Merge with main (#116)

* Stop command

small change so command is available as a constant

* Lots of small updates to enable opening of a secondary configuration for
batch processing control.

src/Acquisition/AcquisitionControl.java

@@ -388,7 +388,7 @@ public class AcquisitionControl extends RawInputControlledUnit implements PamSet
 		message += "\n\nFailure to do so may result in PAMGUARD crashing or features not working correctly";
 		int ans = JOptionPane.showConfirmDialog(parentFrame, message, getArrayErrorMessage(error), JOptionPane.YES_NO_OPTION);
 		if (ans == JOptionPane.YES_OPTION) {
-			ArrayManager.getArrayManager().showArrayDialog(getPamView().getGuiFrame());
+			ArrayManager.getArrayManager().showArrayDialog(getGuiFrame());
 			return checkArrayChannels(parentFrame);
 		}
 

src/IMU/IMUControl.java

@@ -73,7 +73,7 @@ public class IMUControl  extends PamControlledUnit implements PamSettings {
 		}
 
 		public void actionPerformed(ActionEvent e) {
-			IMUSettingsDialog.showDialog(getPamView().getGuiFrame(),THIS);
+			IMUSettingsDialog.showDialog(getGuiFrame(),THIS);
 		}
 	}
 	
@@ -89,7 +89,7 @@ public class IMUControl  extends PamControlledUnit implements PamSettings {
 		}
 
 		public void actionPerformed(ActionEvent e) {
-			IMUParams newIMUParams=IMUImportDialog.showDialog(getPamView().getGuiFrame(),THIS, importCSV);
+			IMUParams newIMUParams=IMUImportDialog.showDialog(getGuiFrame(),THIS, importCSV);
 			//if params are not null try and load data 
 			if (newIMUParams!=null){
 				imuParams=newIMUParams; 
@@ -115,7 +115,7 @@ public class IMUControl  extends PamControlledUnit implements PamSettings {
 		}
 
 		public void actionPerformed(ActionEvent e) {
-			IMUParams newIMUParams=IMUCalibrationDialog.showDialog(getPamView().getGuiFrame(),imuParams);
+			IMUParams newIMUParams=IMUCalibrationDialog.showDialog(getGuiFrame(),imuParams);
 			if (newIMUParams!=null) imuParams=newIMUParams; 
 			updateProcesses(CAL_VALUES_CHANGED);
 		}

src/IMU/IMUImportDialog.java

@@ -91,7 +91,7 @@ public class IMUImportDialog extends PamDialog{
 		}
 		else dir=null;
 			
-		String newFile=PamFileBrowser.csvFileBrowser(imuControl.getPamView().getGuiFrame(),dir,PamFileBrowser.OPEN_FILE);
+		String newFile=PamFileBrowser.csvFileBrowser(imuControl.getGuiFrame(),dir,PamFileBrowser.OPEN_FILE);
 		
 		addNewFileToList( newFile);
 

src/Map/MapPanel.java

@@ -23,6 +23,7 @@ package Map;
 import java.awt.BasicStroke;
 import java.awt.Color;
 import java.awt.Cursor;
+import java.awt.Frame;
 import java.awt.Graphics;
 import java.awt.Graphics2D;
 import java.awt.MouseInfo;
@@ -1636,9 +1637,9 @@ public class MapPanel extends JPanelWithPamKey implements PamObserver, ColorMana
 	class OverlayOptions implements ActionListener {
 
 		public void actionPerformed(ActionEvent e) {
-			JFrame frame = (JFrame) PamController.getMainFrame();
+			Frame frame = (JFrame) PamController.getMainFrame();
 			if (mapController.getPamView() != null) {
-				frame = mapController.getPamView().getGuiFrame();
+				frame = mapController.getGuiFrame();
 			}
 
