
-    retVal += ((memorySegment[pos++] & 0xFF)) << 8;
-    retVal += ((memorySegment[pos++] & 0xFF)) << 0;
-
-    retVal = Integer.reverseBytes(retVal);
-    return retVal;
-  }
 }
diff --git a/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java b/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
index b8bccaf63..a7a8deaf6 100644
--- a/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
+++ b/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
@@ -47,6 +47,7 @@ import org.contikios.cooja.interfaces.ApplicationRadio;
 import org.contikios.cooja.interfaces.ApplicationSerialPort;
 import org.contikios.cooja.interfaces.Radio;
 import org.contikios.cooja.mote.memory.MemoryInterface;
+import org.contikios.cooja.mote.memory.MemoryInterface.Symbol;
 import org.contikios.cooja.mote.memory.MemoryLayout;
 
 /**
@@ -91,7 +92,7 @@ public abstract class AbstractApplicationMote extends AbstractWakeupMote impleme
     setSimulation(sim);
     this.moteType = moteType;
     MemoryLayout.getNative();
-    this.memory = new SectionMoteMemory(new HashMap<String, Integer>(), 0);
+    this.memory = new SectionMoteMemory(new HashMap<String, Symbol>(), 0);
     this.moteInterfaces = new MoteInterfaceHandler(this, moteType.getMoteInterfaceClasses());
     this.moteInterfaces.getRadio().addObserver(radioDataObserver);
     requestImmediateWakeup();
@@ -151,7 +152,7 @@ public abstract class AbstractApplicationMote extends AbstractWakeupMote impleme
   public boolean setConfigXML(Simulation simulation,
       Collection<Element> configXML, boolean visAvailable) {
     setSimulation(simulation);
-    this.memory = new SectionMoteMemory(new HashMap<String, Integer>(), 0);
+    this.memory = new SectionMoteMemory(new HashMap<String, Symbol>(), 0);
     moteInterfaces.getRadio().addObserver(radioDataObserver);
 
     for (Element element : configXML) {

From c5ff3555a02a6b60caacc39e52cd12fad2e992b1 Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Tue, 29 Jul 2014 21:21:39 +0200
Subject: [PATCH 18/28] [cooja] ContikiMoteType: Introduce abstract
 SectionParser

Should encapsulate and decrease both redundancy and code duplication
---
 .../cooja/contikimote/ContikiMoteType.java    | 548 ++++++++----------
 .../cooja/dialogs/ConfigurationWizard.java    |  54 +-
 2 files changed, 270 insertions(+), 332 deletions(-)

diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
index 4049cb85c..2a633f67a 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
@@ -43,6 +43,7 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.HashMap;
+import java.util.Map;
 import java.util.Random;
 import java.util.Vector;
 import java.util.regex.Matcher;
@@ -72,6 +73,7 @@ import org.contikios.cooja.mote.memory.ArrayMemory;
 import org.contikios.cooja.mote.memory.MemoryInterface;
 import org.contikios.cooja.mote.memory.MemoryInterface.Symbol;
 import org.contikios.cooja.mote.memory.MemoryLayout;
+import org.contikios.cooja.mote.memory.UnknownVariableException;
 import org.contikios.cooja.mote.memory.VarMemory;
 import org.contikios.cooja.util.StringUtils;
 
@@ -405,38 +407,35 @@ public class ContikiMoteType implements MoteType {
      */
     boolean useCommand = Boolean.parseBoolean(Cooja.getExternalToolsSetting("PARSE_WITH_COMMAND", "false"));
 
-    int dataSectionRelAddr = -1, dataSectionSize = -1;
-    int bssSectionRelAddr = -1, bssSectionSize = -1;
-    int commonSectionRelAddr = -1, commonSectionSize = -1;
-    int readonlySectionRelAddr = -1, readonlySectionSize = -1;
+    SectionParser dataSecParser;
+    SectionParser bssSecParser;
+    SectionParser commonSecParser;
+    SectionParser readonlySecParser = null;
 
-    HashMap<String, Symbol> addresses = new HashMap<String, Symbol>();
+    HashMap<String, Symbol> variables = new HashMap<>();
     if (useCommand) {
       /* Parse command output */
       String[] output = loadCommandData(getContikiFirmwareFile());
       if (output == null) {
         throw new MoteTypeCreationException("No parse command output loaded");
       }
-      boolean parseOK = parseCommandData(output, addresses);
-      if (!parseOK) {
-        logger.fatal("Command output parsing failed");
-        throw new MoteTypeCreationException("Command output parsing failed");
-      }
 
-      dataSectionRelAddr = parseCommandDataSectionAddr(output);
-      dataSectionSize = parseCommandDataSectionSize(output);
-      bssSectionRelAddr = parseCommandBssSectionAddr(output);
-      bssSectionSize = parseCommandBssSectionSize(output);
-      commonSectionRelAddr = parseCommandCommonSectionAddr(output);
-      commonSectionSize = parseCommandCommonSectionSize(output);
-
-      try {
-        readonlySectionRelAddr = parseCommandReadonlySectionAddr(output);
-        readonlySectionSize = parseCommandReadonlySectionSize(output);
-      } catch (Exception e) {
-        readonlySectionRelAddr = -1;
-        readonlySectionSize = -1;
-      }
+      dataSecParser = new CommandSectionParser(
+              output,
+              Cooja.getExternalToolsSetting("COMMAND_DATA_START"),
+              Cooja.getExternalToolsSetting("COMMAND_DATA_SIZE"));
+      bssSecParser = new CommandSectionParser(
+              output,
+              Cooja.getExternalToolsSetting("COMMAND_BSS_START"),
+              Cooja.getExternalToolsSetting("COMMAND_BSS_SIZE"));
+      commonSecParser = new CommandSectionParser(
+              output,
+              Cooja.getExternalToolsSetting("COMMAND_COMMON_START"),
+              Cooja.getExternalToolsSetting("COMMAND_COMMON_SIZE"));
+      readonlySecParser = new CommandSectionParser(
+              output,
+              Cooja.getExternalToolsSetting("^([0-9A-Fa-f]*)[ \t]t[ \t].text$"),
+              Cooja.getExternalToolsSetting("")); // XXX
 
     } else {
       /* Parse map file */
@@ -449,63 +448,32 @@ public class ContikiMoteType implements MoteType {
         logger.fatal("No map data could be loaded");
         throw new MoteTypeCreationException("No map data could be loaded: " + mapFile);
       }
-      boolean parseOK = parseMapFileData(mapData, addresses);
-      if (!parseOK) {
-        logger.fatal("Map data parsing failed");
-        throw new MoteTypeCreationException("Map data parsing failed: " + mapFile);
-      }
 
-      dataSectionRelAddr = parseMapDataSectionAddr(mapData);
-      dataSectionSize = parseMapDataSectionSize(mapData);
-      bssSectionRelAddr = parseMapBssSectionAddr(mapData);
-      bssSectionSize = parseMapBssSectionSize(mapData);
-      commonSectionRelAddr = parseMapCommonSectionAddr(mapData);
-      commonSectionSize = parseMapCommonSectionSize(mapData);
-      readonlySectionRelAddr = -1;
-      readonlySectionSize = -1;
+      dataSecParser = new MapSectionParser(
+              mapData,
+              Cooja.getExternalToolsSetting("MAPFILE_DATA_START"),
+              Cooja.getExternalToolsSetting("MAPFILE_DATA_SIZE"));
+      bssSecParser = new MapSectionParser(
+              mapData,
+              Cooja.getExternalToolsSetting("MAPFILE_BSS_START"),
+              Cooja.getExternalToolsSetting("MAPFILE_BSS_SIZE"));
+      commonSecParser = new MapSectionParser(
+              mapData,
+              Cooja.getExternalToolsSetting("MAPFILE_COMMON_START"),
+              Cooja.getExternalToolsSetting("MAPFILE_COMMON_SIZE"));
+      readonlySecParser = null;
 
     }
 
-    if (dataSectionRelAddr >= 0) {
-      logger.info(getContikiFirmwareFile().getName()
-              + ": data section at 0x" + Integer.toHexString(dataSectionRelAddr)
-              + " (" + dataSectionSize + " == 0x" + Integer.toHexString(dataSectionSize) + " bytes)");
-    } else {
-      logger.fatal(getContikiFirmwareFile().getName() + ": no data section found");
-    }
-    if (bssSectionRelAddr >= 0) {
-      logger.info(getContikiFirmwareFile().getName()
-              + ": BSS section at 0x" + Integer.toHexString(bssSectionRelAddr)
-              + " (" + bssSectionSize + " == 0x" + Integer.toHexString(bssSectionSize) + " bytes)");
-    } else {
-      logger.fatal(getContikiFirmwareFile().getName() + ": no BSS section found");
-    }
-    if (commonSectionRelAddr >= 0) {
-      logger.info(getContikiFirmwareFile().getName()
-              + ": common section at 0x" + Integer.toHexString(commonSectionRelAddr)
-              + " (" + commonSectionSize + " == 0x" + Integer.toHexString(commonSectionSize) + " bytes)");
-    } else {
-      logger.info(getContikiFirmwareFile().getName() + ": no common section found");
-    }
-    if (readonlySectionRelAddr >= 0) {
-      logger.info(getContikiFirmwareFile().getName()
-              + ": readonly section at 0x" + Integer.toHexString(readonlySectionRelAddr)
-              + " (" + readonlySectionSize + " == 0x" + Integer.toHexString(readonlySectionSize) + " bytes)");
-    } else {
-      logger.warn(getContikiFirmwareFile().getName() + ": no readonly section found");
-    }
-    if (addresses.isEmpty()) {
-      throw new MoteTypeCreationException("Library variables parsing failed");
-    }
-    if (dataSectionRelAddr <= 0 || dataSectionSize <= 0
-        || bssSectionRelAddr <= 0 || bssSectionSize <= 0) {
-      throw new MoteTypeCreationException("Library section addresses parsing failed");
-    }
-
     try {
-      /* Relative <-> absolute addresses offset */
-      int referenceVar = (int) addresses.get("referenceVar").addr;
-      myCoreComm.setReferenceAddress(referenceVar);
+      Map<String, Symbol> vars = bssSecParser.getSymbols();
+      for (Symbol s : vars.values()) {
+        if (s.name.equals("referenceVar")) {
+          /* Relative <-> absolute addresses offset */
+          int referenceVar = (int) s.addr;
+          myCoreComm.setReferenceAddress(referenceVar);
+        }
+      }
     } catch (Exception e) {
       throw new MoteTypeCreationException("JNI call error: " + e.getMessage(), e);
     }
@@ -518,42 +486,185 @@ public class ContikiMoteType implements MoteType {
      * Contiki's and Cooja's address spaces */
     int offset;
     {
-      SectionMoteMemory tmp = new SectionMoteMemory(addresses, 0);
+      SectionMoteMemory tmp = new SectionMoteMemory(variables, 0);
       VarMemory varMem = new VarMemory(tmp);
-      byte[] data = new byte[dataSectionSize];
-      getCoreMemory(dataSectionRelAddr, dataSectionSize, data);
-      tmp.addMemorySection("data", new ArrayMemory(dataSectionRelAddr, MemoryLayout.getNative(), data, null));
-      byte[] bss = new byte[bssSectionSize];
-      getCoreMemory(bssSectionRelAddr, bssSectionSize, bss);
-      tmp.addMemorySection("bss", new ArrayMemory(bssSectionRelAddr, MemoryLayout.getNative(), bss, null));
+      tmp.addMemorySection("tmp.data", dataSecParser.parse());
+
+      tmp.addMemorySection("tmp.bss", bssSecParser.parse());
+
+      try {
+        int referenceVar = (int) varMem.getVariable("referenceVar").addr;
+        myCoreComm.setReferenceAddress(referenceVar);
+      } catch (UnknownVariableException e) {
+        throw new MoteTypeCreationException("JNI call error: " + e.getMessage(), e);
+      }
+
+      
+      getCoreMemory(tmp);
 
       offset = varMem.getIntValueOf("referenceVar");
       logger.info(getContikiFirmwareFile().getName()
-              + ": offsetting Cooja mote address space: " + offset);
+              + ": offsetting Cooja mote address space: " + Long.toHexString(offset));
     }
 