 			MapDetectionsParameters newParams = MapDetectionsDialog.showDialog(frame,

src/PamController/PamConfiguration.java

@@ -0,0 +1,549 @@
+package PamController;
+
+import java.io.File;
+import java.io.Serializable;
+import java.util.ArrayList;
+
+import Array.ArrayManager;
+import PamController.settings.output.xml.PamguardXMLWriter;
+import PamDetection.PamDetection;
+import PamDetection.RawDataUnit;
+import PamView.GeneralProjector;
+import PamView.PanelOverlayDraw;
+import PamguardMVC.PamDataBlock;
+import PamguardMVC.PamDataUnit;
+import PamguardMVC.PamProcess;
+import PamguardMVC.PamRawDataBlock;
+import binaryFileStorage.BinaryStore;
+import fftManager.FFTDataBlock;
+import fftManager.FFTDataUnit;
+import offlineProcessing.OfflineTask;
+import offlineProcessing.OfflineTaskGroup;
+
+/**
+ * Class to take all of the configuration information out of PamController. This 
+ * is because PamController is a singleton class, so there can only every be one of 
+ * them, but for some of the batch processing control, we need to be able to load and
+ * manipulate a second set of modules, which do nothing within the running 
+ * configuration, but are there to allow us to set up a configuration to send to 
+ * other batch processes in viewer mode. 
+ * @author dg50
+ *
+ */
+public class PamConfiguration {
+
+	/**
+	 * List of the current controlled units (PAMGuard modules)
+	 */
+	private ArrayList<PamControlledUnit> pamControlledUnits;
+
+	public PamConfiguration() {
+		super();
+		
+		// create the array list to hold multiple views
+		pamControlledUnits = new ArrayList<PamControlledUnit>();
+	}
+
+	/**
+	 * Call setupControlledUnit() on all modules. 
+	 */
+	public void setupProcesses() {
+		for (int i = 0; i < pamControlledUnits.size(); i++) {
+			pamControlledUnits.get(i).setupControlledUnit();
+		}
+	}
+
+	/**
+	 * Can PAMGUARD shut down. This question is asked in turn to 
+	 * every module. Each module should attempt to make sure it can 
+	 * answer true, e.g. by closing files, but if any module
+	 * returns false, then canClose() will return false;
+	 * @return whether it's possible to close PAMGUARD 
+	 * without corrupting or losing data. 
+	 */
+	public boolean canClose() {
+		for (int i = 0; i < pamControlledUnits.size(); i++) {
+			if (pamControlledUnits.get(i).canClose() == false) {
+				return false;
+			}
+		}
+		return true;
+	}
+
+	/**
+	 * Called after canClose has returned true to finally tell 
+	 * all modules that PAMGUARD is definitely closing down.so they
+	 * can free any resources, etc.  
+	 */
+	public void pamClose() {
+
+		
+		for (int i = 0; i < pamControlledUnits.size(); i++) {
+			pamControlledUnits.get(i).pamClose();
+		}
+	}
+
+	/**
+	 * @return the pamControlledUnits
+	 */
+	public ArrayList<PamControlledUnit> getPamControlledUnits() {
+		return pamControlledUnits;
+	}
+
+	/**
+	 * Add a PamControlledUnit to the main list. 
+	 * @param controlledUnit
+	 */
+	public void addControlledUnit(PamControlledUnit controlledUnit) {
+		pamControlledUnits.add(controlledUnit);
+	}
+
+	public boolean removeControlledUnt(PamControlledUnit controlledUnit) {
+
+		boolean removed = false;
+		while (pamControlledUnits.contains(controlledUnit)) {
+			pamControlledUnits.remove(controlledUnit);
+			removed = true;
+		}
+		return removed;
+		//		getMainFrame().revalidate(); //handled inside the GUIFrameManager by notify model changed. The controller should have 
+		//as few direct GUI calls as possible. 
+	}
+
+	/**
+	 * re-order the modules according to the given list. 
+	 * @param newOrder
+	 * @return
+	 */
+	public boolean reOrderModules(int[] newOrder) {
+
+		if (pamControlledUnits.size() != newOrder.length) return false;
+
+		ArrayList<PamControlledUnit> newList = new ArrayList<PamControlledUnit>();
+
+		for (int i = 0; i < newOrder.length; i++) {
+
+			newList.add(pamControlledUnits.get(newOrder[i]));
+
+		}
+
+		pamControlledUnits = newList;
+
+		return true;
+	}
+
+	public PamControlledUnit getControlledUnit(int iUnit) {
+		if (iUnit < getNumControlledUnits()) {
+			return pamControlledUnits.get(iUnit);
+		}
+		return null;
+	}
+
+	public PamControlledUnit findControlledUnit(String unitType) {
+		for (int i = 0; i < getNumControlledUnits(); i++) {
+			if (pamControlledUnits.get(i).getUnitType().equalsIgnoreCase(unitType)) {
+				return pamControlledUnits.get(i);
+			}
+		}
+		return null;
+	}
+	
+	public int getNumControlledUnits() {
+		return pamControlledUnits.size();
+	}
+
+	public PamRawDataBlock getRawDataBlock(int id) {
+		return (PamRawDataBlock) getDataBlock(RawDataUnit.class, id);
+	}
+	
+	public PamRawDataBlock getRawDataBlock(String name) {
+		return (PamRawDataBlock) getDataBlock(RawDataUnit.class, name);
+	}
+	
+	/** 
+	 * Find a block of a given type with the given name, or null if it
+	 * doesn't exist.