     /* Create initial memory: data+bss+optional common */
-    initialMemory = new SectionMoteMemory(addresses, offset);
+    initialMemory = new SectionMoteMemory(variables, offset);
 
-    byte[] initialDataSection = new byte[dataSectionSize];
-    getCoreMemory(dataSectionRelAddr, dataSectionSize, initialDataSection);
-    initialMemory.addMemorySection("data", new ArrayMemory(dataSectionRelAddr, MemoryLayout.getNative(), initialDataSection, null));
+    initialMemory.addMemorySection("data", dataSecParser.parse());
 
-    byte[] initialBssSection = new byte[bssSectionSize];
-    getCoreMemory(bssSectionRelAddr, bssSectionSize, initialBssSection);
-    initialMemory.addMemorySection("bss", new ArrayMemory(bssSectionRelAddr, MemoryLayout.getNative(), initialBssSection, null));
+    initialMemory.addMemorySection("bss", bssSecParser.parse());
 
-    if (commonSectionRelAddr >= 0 && commonSectionSize > 0) {
-      byte[] initialCommonSection = new byte[commonSectionSize];
-      getCoreMemory(commonSectionRelAddr, commonSectionSize, initialCommonSection);
-      initialMemory.addMemorySection("common", new ArrayMemory(commonSectionRelAddr, MemoryLayout.getNative(), initialCommonSection, null));
+    initialMemory.addMemorySection("common", commonSecParser.parse());
+
+    if (readonlySecParser != null) {
+      initialMemory.addMemorySection("readonly", readonlySecParser.parse());
     }
 
-    /* Read "read-only" memory */
-    if (readonlySectionRelAddr >= 0 && readonlySectionSize > 0) {
-      byte[] readonlySection = new byte[readonlySectionSize];
-      getCoreMemory(readonlySectionRelAddr, readonlySectionSize, readonlySection);
-      initialMemory.addMemorySection("readonly", new ArrayMemory(readonlySectionRelAddr, MemoryLayout.getNative(), readonlySection, true, null));
+    getCoreMemory(initialMemory);
+  }
+
+  public static abstract class SectionParser {
+
+    private final String[] mapFileData;
+
+    public SectionParser(String[] mapFileData) {
+      this.mapFileData = mapFileData;
+    }
+
+    public String[] getData() {
+      return mapFileData;
+    }
+
+    public abstract int parseAddr();
+
+    public abstract int parseSize();
+
+    abstract Map<String, Symbol> getSymbols();
+
+    protected int parseFirstHexInt(String regexp, String[] data) {
+      String retString = getFirstMatchGroup(data, regexp, 1);
+
+      if (retString == null || retString.equals("")) {
+        return -1;
+      }
+
+      return Integer.parseInt(retString.trim(), 16);
+    }
+
+    public MemoryInterface parse() {
+
+      int mapSectionAddr = parseAddr();
+      int mapSectionSize = parseSize();
+
+      if (mapSectionAddr < 0 || mapSectionSize <= 0) {
+        return null;
+      }
+
+      Map<String, Symbol> variables = getMapFileVarsInRange(
+              getData(),
+              mapSectionAddr,
+              mapSectionAddr + mapSectionSize);
+      if (variables == null || variables.isEmpty()) {
+        logger.warn("Map data symbol parsing failed");
+      }
+
+      logger.info(String.format("Parsed section at 0x%x ( %d == 0x%x bytes)",
+//                                getContikiFirmwareFile().getName(),
+                                mapSectionAddr,
+                                mapSectionSize,
+                                mapSectionSize));
+
+      return new ArrayMemory(
+              mapSectionAddr,
+              mapSectionSize,
+              MemoryLayout.getNative(),
+              variables);
+    }
+
+  }
+
+  /**
+   * Parses Map file for seciton data.
+   */
+  public static class MapSectionParser extends SectionParser {
+
+    private final String startRegExp;
+    private final String sizeRegExp;
+
+    public MapSectionParser(String[] mapFileData, String startRegExp, String sizeRegExp) {
+      super(mapFileData);
+      this.startRegExp = startRegExp;
+      this.sizeRegExp = sizeRegExp;
+    }
+
+    @Override
+    public int parseAddr() {
+      if (startRegExp == null) {
+        return -1;
+      }
+      return parseFirstHexInt(startRegExp, getData());
+    }
+
+    @Override
+    public int parseSize() {
+      if (sizeRegExp == null) {
+        return -1;
+      }
+      return parseFirstHexInt(sizeRegExp, getData());
+    }
+
+    @Override
+    public Map<String, Symbol> getSymbols() {
+      return getMapFileVarsInRange(
+              getData(),
+              parseAddr(),
+              parseAddr() + parseSize());
+    }
+  }
+
+  /**
+   * Parses command output for section data.
+   */
+  public static class CommandSectionParser extends SectionParser {
+
+    private final String startRegExp;
+    private final String sizeRegExp;
+
+    public CommandSectionParser(String[] mapFileData, String startRegExp, String sizeRegExp) {
+      super(mapFileData);
+      this.startRegExp = startRegExp;
+      this.sizeRegExp = sizeRegExp;
+    }
+
+    @Override
+    public int parseAddr() {
+      if (startRegExp == null) {
+        return -1;
+      }
+      return parseFirstHexInt(startRegExp, getData());
+    }
+
+    @Override
+    public int parseSize() {
+      if (sizeRegExp == null) {
+        return -1;
+      }
+
+      int start = parseAddr();
+      if (start < 0) {
+        return -1;
+      }
+
+      int end = parseFirstHexInt(sizeRegExp, getData());
+      if (end < 0) {
+        return -1;
+      }
+      return end - start;
+    }
+
+    @Override
+    public Map<String, Symbol> getSymbols() {
+      return parseCommandVariables(getData());
     }
   }
 
@@ -610,46 +721,19 @@ public class ContikiMoteType implements MoteType {
     myCoreComm.setMemory(relAddr, length, mem);
   }
 
-  /**
-   * Parses specified map file data for variable name to addresses mappings. The
-   * mappings are added to the given properties object.
-   *
-   * @param mapFileData
-   * Contents of entire map file
-   * @param varAddresses
-   * Properties that should contain the name to addresses mappings.
-   */
-  public static boolean parseMapFileData(String[] mapFileData, HashMap<String, Symbol> varAddresses) {
-    String[] varNames = getMapFileVarNames(mapFileData);
-    if (varNames == null || varNames.length == 0) {
-      return false;
-    }
-
-    for (String varName : varNames) {
-      int varAddress = getMapFileVarAddress(mapFileData, varName);
-      if (varAddress > 0) {
-        varAddresses.put(varName, new Symbol(Symbol.Type.VARIABLE, varName, varAddress, 1));
-      } else {
-        logger.warn("Parsed Contiki variable '" + varName
-                + "' but could not find address");
-      }
-    }
-
-    return true;
-  }
-
   /**
    * Parses parse command output for variable name to addresses mappings.
    * The mappings are written to the given properties object.
+   * 
+   * TODO: need InRange version!
    *
    * @param output Command output
-   * @param addresses Variable addresses mappings
+   * @return
    */
-  public static boolean parseCommandData(String[] output, HashMap<String, Symbol> addresses) {
+  public static Map<String, Symbol> parseCommandVariables(String[] output) {
     int nrNew = 0, nrOld = 0, nrMismatch = 0;
-
-    Pattern pattern
-            = Pattern.compile(Cooja.getExternalToolsSetting("COMMAND_VAR_NAME_ADDRESS"));
+    HashMap<String, Symbol> addresses = new HashMap<>();
+    Pattern pattern = Pattern.compile(Cooja.getExternalToolsSetting("COMMAND_VAR_NAME_ADDRESS"));
 
     for (String line : output) {
       Matcher matcher = pattern.matcher(line);
@@ -659,6 +743,7 @@ public class ContikiMoteType implements MoteType {
         String symbol = matcher.group(2);
         int address = Integer.parseInt(matcher.group(1), 16);
 
+        /* XXX needs to be checked */
         if (!addresses.containsKey(symbol)) {
           nrNew++;
           addresses.put(symbol, new Symbol(Symbol.Type.VARIABLE, symbol, address, 1));
@@ -682,7 +767,7 @@ public class ContikiMoteType implements MoteType {
      logger.debug("Command response parsing summary: Added " + nrNew
      + " variables. Found " + nrOld + " old variables");
      }*/
-    return (nrNew + nrOld) > 0;
+    return addresses;
   }
 
   @Override
@@ -754,6 +839,9 @@ public class ContikiMoteType implements MoteType {
   }
 
   private static String getFirstMatchGroup(String[] lines, String regexp, int groupNr) {
+    if (regexp == null) {
+      return null;
+    }
     Pattern pattern = Pattern.compile(regexp);
     for (String line : lines) {
       Matcher matcher = pattern.matcher(line);
@@ -764,34 +852,11 @@ public class ContikiMoteType implements MoteType {
     return null;
   }
 
-  /**
-   * Returns all variable names in both data and BSS section by parsing the map
-   * file. These values should not be trusted completely as the parsing may
-   * fail.
-   *
-   * @return Variable names found in the data and bss section
-   */
-  public static String[] getMapFileVarNames(String[] mapFileData) {
-    ArrayList<String> varNames = new ArrayList<>();
-
-    String[] dataVariables = getAllVariableNames(
-            mapFileData,
-            parseMapDataSectionAddr(mapFileData),
-            parseMapDataSectionAddr(mapFileData) + parseMapDataSectionSize(mapFileData));
-    varNames.addAll(Arrays.asList(dataVariables));
-
-    String[] bssVariables = getAllVariableNames(
-            mapFileData,
-            parseMapBssSectionAddr(mapFileData),
-            parseMapBssSectionAddr(mapFileData) + parseMapBssSectionSize(mapFileData));
-    varNames.addAll(Arrays.asList(bssVariables));
-
-    return varNames.toArray(new String[0]);
-  }
-
-  private static String[] getAllVariableNames(String[] lines,
-                                              int startAddress, int endAddress) {
-    ArrayList<String> varNames = new ArrayList<>();
+  private static Map<String, Symbol> getMapFileVarsInRange(
+          String[] lines,
+          int startAddress,
+          int endAddress) {
+    Map<String, Symbol> varNames = new HashMap<>();
 
     Pattern pattern = Pattern.compile(Cooja.getExternalToolsSetting("MAPFILE_VAR_NAME"));
     for (String line : lines) {
@@ -799,11 +864,16 @@ public class ContikiMoteType implements MoteType {
       if (matcher.find()) {
         if (Integer.decode(matcher.group(1)).intValue() >= startAddress
                 && Integer.decode(matcher.group(1)).intValue() <= endAddress) {
-          varNames.add(matcher.group(2));
+          String varName = matcher.group(2);
+          varNames.put(varName, new Symbol(
+                  Symbol.Type.VARIABLE,
+                  varName,
+                  getMapFileVarAddress(lines, varName),
+                  getMapFileVarSize(lines, varName)));
         }
       }
     }
-    return varNames.toArray(new String[0]);
+    return varNames;
   }
 
   /**
@@ -841,156 +911,6 @@ public class ContikiMoteType implements MoteType {
     return -1;
   }
 
-  private static int parseFirstHexInt(String regexp, String[] data) {
-    String retString
-            = getFirstMatchGroup(data, regexp, 1);
-
-    if (retString != null) {
-      return Integer.parseInt(retString.trim(), 16);
-    } else {
-      return -1;
-    }
-  }
-
-  public static int parseMapDataSectionAddr(String[] mapFileData) {
-    String regexp = Cooja.getExternalToolsSetting("MAPFILE_DATA_START", "");
-    if (regexp.equals("")) {
-      return -1;
-    }
-    return parseFirstHexInt(regexp, mapFileData);
-  }
-
-  public static int parseMapDataSectionSize(String[] mapFileData) {
-    String regexp = Cooja.getExternalToolsSetting("MAPFILE_DATA_SIZE", "");
-    if (regexp.equals("")) {
-      return -1;
-    }
-    return parseFirstHexInt(regexp, mapFileData);
-  }
-
-  public static int parseMapBssSectionAddr(String[] mapFileData) {
-    String regexp = Cooja.getExternalToolsSetting("MAPFILE_BSS_START", "");
-    if (regexp.equals("")) {
-      return -1;
-    }
-    return parseFirstHexInt(regexp, mapFileData);
-  }
-
-  public static int parseMapBssSectionSize(String[] mapFileData) {
-    String regexp = Cooja.getExternalToolsSetting("MAPFILE_BSS_SIZE", "");
-    if (regexp.equals("")) {
-      return -1;
-    }
-    return parseFirstHexInt(regexp, mapFileData);
-  }
-
-  public static int parseMapCommonSectionAddr(String[] mapFileData) {
-    String regexp = Cooja.getExternalToolsSetting("MAPFILE_COMMON_START", "");
-    if (regexp.equals("")) {
-      return -1;
-    }
-    return parseFirstHexInt(regexp, mapFileData);
-  }
-
-  public static int parseMapCommonSectionSize(String[] mapFileData) {
-    String regexp = Cooja.getExternalToolsSetting("MAPFILE_COMMON_SIZE", "");
-    if (regexp.equals("")) {
-      return -1;
-    }
-    return parseFirstHexInt(regexp, mapFileData);
-  }
-
-  public static int parseCommandDataSectionAddr(String[] output) {
-    String regexp = Cooja.getExternalToolsSetting("COMMAND_DATA_START", "");
-    if (regexp.equals("")) {
-      return -1;
-    }
-    return parseFirstHexInt(regexp, output);
-  }
-
-  public static int parseCommandDataSectionSize(String[] output) {
-    String regexp = Cooja.getExternalToolsSetting("COMMAND_DATA_END", "");
-    if (regexp.equals("")) {
-      return -1;
-    }
-    int start = parseCommandDataSectionAddr(output);
-    if (start < 0) {
-      return -1;
-    }
-
-    int end = parseFirstHexInt(regexp, output);
-    if (end < 0) {
-      return -1;
-    }
-    return end - start;
-  }
-
-  public static int parseCommandBssSectionAddr(String[] output) {
-    String regexp = Cooja.getExternalToolsSetting("COMMAND_BSS_START", "");
-    if (regexp.equals("")) {
-      return -1;
-    }
-    return parseFirstHexInt(regexp, output);
-  }
-
-  public static int parseCommandBssSectionSize(String[] output) {
-    String regexp = Cooja.getExternalToolsSetting("COMMAND_BSS_END", "");
-    if (regexp.equals("")) {
-      return -1;
-    }
-    int start = parseCommandBssSectionAddr(output);
-    if (start < 0) {
-      return -1;
-    }
-
-    int end = parseFirstHexInt(regexp, output);
-    if (end < 0) {
-      return -1;
-    }
-    return end - start;
-  }
-
-  public static int parseCommandCommonSectionAddr(String[] output) {
-    String regexp = Cooja.getExternalToolsSetting("COMMAND_COMMON_START", "");
-    if (regexp.equals("")) {
-      return -1;
-    }
-    return parseFirstHexInt(regexp, output);
-  }
-
-  public static int parseCommandCommonSectionSize(String[] output) {
-    String regexp = Cooja.getExternalToolsSetting("COMMAND_COMMON_END", "");
-    if (regexp.equals("")) {
-      return -1;
-    }
-    int start = parseCommandCommonSectionAddr(output);
-    if (start < 0) {
-      return -1;
-    }
-
-    int end = parseFirstHexInt(regexp, output);
-    if (end < 0) {
-      return -1;
-    }
-    return end - start;
-  }
-
-  private static int parseCommandReadonlySectionAddr(String[] output) {
-    return parseFirstHexInt("^([0-9A-Fa-f]*)[ \t]t[ \t].text$", output);
-  }
-
-  private static int parseCommandReadonlySectionSize(String[] output) {
-    int start = parseCommandReadonlySectionAddr(output);
-    if (start < 0) {
-      return -1;
-    }
-
-    /* Extract the last specified address, assuming that the interval covers all the memory */
-    String last = output[output.length - 1];
-    int lastAddress = Integer.parseInt(last.split("[ \t]")[0], 16);
-    return lastAddress - start;
-  }
-
   private static int getRelVarAddr(String mapFileData[], String varName) {
     String regExp
             = Cooja.getExternalToolsSetting("MAPFILE_VAR_ADDRESS_1")
diff --git a/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java b/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
index 946d0f88c..de4beff02 100644
--- a/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
+++ b/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
@@ -68,6 +68,7 @@ import org.contikios.cooja.Cooja;
 import org.contikios.cooja.MoteType.MoteTypeCreationException;
 import org.contikios.cooja.mote.memory.SectionMoteMemory;
 import org.contikios.cooja.contikimote.ContikiMoteType;
+import org.contikios.cooja.contikimote.ContikiMoteType.SectionParser;
 import org.contikios.cooja.mote.memory.MemoryInterface.Symbol;
 import org.contikios.cooja.mote.memory.VarMemory;
 
@@ -760,17 +761,25 @@ public class ConfigurationWizard extends JDialog {
 
     testOutput.addMessage("### Parsing map file data for addresses");
     addresses = new HashMap<String, Symbol>();
-    boolean parseOK = ContikiMoteType.parseMapFileData(mapData, addresses);
-    if (!parseOK) {
-      testOutput.addMessage("### Error: Failed parsing map file data", MessageList.ERROR);
-      return false;
-    }
+//    boolean parseOK = ContikiMoteType.parseMapFileData(mapData, addresses);
+//    if (!parseOK) {
+//      testOutput.addMessage("### Error: Failed parsing map file data", MessageList.ERROR);
+//      return false;
+//    }
 
     testOutput.addMessage("### Validating section addresses");
-    relDataSectionAddr = ContikiMoteType.parseMapDataSectionAddr(mapData);
-    dataSectionSize = ContikiMoteType.parseMapDataSectionSize(mapData);
-    relBssSectionAddr = ContikiMoteType.parseMapBssSectionAddr(mapData);
-    bssSectionSize = ContikiMoteType.parseMapBssSectionSize(mapData);
+    SectionParser dataSecParser = new ContikiMoteType.MapSectionParser(
+            mapData,
+            Cooja.getExternalToolsSetting("MAPFILE_DATA_START"),
+            Cooja.getExternalToolsSetting("MAPFILE_DATA_SIZE"));
+    SectionParser bssSecParser = new ContikiMoteType.MapSectionParser(
+            mapData,
+            Cooja.getExternalToolsSetting("MAPFILE_BSS_START"),
+            Cooja.getExternalToolsSetting("MAPFILE_BSS_SIZE"));
+    relDataSectionAddr = dataSecParser.parseAddr();
+    dataSectionSize = dataSecParser.parseSize();
+    relBssSectionAddr = bssSecParser.parseAddr();
+    bssSectionSize = bssSecParser.parseSize();
     testOutput.addMessage("Data section address: 0x" + Integer.toHexString(relDataSectionAddr));
     testOutput.addMessage("Data section size: 0x" + Integer.toHexString(dataSectionSize));
     testOutput.addMessage("BSS section address: 0x" + Integer.toHexString(relBssSectionAddr));
@@ -840,17 +849,26 @@ public class ConfigurationWizard extends JDialog {
 
     testOutput.addMessage("### Parsing command output for addresses");
     addresses = new HashMap<String, Symbol>();
-    boolean parseOK = ContikiMoteType.parseCommandData(commandData, addresses);
-    if (!parseOK) {
-      testOutput.addMessage("### Error: Failed parsing command output", MessageList.ERROR);
-      return false;
-    }
+//    boolean parseOK = ContikiMoteType.parseCommandData(commandData, addresses);
+//    if (!parseOK) {
+//      testOutput.addMessage("### Error: Failed parsing command output", MessageList.ERROR);
+//      return false;
+//    }
 
     testOutput.addMessage("### Validating section addresses");
-    relDataSectionAddr = ContikiMoteType.parseCommandDataSectionAddr(commandData);
-    dataSectionSize = ContikiMoteType.parseCommandDataSectionSize(commandData);
-    relBssSectionAddr = ContikiMoteType.parseCommandBssSectionAddr(commandData);
-    bssSectionSize = ContikiMoteType.parseCommandBssSectionSize(commandData);
+    SectionParser dataSecParser = new ContikiMoteType.CommandSectionParser(
+            commandData,
+            Cooja.getExternalToolsSetting("COMMAND_DATA_START"),
+            Cooja.getExternalToolsSetting("COMMAND_DATA_SIZE"));
+    SectionParser bssSecParser = new ContikiMoteType.CommandSectionParser(
+            commandData,
+            Cooja.getExternalToolsSetting("COMMAND_BSS_START"),
+            Cooja.getExternalToolsSetting("COMMAND_BSS_SIZE"));
+
+    relDataSectionAddr = dataSecParser.parseAddr();
+    dataSectionSize = dataSecParser.parseSize();
+    relBssSectionAddr = bssSecParser.parseAddr();
+    bssSectionSize = bssSecParser.parseSize();
     testOutput.addMessage("Data section address: 0x" + Integer.toHexString(relDataSectionAddr));
     testOutput.addMessage("Data section size: 0x" + Integer.toHexString(dataSectionSize));
     testOutput.addMessage("BSS section address: 0x" + Integer.toHexString(relBssSectionAddr));

From 66d4dad1e179e11618dee3ab33f695b40a06cb10 Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Tue, 29 Jul 2014 21:31:32 +0200
Subject: [PATCH 19/28] [cooja] Removed offset from SectionMoteMemory to make
 it more generic

---
 .../cooja/contikimote/ContikiMoteType.java          |  8 +++++---
 .../cooja/dialogs/ConfigurationWizard.java          |  2 +-
 .../cooja/mote/memory/SectionMoteMemory.java        | 13 ++-----------
 .../cooja/motes/AbstractApplicationMote.java        |  4 ++--
 4 files changed, 10 insertions(+), 17 deletions(-)

diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
index 2a633f67a..adeed023d 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
@@ -212,6 +212,9 @@ public class ContikiMoteType implements MoteType {
   // Initial memory for all motes of this type
   private SectionMoteMemory initialMemory = null;
 
+  /** Offset between native (cooja) and contiki address space */
+  long offset;
+
   /**
    * Creates a new uninitialized Cooja mote type. This mote type needs to load
    * a library file and parse a map file before it can be used.
@@ -484,9 +487,8 @@ public class ContikiMoteType implements MoteType {
      *
      * This offset will be used in Cooja in the memory abstraction to match
      * Contiki's and Cooja's address spaces */
-    int offset;
     {
-      SectionMoteMemory tmp = new SectionMoteMemory(variables, 0);
+      SectionMoteMemory tmp = new SectionMoteMemory(variables);
       VarMemory varMem = new VarMemory(tmp);
       tmp.addMemorySection("tmp.data", dataSecParser.parse());
 
@@ -508,7 +510,7 @@ public class ContikiMoteType implements MoteType {
     }
 
     /* Create initial memory: data+bss+optional common */
-    initialMemory = new SectionMoteMemory(variables, offset);
+    initialMemory = new SectionMoteMemory(variables);
 
     initialMemory.addMemorySection("data", dataSecParser.parse());
 
diff --git a/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java b/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
index de4beff02..40202fc7a 100644
--- a/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
+++ b/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
@@ -963,7 +963,7 @@ public class ConfigurationWizard extends JDialog {
     byte[] initialBssSection = new byte[bssSectionSize];
     javaLibrary.getMemory(relDataSectionAddr, dataSectionSize, initialDataSection);
     javaLibrary.getMemory(relBssSectionAddr, bssSectionSize, initialBssSection);
-    SectionMoteMemory memory = new SectionMoteMemory(addresses, 0);
+    SectionMoteMemory memory = new SectionMoteMemory(addresses);
     VarMemory varMem = new VarMemory(memory);
     memory.setMemorySegment(relDataSectionAddr, initialDataSection);
     memory.setMemorySegment(relBssSectionAddr, initialBssSection);
diff --git a/tools/cooja/java/org/contikios/cooja/mote/memory/SectionMoteMemory.java b/tools/cooja/java/org/contikios/cooja/mote/memory/SectionMoteMemory.java
index f1a43cebe..62c12df24 100644
--- a/tools/cooja/java/org/contikios/cooja/mote/memory/SectionMoteMemory.java
+++ b/tools/cooja/java/org/contikios/cooja/mote/memory/SectionMoteMemory.java
@@ -57,16 +57,11 @@ public class SectionMoteMemory implements MemoryInterface {
   private MemoryLayout memLayout;
   private long startAddr = Long.MAX_VALUE;
 
-  /* used to map Cooja's address space to native (Contiki's) addresses */
-  private final int offset;
-  
   /**
    * @param symbols Symbol addresses
-   * @param offset Offset for internally used addresses
    */
-  public SectionMoteMemory(Map<String, Symbol> symbols, int offset) {
+  public SectionMoteMemory(Map<String, Symbol> symbols) {
     this.symbols = symbols;
-    this.offset = offset;
   }
 
   /**
@@ -248,10 +243,6 @@ public class SectionMoteMemory implements MemoryInterface {
             address, address + data.length - 1);
   }
 
-  public void setMemorySegmentNative(long address, byte[] data) throws MoteMemoryException {
-    setMemorySegment(address + offset, data);
-  }
-
   @Override
   public long getStartAddr() {
     return startAddr;
@@ -292,7 +283,7 @@ public class SectionMoteMemory implements MemoryInterface {
   @Override
   public SectionMoteMemory clone() {
 
-    SectionMoteMemory clone = new SectionMoteMemory(symbols, offset);
+    SectionMoteMemory clone = new SectionMoteMemory(symbols);
 
     for (String secname : sections.keySet()) {
       // Copy section memory to new ArrayMemory
diff --git a/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java b/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
index a7a8deaf6..98de78327 100644
--- a/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
+++ b/tools/cooja/java/org/contikios/cooja/motes/AbstractApplicationMote.java
@@ -92,7 +92,7 @@ public abstract class AbstractApplicationMote extends AbstractWakeupMote impleme
     setSimulation(sim);
     this.moteType = moteType;
     MemoryLayout.getNative();
-    this.memory = new SectionMoteMemory(new HashMap<String, Symbol>(), 0);
+    this.memory = new SectionMoteMemory(new HashMap<String, Symbol>());
     this.moteInterfaces = new MoteInterfaceHandler(this, moteType.getMoteInterfaceClasses());
     this.moteInterfaces.getRadio().addObserver(radioDataObserver);
     requestImmediateWakeup();
@@ -152,7 +152,7 @@ public abstract class AbstractApplicationMote extends AbstractWakeupMote impleme
   public boolean setConfigXML(Simulation simulation,
       Collection<Element> configXML, boolean visAvailable) {
     setSimulation(simulation);
-    this.memory = new SectionMoteMemory(new HashMap<String, Symbol>(), 0);
+    this.memory = new SectionMoteMemory(new HashMap<String, Symbol>());
     moteInterfaces.getRadio().addObserver(radioDataObserver);
 
     for (Element element : configXML) {

From defcd1a34c31f03b6200b392a3e24704cecb8b4d Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Wed, 30 Jul 2014 00:09:35 +0200
Subject: [PATCH 20/28] [cooja] ContikiMoteType: Moved further parse functions
 to SectionParser classes

---
 .../cooja/contikimote/ContikiMoteType.java    | 234 +++++++-----------
 .../cooja/dialogs/ConfigurationWizard.java    |   8 +-
 2 files changed, 95 insertions(+), 147 deletions(-)

diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
index adeed023d..96bbaf27c 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
@@ -469,7 +469,7 @@ public class ContikiMoteType implements MoteType {
     }
 
     try {
-      Map<String, Symbol> vars = bssSecParser.getSymbols();
+      Map<String, Symbol> vars = bssSecParser.parseSymbols();
       for (Symbol s : vars.values()) {
         if (s.name.equals("referenceVar")) {
           /* Relative <-> absolute addresses offset */
@@ -525,6 +525,9 @@ public class ContikiMoteType implements MoteType {
     getCoreMemory(initialMemory);
   }
 
+  /**
+   * 
+   */
   public static abstract class SectionParser {
 
     private final String[] mapFileData;
@@ -537,11 +540,11 @@ public class ContikiMoteType implements MoteType {
       return mapFileData;
     }
 
-    public abstract int parseAddr();
+    public abstract int parseStartAddr();
 
     public abstract int parseSize();
 
-    abstract Map<String, Symbol> getSymbols();
+    abstract Map<String, Symbol> parseSymbols();
 
     protected int parseFirstHexInt(String regexp, String[] data) {
       String retString = getFirstMatchGroup(data, regexp, 1);
@@ -555,20 +558,15 @@ public class ContikiMoteType implements MoteType {
 
     public MemoryInterface parse() {
 
-      int mapSectionAddr = parseAddr();
+      /* Parse start address and size of section */
+      int mapSectionAddr = parseStartAddr();
       int mapSectionSize = parseSize();
 
       if (mapSectionAddr < 0 || mapSectionSize <= 0) {
         return null;
       }
 
-      Map<String, Symbol> variables = getMapFileVarsInRange(
-              getData(),
-              mapSectionAddr,
-              mapSectionAddr + mapSectionSize);
-      if (variables == null || variables.isEmpty()) {
-        logger.warn("Map data symbol parsing failed");
-      }
+      Map<String, Symbol> variables = parseSymbols();
 
       logger.info(String.format("Parsed section at 0x%x ( %d == 0x%x bytes)",
 //                                getContikiFirmwareFile().getName(),
@@ -600,7 +598,7 @@ public class ContikiMoteType implements MoteType {
     }
 
     @Override
-    public int parseAddr() {
+    public int parseStartAddr() {
       if (startRegExp == null) {
         return -1;
       }
@@ -616,11 +614,59 @@ public class ContikiMoteType implements MoteType {
     }
 
     @Override
-    public Map<String, Symbol> getSymbols() {
-      return getMapFileVarsInRange(
-              getData(),
-              parseAddr(),
-              parseAddr() + parseSize());
+    public Map<String, Symbol> parseSymbols() {
+      Map<String, Symbol> varNames = new HashMap<>();
+
+      Pattern pattern = Pattern.compile(Cooja.getExternalToolsSetting("MAPFILE_VAR_NAME"));
+      for (String line : getData()) {
+        Matcher matcher = pattern.matcher(line);
+        if (matcher.find()) {
+          if (Integer.decode(matcher.group(1)).intValue() >= parseStartAddr()
+                  && Integer.decode(matcher.group(1)).intValue() <= parseStartAddr() + parseSize()) {
+            String varName = matcher.group(2);
+            varNames.put(varName, new Symbol(
+                    Symbol.Type.VARIABLE,
+                    varName,
+                    getMapFileVarAddress(getData(), varName),
+                    getMapFileVarSize(getData(), varName)));
+          }
+        }
+      }
+      return varNames;
+    }
+
+    /**
+     * Get relative address of variable with given name.
+     *
+     * @param varName Name of variable
+     * @return Relative memory address of variable or -1 if not found
+     */
+    private int getMapFileVarAddress(String[] mapFileData, String varName) {
+
+      String regExp = Cooja.getExternalToolsSetting("MAPFILE_VAR_ADDRESS_1")
+              + varName
+              + Cooja.getExternalToolsSetting("MAPFILE_VAR_ADDRESS_2");
+      String retString = getFirstMatchGroup(mapFileData, regExp, 1);
+
+      if (retString != null) {
+        return Integer.parseInt(retString.trim(), 16);
+      } else {
+        return -1;
+      }
+    }
+
+    private int getMapFileVarSize(String[] mapFileData, String varName) {
+      Pattern pattern = Pattern.compile(
+              Cooja.getExternalToolsSetting("MAPFILE_VAR_SIZE_1")
+              + varName
+              + Cooja.getExternalToolsSetting("MAPFILE_VAR_SIZE_2"));
+      for (String line : mapFileData) {
+        Matcher matcher = pattern.matcher(line);
+        if (matcher.find()) {
+          return Integer.decode(matcher.group(1));
+        }
+      }
+      return -1;
     }
   }
 
@@ -639,7 +685,7 @@ public class ContikiMoteType implements MoteType {
     }
 
     @Override
-    public int parseAddr() {
+    public int parseStartAddr() {
       if (startRegExp == null) {
         return -1;
       }
@@ -652,7 +698,7 @@ public class ContikiMoteType implements MoteType {
         return -1;
       }
 
-      int start = parseAddr();
+      int start = parseStartAddr();
       if (start < 0) {
         return -1;
       }
@@ -665,8 +711,32 @@ public class ContikiMoteType implements MoteType {
     }
 
     @Override
-    public Map<String, Symbol> getSymbols() {
-      return parseCommandVariables(getData());
+    public Map<String, Symbol> parseSymbols() {
+      HashMap<String, Symbol> addresses = new HashMap<>();
+      Pattern pattern = Pattern.compile(Cooja.getExternalToolsSetting("COMMAND_VAR_NAME_ADDRESS"));
+
+      for (String line : getData()) {
+        Matcher matcher = pattern.matcher(line);
+
+        if (matcher.find()) {
+          /* Line matched variable address */
+          String symbol = matcher.group(2);
+          int address = Integer.parseInt(matcher.group(1), 16);
+
+          /* XXX needs to be checked */
+          if (!addresses.containsKey(symbol)) {
+            addresses.put(symbol, new Symbol(Symbol.Type.VARIABLE, symbol, address, 1));
+          } else {
+            int oldAddress = (int) addresses.get(symbol).addr;
+            if (oldAddress != address) {
+              /*logger.warn("Warning, command response not matching previous entry of: "
+               + varName);*/
+            }
+          }
+        }
+      }
+
+      return addresses;
     }
   }
 
@@ -723,55 +793,6 @@ public class ContikiMoteType implements MoteType {
     myCoreComm.setMemory(relAddr, length, mem);
   }
 
-  /**
-   * Parses parse command output for variable name to addresses mappings.
-   * The mappings are written to the given properties object.
-   * 
-   * TODO: need InRange version!
-   *
-   * @param output Command output
-   * @return
-   */
-  public static Map<String, Symbol> parseCommandVariables(String[] output) {
-    int nrNew = 0, nrOld = 0, nrMismatch = 0;
-    HashMap<String, Symbol> addresses = new HashMap<>();
-    Pattern pattern = Pattern.compile(Cooja.getExternalToolsSetting("COMMAND_VAR_NAME_ADDRESS"));
-
-    for (String line : output) {
-      Matcher matcher = pattern.matcher(line);
-
-      if (matcher.find()) {
-        /* Line matched variable address */
-        String symbol = matcher.group(2);
-        int address = Integer.parseInt(matcher.group(1), 16);
-
-        /* XXX needs to be checked */
-        if (!addresses.containsKey(symbol)) {
-          nrNew++;
-          addresses.put(symbol, new Symbol(Symbol.Type.VARIABLE, symbol, address, 1));
-        } else {
-          int oldAddress = (int) addresses.get(symbol).addr;
-          if (oldAddress != address) {
-            /*logger.warn("Warning, command response not matching previous entry of: "
-             + varName);*/
-            nrMismatch++;
-          }
-          nrOld++;
-        }
-      }
-    }
-
-    /*if (nrMismatch > 0) {
-     logger.debug("Command response parsing summary: Added " + nrNew
-     + " variables. Found " + nrOld
-     + " old variables. Mismatching addresses: " + nrMismatch);
-     } else {
-     logger.debug("Command response parsing summary: Added " + nrNew
-     + " variables. Found " + nrOld + " old variables");
-     }*/
-    return addresses;
-  }
-
   @Override
   public String getIdentifier() {
     return identifier;
@@ -854,79 +875,6 @@ public class ContikiMoteType implements MoteType {
     return null;
   }
 
-  private static Map<String, Symbol> getMapFileVarsInRange(
-          String[] lines,
-          int startAddress,
-          int endAddress) {
-    Map<String, Symbol> varNames = new HashMap<>();
-
-    Pattern pattern = Pattern.compile(Cooja.getExternalToolsSetting("MAPFILE_VAR_NAME"));
-    for (String line : lines) {
-      Matcher matcher = pattern.matcher(line);
-      if (matcher.find()) {
-        if (Integer.decode(matcher.group(1)).intValue() >= startAddress
-                && Integer.decode(matcher.group(1)).intValue() <= endAddress) {
-          String varName = matcher.group(2);
-          varNames.put(varName, new Symbol(
-                  Symbol.Type.VARIABLE,
-                  varName,
-                  getMapFileVarAddress(lines, varName),
-                  getMapFileVarSize(lines, varName)));
-        }
-      }
-    }
-    return varNames;
-  }
-
-  /**
-   * Get relative address of variable with given name.
-   *
-   * @param varName Name of variable
-   * @return Relative memory address of variable or -1 if not found
-   */
-  private static int getMapFileVarAddress(String[] mapFileData, String varName) {
-
-    String regExp = Cooja.getExternalToolsSetting("MAPFILE_VAR_ADDRESS_1")
-            + varName
-            + Cooja.getExternalToolsSetting("MAPFILE_VAR_ADDRESS_2");
-    String retString = getFirstMatchGroup(mapFileData, regExp, 1);
-
-    if (retString != null) {
-      return Integer.parseInt(retString.trim(), 16);
-    }
-    else {
-      return -1;
-    }
-  }
-
-  protected static int getMapFileVarSize(String[] mapFileData, String varName) {
-    Pattern pattern = Pattern.compile(
-            Cooja.getExternalToolsSetting("MAPFILE_VAR_SIZE_1")
-            + varName
-            + Cooja.getExternalToolsSetting("MAPFILE_VAR_SIZE_2"));
-    for (String line : mapFileData) {
-      Matcher matcher = pattern.matcher(line);
-      if (matcher.find()) {
-        return Integer.decode(matcher.group(1));
-      }
-    }
-    return -1;
-  }
-
-  private static int getRelVarAddr(String mapFileData[], String varName) {
-    String regExp
-            = Cooja.getExternalToolsSetting("MAPFILE_VAR_ADDRESS_1")
-            + varName
-            + Cooja.getExternalToolsSetting("MAPFILE_VAR_ADDRESS_2");
-    String retString = getFirstMatchGroup(mapFileData, regExp, 1);
-
-    if (retString != null) {
-      return Integer.parseInt(retString.trim(), 16);
-    } else {
-      return -1;
-    }
-  }
-
   public static String[] loadMapFile(File mapFile) {
     String contents = StringUtils.loadFromFile(mapFile);
     if (contents == null) {
diff --git a/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java b/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
index 40202fc7a..cdb7ef8c3 100644
--- a/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
+++ b/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
@@ -776,9 +776,9 @@ public class ConfigurationWizard extends JDialog {
             mapData,
             Cooja.getExternalToolsSetting("MAPFILE_BSS_START"),
             Cooja.getExternalToolsSetting("MAPFILE_BSS_SIZE"));
-    relDataSectionAddr = dataSecParser.parseAddr();
+    relDataSectionAddr = dataSecParser.parseStartAddr();
     dataSectionSize = dataSecParser.parseSize();
-    relBssSectionAddr = bssSecParser.parseAddr();
+    relBssSectionAddr = bssSecParser.parseStartAddr();
     bssSectionSize = bssSecParser.parseSize();
     testOutput.addMessage("Data section address: 0x" + Integer.toHexString(relDataSectionAddr));
     testOutput.addMessage("Data section size: 0x" + Integer.toHexString(dataSectionSize));
@@ -865,9 +865,9 @@ public class ConfigurationWizard extends JDialog {
             Cooja.getExternalToolsSetting("COMMAND_BSS_START"),
             Cooja.getExternalToolsSetting("COMMAND_BSS_SIZE"));
 
-    relDataSectionAddr = dataSecParser.parseAddr();
+    relDataSectionAddr = dataSecParser.parseStartAddr();
     dataSectionSize = dataSecParser.parseSize();
-    relBssSectionAddr = bssSecParser.parseAddr();
+    relBssSectionAddr = bssSecParser.parseStartAddr();
     bssSectionSize = bssSecParser.parseSize();
     testOutput.addMessage("Data section address: 0x" + Integer.toHexString(relDataSectionAddr));
     testOutput.addMessage("Data section size: 0x" + Integer.toHexString(dataSectionSize));

From f5531dfa74a470cf722e63ff49be9c0a2e5b418d Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Tue, 5 Aug 2014 17:25:38 +0200
Subject: [PATCH 21/28] [cooja] ContikiMoteType: Fix mapfile variable size
 parsing

For some longer variable names the lines are wrapped after the name
to display size information vertical aligned.
---
 .../cooja/contikimote/ContikiMoteType.java          | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
index 96bbaf27c..46d94ddf9 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
@@ -660,8 +660,17 @@ public class ContikiMoteType implements MoteType {
               Cooja.getExternalToolsSetting("MAPFILE_VAR_SIZE_1")
               + varName
               + Cooja.getExternalToolsSetting("MAPFILE_VAR_SIZE_2"));
-      for (String line : mapFileData) {
-        Matcher matcher = pattern.matcher(line);
+      for (int idx = 0; idx < mapFileData.length; idx++) {
+        String parseString = mapFileData[idx];
+        Matcher matcher = pattern.matcher(parseString);
+        if (matcher.find()) {
+          return Integer.decode(matcher.group(1));
+        }
+        // second approach with lines joined
+        if (idx < mapFileData.length - 1) {
+          parseString += mapFileData[idx + 1];
+        }
+        matcher = pattern.matcher(parseString);
         if (matcher.find()) {
           return Integer.decode(matcher.group(1));
         }

From d4e36dcd4782745dd4a07a5025eb7f8ac1a8d3d7 Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Tue, 5 Aug 2014 18:22:34 +0200
Subject: [PATCH 22/28] [cooja] logging: default logging level should not be
 highest

---
 tools/cooja/config/log4j_config.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/cooja/config/log4j_config.xml b/tools/cooja/config/log4j_config.xml
index ff9741f0c..d3d269bb8 100644
--- a/tools/cooja/config/log4j_config.xml
+++ b/tools/cooja/config/log4j_config.xml
@@ -18,7 +18,7 @@
   </appender>
 
   <root>
-    <priority value="debug"/>
+    <priority value="info"/>
     <appender-ref ref="logfile"/>
     <appender-ref ref="stdout"/>
   </root>

From 3da6c6d55a157d515a7c32cc190cc809df37a617 Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Wed, 6 Aug 2014 16:07:52 +0200
Subject: [PATCH 23/28] [cooja] ContikiMoteType: Fixed Command parsing

- Use `nm -aP` for parsing both addres and size information
- Use symbol section information for parsing
---
 tools/cooja/config/external_tools.config      |  19 ++-
 .../cooja/java/org/contikios/cooja/Cooja.java |   2 +-
 .../cooja/contikimote/ContikiMoteType.java    | 148 ++++++++++++------
 .../cooja/dialogs/ConfigurationWizard.java    |  26 +--
 4 files changed, 129 insertions(+), 66 deletions(-)

diff --git a/tools/cooja/config/external_tools.config b/tools/cooja/config/external_tools.config
index 18ad0be46..89d9c4f7d 100644
--- a/tools/cooja/config/external_tools.config
+++ b/tools/cooja/config/external_tools.config
@@ -25,7 +25,6 @@ PATH_JAVAC = javac
 DEFAULT_PROJECTDIRS = [CONTIKI_DIR]/tools/cooja/apps/mrm;[CONTIKI_DIR]/tools/cooja/apps/mspsim;[CONTIKI_DIR]/tools/cooja/apps/avrora;[CONTIKI_DIR]/tools/cooja/apps/serial_socket;[CONTIKI_DIR]/tools/cooja/apps/collect-view;[CONTIKI_DIR]/tools/cooja/apps/powertracker
 
 PARSE_WITH_COMMAND=false
-PARSE_COMMAND=nm -a $(LIBFILE)
 MAPFILE_DATA_START = ^.data[ \t]*0x([0-9A-Fa-f]*)[ \t]*0x[0-9A-Fa-f]*[ \t]*$
 MAPFILE_DATA_SIZE = ^.data[ \t]*0x[0-9A-Fa-f]*[ \t]*0x([0-9A-Fa-f]*)[ \t]*$
 MAPFILE_BSS_START = ^.bss[ \t]*0x([0-9A-Fa-f]*)[ \t]*0x[0-9A-Fa-f]*[ \t]*$
@@ -35,11 +34,19 @@ MAPFILE_VAR_ADDRESS_1 = ^[ \t]*0x([0-9A-Fa-f]*)[ \t]*
 MAPFILE_VAR_ADDRESS_2 = [ \t]*$
 MAPFILE_VAR_SIZE_1 = ^
 MAPFILE_VAR_SIZE_2 = [ \t]*(0x[0-9A-Fa-f]*)[ \t]*[^ ]*[ \t]*$
-COMMAND_VAR_NAME_ADDRESS = ^([0-9A-Fa-f][0-9A-Fa-f]*)[ \t][^Tt][ \t]([^ ._][^ ]*)
-COMMAND_DATA_START = ^([0-9A-Fa-f]*)[ \t]d[ \t].data$
-COMMAND_DATA_END = ^([0-9A-Fa-f]*)[ \t]A[ \t]_edata$
-COMMAND_BSS_START = ^([0-9A-Fa-f]*)[ \t]A[ \t]__bss_start$
-COMMAND_BSS_END = ^([0-9A-Fa-f]*)[ \t]A[ \t]_end$
+
+PARSE_COMMAND=nm -aP $(LIBFILE)
+COMMAND_VAR_NAME_ADDRESS_SIZE = ^([^.].*?) <SECTION> ([0-9a-fA-F]+) ([0-9a-fA-F])*
+COMMAND_VAR_SEC_DATA = [DdGg]
+COMMAND_VAR_SEC_BSS = [Bb]
+COMMAND_VAR_SEC_COMMON = [C]
+COMMAND_VAR_SEC_READONLY = [Rr]
+COMMAND_DATA_START = ^.data[ \t]d[ \t]([0-9A-Fa-f]*)[ \t]*$
+COMMAND_DATA_END = ^_edata[ \t]A[ \t]([0-9A-Fa-f]*)[ \t]*$
+COMMAND_BSS_START = ^__bss_start[ \t]A[ \t]([0-9A-Fa-f]*)[ \t]*$
+COMMAND_BSS_END = ^_end[ \t]A[ \t]([0-9A-Fa-f]*)[ \t]*$
+COMMAND_READONLY_START = ^.rodata[ \t]r[ \t]([0-9A-Fa-f]*)[ \t]*$
+COMMAND_READONLY_END = ^.eh_frame_hdr[ \t]r[ \t]([0-9A-Fa-f]*)[ \t]*$
 
 VISUALIZER_DEFAULT_SKINS=\
 org.contikios.cooja.plugins.skins.IDVisualizerSkin;\
diff --git a/tools/cooja/java/org/contikios/cooja/Cooja.java b/tools/cooja/java/org/contikios/cooja/Cooja.java
index 4d1770b6b..055cb46f4 100644
--- a/tools/cooja/java/org/contikios/cooja/Cooja.java
+++ b/tools/cooja/java/org/contikios/cooja/Cooja.java
@@ -274,7 +274,7 @@ public class Cooja extends Observable {
     "MAPFILE_VAR_SIZE_1", "MAPFILE_VAR_SIZE_2",
 
     "PARSE_COMMAND",
-    "COMMAND_VAR_NAME_ADDRESS",
+    "COMMAND_VAR_NAME_ADDRESS_SIZE",
     "COMMAND_DATA_START", "COMMAND_DATA_END",
     "COMMAND_BSS_START", "COMMAND_BSS_END",
     "COMMAND_COMMON_START", "COMMAND_COMMON_END",
diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
index 46d94ddf9..f587003f0 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
@@ -51,6 +51,7 @@ import java.util.regex.Pattern;
 
 import javax.swing.JComponent;
 import javax.swing.JLabel;
+import org.apache.log4j.Level;
 
 import org.apache.log4j.Logger;
 import org.jdom.Element;
@@ -426,19 +427,24 @@ public class ContikiMoteType implements MoteType {
       dataSecParser = new CommandSectionParser(
               output,
               Cooja.getExternalToolsSetting("COMMAND_DATA_START"),
-              Cooja.getExternalToolsSetting("COMMAND_DATA_SIZE"));
+              Cooja.getExternalToolsSetting("COMMAND_DATA_END"),
+              Cooja.getExternalToolsSetting("COMMAND_VAR_SEC_DATA"));
       bssSecParser = new CommandSectionParser(
               output,
               Cooja.getExternalToolsSetting("COMMAND_BSS_START"),
-              Cooja.getExternalToolsSetting("COMMAND_BSS_SIZE"));
+              Cooja.getExternalToolsSetting("COMMAND_BSS_END"),
+              Cooja.getExternalToolsSetting("COMMAND_VAR_SEC_BSS"));
       commonSecParser = new CommandSectionParser(
               output,
               Cooja.getExternalToolsSetting("COMMAND_COMMON_START"),
-              Cooja.getExternalToolsSetting("COMMAND_COMMON_SIZE"));
-      readonlySecParser = new CommandSectionParser(
+              Cooja.getExternalToolsSetting("COMMAND_COMMON_END"),
+              Cooja.getExternalToolsSetting("COMMAND_VAR_SEC_COMMON"));
+      /* XXX Currently Cooja tries to sync readonly memory */
+      readonlySecParser = null;/* new CommandSectionParser(
               output,
-              Cooja.getExternalToolsSetting("^([0-9A-Fa-f]*)[ \t]t[ \t].text$"),
-              Cooja.getExternalToolsSetting("")); // XXX
+              Cooja.getExternalToolsSetting("COMMAND_READONLY_START"),
+              Cooja.getExternalToolsSetting("COMMAND_READONLY_END"),
+              Cooja.getExternalToolsSetting("COMMAND_VAR_SEC_READONLY"));*/
 
     } else {
       /* Parse map file */
@@ -526,11 +532,13 @@ public class ContikiMoteType implements MoteType {
   }
 
   /**
-   * 
+   * Abstract base class for concrete section parser class.
    */
   public static abstract class SectionParser {
 
     private final String[] mapFileData;
+    protected int startAddr;
+    protected int size;
 
     public SectionParser(String[] mapFileData) {
       this.mapFileData = mapFileData;
@@ -540,9 +548,17 @@ public class ContikiMoteType implements MoteType {
       return mapFileData;
     }
 
-    public abstract int parseStartAddr();
+    public int getStartAddr() {
+      return startAddr;
+    }
 
-    public abstract int parseSize();
+    public int getSize() {
+      return size;
+    }
+
+    protected abstract void parseStartAddr();
+
+    protected abstract void parseSize();
 
     abstract Map<String, Symbol> parseSymbols();
 
@@ -559,24 +575,33 @@ public class ContikiMoteType implements MoteType {
     public MemoryInterface parse() {
 
       /* Parse start address and size of section */
-      int mapSectionAddr = parseStartAddr();
-      int mapSectionSize = parseSize();
+      parseStartAddr();
+      parseSize();
 
-      if (mapSectionAddr < 0 || mapSectionSize <= 0) {
+      if (getStartAddr() < 0 || getSize() <= 0) {
         return null;
       }
 
       Map<String, Symbol> variables = parseSymbols();
 
       logger.info(String.format("Parsed section at 0x%x ( %d == 0x%x bytes)",
-//                                getContikiFirmwareFile().getName(),
-                                mapSectionAddr,
-                                mapSectionSize,
-                                mapSectionSize));
+                                getStartAddr(),
+                                getSize(),
+                                getSize()));
+
+      if (logger.isDebugEnabled()) {
+        for (String var : variables.keySet()) {
+          logger.debug(String.format("Found Symbol: %s, 0x%x, %d",
+                                     var,
+                                     variables.get(var).addr,
+                                     variables.get(var).size));
+        }
+      }
+
 
       return new ArrayMemory(
-              mapSectionAddr,
-              mapSectionSize,
+              getStartAddr(),
+              getSize(),
               MemoryLayout.getNative(),
               variables);
     }
@@ -598,19 +623,21 @@ public class ContikiMoteType implements MoteType {
     }
 
     @Override
-    public int parseStartAddr() {
-      if (startRegExp == null) {
-        return -1;
+    protected void parseStartAddr() {
+      if (startRegExp == null || startRegExp.equals("")) {
+        startAddr = -1;
+        return;
       }
-      return parseFirstHexInt(startRegExp, getData());
+      startAddr = parseFirstHexInt(startRegExp, getData());
     }
 
     @Override
-    public int parseSize() {
-      if (sizeRegExp == null) {
-        return -1;
+    protected void parseSize() {
+      if (sizeRegExp == null || sizeRegExp.equals("")) {
+        size = -1;
+        return;
       }
-      return parseFirstHexInt(sizeRegExp, getData());
+      size = parseFirstHexInt(sizeRegExp, getData());
     }
 
     @Override
@@ -621,8 +648,8 @@ public class ContikiMoteType implements MoteType {
       for (String line : getData()) {
         Matcher matcher = pattern.matcher(line);
         if (matcher.find()) {
-          if (Integer.decode(matcher.group(1)).intValue() >= parseStartAddr()
-                  && Integer.decode(matcher.group(1)).intValue() <= parseStartAddr() + parseSize()) {
+          if (Integer.decode(matcher.group(1)).intValue() >= getStartAddr()
+                  && Integer.decode(matcher.group(1)).intValue() <= getStartAddr() + getSize()) {
             String varName = matcher.group(2);
             varNames.put(varName, new Symbol(
                     Symbol.Type.VARIABLE,
@@ -685,59 +712,82 @@ public class ContikiMoteType implements MoteType {
   public static class CommandSectionParser extends SectionParser {
 
     private final String startRegExp;
-    private final String sizeRegExp;
+    private final String endRegExp;
+    private final String sectionRegExp;
 
-    public CommandSectionParser(String[] mapFileData, String startRegExp, String sizeRegExp) {
+    /**
+     * Creates SectionParser based on output of configurable command.
+     * 
+     * @param mapFileData Map file lines as array of String
+     * @param startRegExp Regular expression for parsing start of section
+     * @param endRegExp Regular expression for parsing end of section
+     * @param sectionRegExp Reqular expression describing symbol table section identifier (e.g. '[Rr]' for readonly)
+     *        Will be used to replaced '<SECTION>'in 'COMMAND_VAR_NAME_ADDRESS_SIZE'
+     */
+    public CommandSectionParser(String[] mapFileData, String startRegExp, String endRegExp, String sectionRegExp) {
       super(mapFileData);
       this.startRegExp = startRegExp;
-      this.sizeRegExp = sizeRegExp;
+      this.endRegExp = endRegExp;
+      this.sectionRegExp = sectionRegExp;
     }
 
     @Override
-    public int parseStartAddr() {
-      if (startRegExp == null) {
-        return -1;
+    protected void parseStartAddr() {
+      if (startRegExp == null || startRegExp.equals("")) {
+        startAddr = -1;
+        return;
       }
-      return parseFirstHexInt(startRegExp, getData());
+      startAddr = parseFirstHexInt(startRegExp, getData());
     }
 
     @Override
-    public int parseSize() {
-      if (sizeRegExp == null) {
-        return -1;
+    public void parseSize() {
+      if (endRegExp == null || endRegExp.equals("")) {
+        size = -1;
+        return;
       }
 
-      int start = parseStartAddr();
-      if (start < 0) {
-        return -1;
+      if (getStartAddr() < 0) {
+        size = -1;
+        return;
       }
 
-      int end = parseFirstHexInt(sizeRegExp, getData());
+      int end = parseFirstHexInt(endRegExp, getData());
       if (end < 0) {
-        return -1;
+        size = -1;
+        return;
       }
-      return end - start;
+      size = end - getStartAddr();
     }
 
     @Override
     public Map<String, Symbol> parseSymbols() {
       HashMap<String, Symbol> addresses = new HashMap<>();
-      Pattern pattern = Pattern.compile(Cooja.getExternalToolsSetting("COMMAND_VAR_NAME_ADDRESS"));
+      /* Replace "<SECTION>" in regexp by section specific regex */
+      Pattern pattern = Pattern.compile(
+              Cooja.getExternalToolsSetting("COMMAND_VAR_NAME_ADDRESS_SIZE")
+                      .replace("<SECTION>", sectionRegExp));
 
       for (String line : getData()) {
         Matcher matcher = pattern.matcher(line);
 
         if (matcher.find()) {
           /* Line matched variable address */
-          String symbol = matcher.group(2);
-          int address = Integer.parseInt(matcher.group(1), 16);
+          String symbol = matcher.group(1);
+          int varAddr = Integer.parseInt(matcher.group(2), 16);
+          int varSize;
+          if (matcher.group(3) != null) {
+           varSize = Integer.parseInt(matcher.group(3), 16);
+          } else {
+            varSize = -1;
+          }
 
           /* XXX needs to be checked */
           if (!addresses.containsKey(symbol)) {
-            addresses.put(symbol, new Symbol(Symbol.Type.VARIABLE, symbol, address, 1));
+            addresses.put(symbol, new Symbol(Symbol.Type.VARIABLE, symbol, varAddr, varSize));
           } else {
             int oldAddress = (int) addresses.get(symbol).addr;
-            if (oldAddress != address) {
+            if (oldAddress != varAddr) {
               /*logger.warn("Warning, command response not matching previous entry of: "
                + varName);*/
             }
diff --git a/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java b/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
index cdb7ef8c3..340a3471f 100644
--- a/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
+++ b/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
@@ -776,10 +776,12 @@ public class ConfigurationWizard extends JDialog {
             mapData,
             Cooja.getExternalToolsSetting("MAPFILE_BSS_START"),
             Cooja.getExternalToolsSetting("MAPFILE_BSS_SIZE"));
-    relDataSectionAddr = dataSecParser.parseStartAddr();
-    dataSectionSize = dataSecParser.parseSize();
-    relBssSectionAddr = bssSecParser.parseStartAddr();
-    bssSectionSize = bssSecParser.parseSize();
+    dataSecParser.parse();
+    bssSecParser.parse();
+    relDataSectionAddr = dataSecParser.getStartAddr();
+    dataSectionSize = dataSecParser.getSize();
+    relBssSectionAddr = bssSecParser.getStartAddr();
+    bssSectionSize = bssSecParser.getSize();
     testOutput.addMessage("Data section address: 0x" + Integer.toHexString(relDataSectionAddr));
     testOutput.addMessage("Data section size: 0x" + Integer.toHexString(dataSectionSize));
     testOutput.addMessage("BSS section address: 0x" + Integer.toHexString(relBssSectionAddr));
@@ -859,16 +861,20 @@ public class ConfigurationWizard extends JDialog {
     SectionParser dataSecParser = new ContikiMoteType.CommandSectionParser(
             commandData,
             Cooja.getExternalToolsSetting("COMMAND_DATA_START"),
-            Cooja.getExternalToolsSetting("COMMAND_DATA_SIZE"));
+            Cooja.getExternalToolsSetting("COMMAND_DATA_SIZE"),
+            Cooja.getExternalToolsSetting("COMMAND_VAR_SEC_DATA"));
     SectionParser bssSecParser = new ContikiMoteType.CommandSectionParser(
             commandData,
             Cooja.getExternalToolsSetting("COMMAND_BSS_START"),
-            Cooja.getExternalToolsSetting("COMMAND_BSS_SIZE"));
+            Cooja.getExternalToolsSetting("COMMAND_BSS_SIZE"),
+            Cooja.getExternalToolsSetting("COMMAND_VAR_SEC_BSS"));
 
-    relDataSectionAddr = dataSecParser.parseStartAddr();
-    dataSectionSize = dataSecParser.parseSize();
-    relBssSectionAddr = bssSecParser.parseStartAddr();
-    bssSectionSize = bssSecParser.parseSize();
+    dataSecParser.parse();
+    bssSecParser.parse();
+    relDataSectionAddr = dataSecParser.getStartAddr();
+    dataSectionSize = dataSecParser.getSize();
+    relBssSectionAddr = bssSecParser.getStartAddr();
+    bssSectionSize = bssSecParser.getSize();
     testOutput.addMessage("Data section address: 0x" + Integer.toHexString(relDataSectionAddr));
     testOutput.addMessage("Data section size: 0x" + Integer.toHexString(dataSectionSize));
     testOutput.addMessage("BSS section address: 0x" + Integer.toHexString(relBssSectionAddr));

From 0f2837320c7bf91d9c4c3fe5c83f8ad3b7a10893 Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Wed, 6 Aug 2014 19:01:28 +0200
Subject: [PATCH 24/28] [cooja] Reintroduced offset handling for absolute
 address space

---
 .../cooja/contikimote/ContikiMoteType.java    | 59 ++++++++-----------
 .../cooja/dialogs/ConfigurationWizard.java    |  8 +--
 .../cooja/mote/memory/SectionMoteMemory.java  |  6 +-
 3 files changed, 32 insertions(+), 41 deletions(-)

diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
index f587003f0..8256f0580 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
@@ -474,19 +474,6 @@ public class ContikiMoteType implements MoteType {
 
     }
 
-    try {
-      Map<String, Symbol> vars = bssSecParser.parseSymbols();
-      for (Symbol s : vars.values()) {
-        if (s.name.equals("referenceVar")) {
-          /* Relative <-> absolute addresses offset */
-          int referenceVar = (int) s.addr;
-          myCoreComm.setReferenceAddress(referenceVar);
-        }
-      }
-    } catch (Exception e) {
-      throw new MoteTypeCreationException("JNI call error: " + e.getMessage(), e);
-    }
-
     /* We first need the value of Contiki's referenceVar, which tells us the
      * memory offset between Contiki's variable and the relative addresses that
      * were calculated directly from the library file.
@@ -496,9 +483,9 @@ public class ContikiMoteType implements MoteType {
     {
       SectionMoteMemory tmp = new SectionMoteMemory(variables);
       VarMemory varMem = new VarMemory(tmp);
-      tmp.addMemorySection("tmp.data", dataSecParser.parse());
+      tmp.addMemorySection("tmp.data", dataSecParser.parse(0));
 
-      tmp.addMemorySection("tmp.bss", bssSecParser.parse());
+      tmp.addMemorySection("tmp.bss", bssSecParser.parse(0));
 
       try {
         int referenceVar = (int) varMem.getVariable("referenceVar").addr;
@@ -507,25 +494,24 @@ public class ContikiMoteType implements MoteType {
         throw new MoteTypeCreationException("JNI call error: " + e.getMessage(), e);
       }
 
-      
       getCoreMemory(tmp);
 
-      offset = varMem.getIntValueOf("referenceVar");
+      offset = varMem.getIntValueOf("referenceVar") & 0xFFFFFFFFL;
       logger.info(getContikiFirmwareFile().getName()
-              + ": offsetting Cooja mote address space: " + Long.toHexString(offset));
+              + ": offsetting Cooja mote address space: 0x" + Long.toHexString(offset));
     }
 
     /* Create initial memory: data+bss+optional common */
     initialMemory = new SectionMoteMemory(variables);
 
-    initialMemory.addMemorySection("data", dataSecParser.parse());
+    initialMemory.addMemorySection("data", dataSecParser.parse(offset));
 
-    initialMemory.addMemorySection("bss", bssSecParser.parse());
+    initialMemory.addMemorySection("bss", bssSecParser.parse(offset));
 
-    initialMemory.addMemorySection("common", commonSecParser.parse());
+    initialMemory.addMemorySection("common", commonSecParser.parse(offset));
 
     if (readonlySecParser != null) {
-      initialMemory.addMemorySection("readonly", readonlySecParser.parse());
+      initialMemory.addMemorySection("readonly", readonlySecParser.parse(offset));
     }
 
     getCoreMemory(initialMemory);
@@ -560,7 +546,7 @@ public class ContikiMoteType implements MoteType {
 
     protected abstract void parseSize();
 
-    abstract Map<String, Symbol> parseSymbols();
+    abstract Map<String, Symbol> parseSymbols(long offset);
 
     protected int parseFirstHexInt(String regexp, String[] data) {
       String retString = getFirstMatchGroup(data, regexp, 1);
@@ -572,7 +558,7 @@ public class ContikiMoteType implements MoteType {
       return Integer.parseInt(retString.trim(), 16);
     }
 
-    public MemoryInterface parse() {
+    public MemoryInterface parse(long offset) {
 
       /* Parse start address and size of section */
       parseStartAddr();
@@ -582,10 +568,10 @@ public class ContikiMoteType implements MoteType {
         return null;
       }
 
-      Map<String, Symbol> variables = parseSymbols();
+      Map<String, Symbol> variables = parseSymbols(offset);
 
       logger.info(String.format("Parsed section at 0x%x ( %d == 0x%x bytes)",
-                                getStartAddr(),
+                                getStartAddr() + offset,
                                 getSize(),
                                 getSize()));
 
@@ -598,9 +584,8 @@ public class ContikiMoteType implements MoteType {
         }
       }
 
-
       return new ArrayMemory(
-              getStartAddr(),
+              getStartAddr() + offset,
               getSize(),
               MemoryLayout.getNative(),
               variables);
@@ -641,7 +626,7 @@ public class ContikiMoteType implements MoteType {
     }
 
     @Override
-    public Map<String, Symbol> parseSymbols() {
+    public Map<String, Symbol> parseSymbols(long offset) {
       Map<String, Symbol> varNames = new HashMap<>();
 
       Pattern pattern = Pattern.compile(Cooja.getExternalToolsSetting("MAPFILE_VAR_NAME"));
@@ -654,7 +639,7 @@ public class ContikiMoteType implements MoteType {
             varNames.put(varName, new Symbol(
                     Symbol.Type.VARIABLE,
                     varName,
-                    getMapFileVarAddress(getData(), varName),
+                    getMapFileVarAddress(getData(), varName) + offset,
                     getMapFileVarSize(getData(), varName)));
           }
         }
@@ -761,7 +746,7 @@ public class ContikiMoteType implements MoteType {
     }
 
     @Override
-    public Map<String, Symbol> parseSymbols() {
+    public Map<String, Symbol> parseSymbols(long offset) {
       HashMap<String, Symbol> addresses = new HashMap<>();
       /* Replace "<SECTION>" in regexp by section specific regex */
       Pattern pattern = Pattern.compile(
@@ -774,7 +759,7 @@ public class ContikiMoteType implements MoteType {
         if (matcher.find()) {
           /* Line matched variable address */
           String symbol = matcher.group(1);
-          int varAddr = Integer.parseInt(matcher.group(2), 16);
+          long varAddr = Integer.parseInt(matcher.group(2), 16) + offset;
           int varSize;
           if (matcher.group(3) != null) {
            varSize = Integer.parseInt(matcher.group(3), 16);
@@ -827,7 +812,10 @@ public class ContikiMoteType implements MoteType {
    */
   public void getCoreMemory(SectionMoteMemory mem) {
     for (MemoryInterface section : mem.getSections().values()) {
-      getCoreMemory((int) section.getStartAddr(), section.getTotalSize(), section.getMemory());
+      getCoreMemory(
+              (int) (section.getStartAddr() - offset),
+              section.getTotalSize(),
+              section.getMemory());
     }
   }
 
@@ -844,7 +832,10 @@ public class ContikiMoteType implements MoteType {
    */
   public void setCoreMemory(SectionMoteMemory mem) {
     for (MemoryInterface section : mem.getSections().values()) {
-      setCoreMemory((int) section.getStartAddr(), section.getTotalSize(), section.getMemory());
+      setCoreMemory(
+              (int) (section.getStartAddr() - offset),
+              section.getTotalSize(),
+              section.getMemory());
     }
   }
 
diff --git a/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java b/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
index 340a3471f..a677c07a9 100644
--- a/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
+++ b/tools/cooja/java/org/contikios/cooja/dialogs/ConfigurationWizard.java
@@ -776,8 +776,8 @@ public class ConfigurationWizard extends JDialog {
             mapData,
             Cooja.getExternalToolsSetting("MAPFILE_BSS_START"),
             Cooja.getExternalToolsSetting("MAPFILE_BSS_SIZE"));
-    dataSecParser.parse();
-    bssSecParser.parse();
+    dataSecParser.parse(0);
+    bssSecParser.parse(0);
     relDataSectionAddr = dataSecParser.getStartAddr();
     dataSectionSize = dataSecParser.getSize();
     relBssSectionAddr = bssSecParser.getStartAddr();
@@ -869,8 +869,8 @@ public class ConfigurationWizard extends JDialog {
             Cooja.getExternalToolsSetting("COMMAND_BSS_SIZE"),
             Cooja.getExternalToolsSetting("COMMAND_VAR_SEC_BSS"));
 
-    dataSecParser.parse();
-    bssSecParser.parse();
+    dataSecParser.parse(0);
+    bssSecParser.parse(0);
     relDataSectionAddr = dataSecParser.getStartAddr();
     dataSectionSize = dataSecParser.getSize();
     relBssSectionAddr = bssSecParser.getStartAddr();
diff --git a/tools/cooja/java/org/contikios/cooja/mote/memory/SectionMoteMemory.java b/tools/cooja/java/org/contikios/cooja/mote/memory/SectionMoteMemory.java
index 62c12df24..0a335b15e 100644
--- a/tools/cooja/java/org/contikios/cooja/mote/memory/SectionMoteMemory.java
+++ b/tools/cooja/java/org/contikios/cooja/mote/memory/SectionMoteMemory.java
@@ -260,7 +260,7 @@ public class SectionMoteMemory implements MemoryInterface {
 
   @Override
   public boolean addSegmentMonitor(SegmentMonitor.EventType flag, long address, int size, SegmentMonitor monitor) {
-    PolledMemorySegments t = new PolledMemorySegments(monitor, (int) address, size);
+    PolledMemorySegments t = new PolledMemorySegments(monitor, address, size);
     polledMemories.add(t);
     return true;
   }
@@ -304,11 +304,11 @@ public class SectionMoteMemory implements MemoryInterface {
 
   private class PolledMemorySegments {
     public final SegmentMonitor mm;
-    public final int address;
+    public final long address;
     public final int size;
     private byte[] oldMem;
 
-    public PolledMemorySegments(SegmentMonitor mm, int address, int size) {
+    public PolledMemorySegments(SegmentMonitor mm, long address, int size) {
       this.mm = mm;
       this.address = address;
       this.size = size;

From b9ac2953b701c254f5c513289857fdeee94caff8 Mon Sep 17 00:00:00 2001
From: Enrico Joerns <e.joerns@tu-bs.de>
Date: Thu, 7 Aug 2014 13:01:50 +0200
Subject: [PATCH 25/28] [cooja] VarMemory: Actually throw
 UnknownVariableException

---
 .../java/org/contikios/cooja/mote/memory/VarMemory.java     | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tools/cooja/java/org/contikios/cooja/mote/memory/VarMemory.java b/tools/cooja/java/org/contikios/cooja/mote/memory/VarMemory.java
index c8866eeef..2559fe2f1 100644
--- a/tools/cooja/java/org/contikios/cooja/mote/memory/VarMemory.java
+++ b/tools/cooja/java/org/contikios/cooja/mote/memory/VarMemory.java
@@ -99,7 +99,11 @@ public class VarMemory extends Memory {
    * @return Variable address
    */
   public Symbol getVariable(String varName) throws UnknownVariableException {
-    return memIntf.getSymbolMap().get(varName);
+    Symbol sym = memIntf.getSymbolMap().get(varName);
+    if (sym == null) {
+      throw new UnknownVariableException(varName);
+    }
+    return sym;
   }
 
   /**

From 77d17196a76c4ca395e3b0d3248e14f6af3677b9 Mon Sep 17 00:00:00 2001
From: Fredrik Osterlind <fredrik@thingsquare.com>
Date: Thu, 7 Aug 2014 11:41:26 +0200
Subject: [PATCH 26/28] section address parsing configuration for windows

---
 tools/cooja/config/external_tools_win32.config | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/tools/cooja/config/external_tools_win32.config b/tools/cooja/config/external_tools_win32.config
index 484f95a21..d6c61cac2 100644
--- a/tools/cooja/config/external_tools_win32.config
+++ b/tools/cooja/config/external_tools_win32.config
@@ -6,8 +6,11 @@ COMPILER_ARGS=-D__int64\="long long" -Wall -I'$(JAVA_HOME)/include' -I'$(JAVA_HO
 LINK_COMMAND_1 = mingw32-gcc -shared -Wl,-Map=$(MAPFILE) -Wl,--add-stdcall-alias -o $(LIBFILE)
 LINK_COMMAND_2 = -L/usr/lib/mingw
 PARSE_WITH_COMMAND = true
-PARSE_COMMAND=nm -n -C $(LIBFILE)
-COMMAND_DATA_START = ^([0-9A-Fa-f]*)[ \t]D[ \t].*_data_start__$
-COMMAND_DATA_END = ^([0-9A-Fa-f]*)[ \t]D[ \t].*_data_end__$
-COMMAND_BSS_START = ^([0-9A-Fa-f]*)[ \t]B[ \t].*_bss_start__$
-COMMAND_BSS_END = ^([0-9A-Fa-f]*)[ \t]B[ \t].*_bss_end__$
+
+COMMAND_VAR_NAME_ADDRESS_SIZE = ^[_]([^.].*?) <SECTION> ([0-9a-fA-F]+) ([0-9a-fA-F])*
+COMMAND_DATA_START = ^__data_start__[ \t]D[ \t]([0-9A-Fa-f]*)[ \t]*$
+COMMAND_DATA_END = ^__data_end__[ \t]D[ \t]([0-9A-Fa-f]*)[ \t]*$
+COMMAND_BSS_START = ^__bss_start__[ \t]B[ \t]([0-9A-Fa-f]*)[ \t]*$
+COMMAND_BSS_END = ^__bss_end__[ \t]B[ \t]([0-9A-Fa-f]*)[ \t]*$
+COMMAND_READONLY_START = ^.rodata[ \t]r[ \t]([0-9A-Fa-f]*)[ \t]*$
+COMMAND_READONLY_END = ^.eh_frame_hdr[ \t]r[ \t]([0-9A-Fa-f]*)[ \t]*$

From b8d0b13ccff16586fcafcced4687d05332d5a50f Mon Sep 17 00:00:00 2001
From: Fredrik Osterlind <fredrik@thingsquare.com>
Date: Thu, 7 Aug 2014 11:41:44 +0200
Subject: [PATCH 27/28] improved debugging output at referenceVar errors

---
 .../java/org/contikios/cooja/contikimote/ContikiMoteType.java | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
index 8256f0580..c80c375b1 100644
--- a/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
+++ b/tools/cooja/java/org/contikios/cooja/contikimote/ContikiMoteType.java
@@ -491,7 +491,9 @@ public class ContikiMoteType implements MoteType {
         int referenceVar = (int) varMem.getVariable("referenceVar").addr;
         myCoreComm.setReferenceAddress(referenceVar);
       } catch (UnknownVariableException e) {
-        throw new MoteTypeCreationException("JNI call error: " + e.getMessage(), e);
+        throw new MoteTypeCreationException("Error setting reference variable: " + e.getMessage(), e);
+      } catch (RuntimeException e) {
+          throw new MoteTypeCreationException("Error setting reference variable: " + e.getMessage(), e);
       }
 
       getCoreMemory(tmp);

From a4271f43276d0b83df9d18534163749445530b87 Mon Sep 17 00:00:00 2001
From: Fredrik Osterlind <fredrik@thingsquare.com>
Date: Thu, 7 Aug 2014 13:06:25 +0200
Subject: [PATCH 28/28] hack to support symbol size parsing under cygwin

---
 tools/cooja/config/external_tools_win32.config | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/tools/cooja/config/external_tools_win32.config b/tools/cooja/config/external_tools_win32.config
index d6c61cac2..2d5dd7e4a 100644
--- a/tools/cooja/config/external_tools_win32.config
+++ b/tools/cooja/config/external_tools_win32.config
@@ -7,10 +7,13 @@ LINK_COMMAND_1 = mingw32-gcc -shared -Wl,-Map=$(MAPFILE) -Wl,--add-stdcall-alias
 LINK_COMMAND_2 = -L/usr/lib/mingw
 PARSE_WITH_COMMAND = true
 
-COMMAND_VAR_NAME_ADDRESS_SIZE = ^[_]([^.].*?) <SECTION> ([0-9a-fA-F]+) ([0-9a-fA-F])*
-COMMAND_DATA_START = ^__data_start__[ \t]D[ \t]([0-9A-Fa-f]*)[ \t]*$
-COMMAND_DATA_END = ^__data_end__[ \t]D[ \t]([0-9A-Fa-f]*)[ \t]*$
-COMMAND_BSS_START = ^__bss_start__[ \t]B[ \t]([0-9A-Fa-f]*)[ \t]*$
-COMMAND_BSS_END = ^__bss_end__[ \t]B[ \t]([0-9A-Fa-f]*)[ \t]*$
-COMMAND_READONLY_START = ^.rodata[ \t]r[ \t]([0-9A-Fa-f]*)[ \t]*$
-COMMAND_READONLY_END = ^.eh_frame_hdr[ \t]r[ \t]([0-9A-Fa-f]*)[ \t]*$
+# Hack: nm with arguments -S --size-sort does not display __data_start symbols
+PARSE_COMMAND=sh -c "/bin/nm -aP --size-sort -S $(LIBFILE) && /bin/nm -aP $(LIBFILE)"
+
+COMMAND_VAR_NAME_ADDRESS_SIZE = ^[_]([^.].*?)[ \t]<SECTION>[ \t]([0-9a-fA-F]+)[ \t]([0-9a-fA-F]+)
+COMMAND_DATA_START = ^__data_start__[ \t]D[ \t]([0-9A-Fa-f]*)
+COMMAND_DATA_END = ^__data_end__[ \t]D[ \t]([0-9A-Fa-f]*)
+COMMAND_BSS_START = ^__bss_start__[ \t]B[ \t]([0-9A-Fa-f]*)
+COMMAND_BSS_END = ^__bss_end__[ \t]B[ \t]([0-9A-Fa-f]*)
+COMMAND_READONLY_START = ^.rodata[ \t]r[ \t]([0-9A-Fa-f]*)
+COMMAND_READONLY_END = ^.eh_frame_hdr[ \t]r[ \t]([0-9A-Fa-f]*)