+	 * @param  blockType -- RAW, FFT, DETECTOR, null, etc.
+	 * @param  name -- the block name
+	 * @return  block, which you may want to cast to a subtype
+	 */
+	public PamDataBlock getDataBlock(Class blockType, String name) {
+		if (name == null) return null;
+		ArrayList<PamDataBlock> blocks = getDataBlocks(blockType, true);
+		for (PamDataBlock dataBlock:blocks) {
+			if (name.equals(dataBlock.getLongDataName())) { // check for a long name match first 
+				return dataBlock;
+			}
+			if (dataBlock instanceof FFTDataBlock) {
+				FFTDataBlock fb = (FFTDataBlock) dataBlock;
+				if (name.equals(fb.getOldLongDataName())) {
+					return dataBlock;
+				}
+			}
+			if (name.equals(dataBlock.toString())) {
+				return dataBlock;
+			}
+		}
+		return null;
+	}
+
+	public ArrayList<PamDataBlock> getDataBlocks(Class blockType, boolean includeSubClasses) {
+		return makeDataBlockList(blockType, includeSubClasses);
+	}
+
+	public ArrayList<PamDataBlock> getDetectorDataBlocks() {
+		return makeDataBlockList(PamDetection.class, true);
+	}
+
+	public ArrayList<PamDataBlock> getFFTDataBlocks() {
+		return makeDataBlockList(FFTDataUnit.class, true);
+	}
+
+	public PamDataBlock getFFTDataBlock(int id) {
+		return getDataBlock(FFTDataUnit.class, id);
+	}
+
+	public PamDataBlock getFFTDataBlock(String name) {
+		return getDataBlock(FFTDataUnit.class, name);
+	}
+	
+	/** 
+	 * Find a block of a given type with the id number, or null if the number
+	 * is out of range.
+	 * 
+	 * @param  blockType
+	 * @param  id -- the block id number
+	 * @return  block, which you may want to cast to a subtype
+	 */
+	public PamDataBlock getDataBlock(Class blockType, int id) {
+
+		ArrayList<PamDataBlock> blocks = getDataBlocks(blockType, true);
+		if (id >= 0 && id < blocks.size()) return blocks.get(id);
+		return null;
+	}
+	public ArrayList<PamDataBlock> getRawDataBlocks() {
+		return makeDataBlockList(RawDataUnit.class, true);
+	}
+	/**
+	 * Find a block with the given long name, or null if it doesn't exist.
+	 * @param longName the long name of the PamDataBlock
+	 * @return block
+	 */
+	public PamDataBlock getDataBlockByLongName(String longName) {
+		if (longName == null) return null;
+		ArrayList<PamDataBlock> allBlocks = getDataBlocks();
+		for (PamDataBlock dataBlock:allBlocks) {
+			if (longName.equals(dataBlock.getLongDataName())) {
+				return dataBlock;
+			}
+			if (dataBlock instanceof FFTDataBlock) {
+				FFTDataBlock fb = (FFTDataBlock) dataBlock;
+				if (longName.equals(fb.getOldLongDataName())) {
+					return dataBlock;
+				}
+			}
+		}
+		return null;
+	}
+
+	public ArrayList<PamDataBlock> getDataBlocks() {
+		return makeDataBlockList(PamDataUnit.class, true);
+	}
+	
+	/**
+	 * Get a list of PamControlledUnit units of a given type
+	 * @param unitType Controlled unit type
+	 * @return list of units. 
+	 */
+	public ArrayList<PamControlledUnit> findControlledUnits(String unitType) {
+		ArrayList<PamControlledUnit> l = new ArrayList<PamControlledUnit>();
+		int n = getNumControlledUnits();
+		PamControlledUnit pcu;
+		for (int i = 0; i < n; i++) {
+			pcu = getControlledUnit(i);
+			if (pcu.getUnitType().equals(unitType)) {
+				l.add(pcu);
+			}
+		}
+
+		return l;
+	}
+	
+	/**
+	 * Get a list of PamControlledUnit units of a given type and name, allowing for nulls. 
+	 * @param unitType Controlled unit type, can be null for all units of name
+	 * @param unitName Controlled unit name, can be null for all units of type
+	 * @return list of units. 
+	 */
+	public ArrayList<PamControlledUnit> findControlledUnits(String unitType, String unitName) {
+		ArrayList<PamControlledUnit> l = new ArrayList<PamControlledUnit>();
+		int n = getNumControlledUnits();
+		PamControlledUnit pcu;
+		for (int i = 0; i < n; i++) {
+			pcu = getControlledUnit(i);
+			if (unitType != null && !unitType.equals(pcu.getUnitType())) {
+				continue;
+			}
+			if (unitName != null && !unitName.equals(pcu.getUnitName())) {
+				continue;
+			}
+			l.add(pcu);
+		}
+
+		return l;
+	}
+
+	/**
+	 * find the first controlled unit with the given type and name. 
+	 * @param unitType
+	 * @param unitName
+	 * @return
+	 */
+	public PamControlledUnit findControlledUnit(String unitType, String unitName) {
+		for (int i = 0; i < getNumControlledUnits(); i++) {
+			if (pamControlledUnits.get(i).getUnitType().equalsIgnoreCase(unitType) &&
+					pamControlledUnits.get(i).getUnitName().equalsIgnoreCase(unitName)) {
+				return pamControlledUnits.get(i);
+			}
+		}
+		return null;
+	}
+	
+	/**
+	 * Find the first instance of a module with a given class type and name.
+	 * <p>Name can be null in which case the first module with the correct class
+	 * will be returned
+	 * @param unitClass Module class (sub class of PamControlledUnit)
+	 * @param unitName Module Name
+	 * @return Existing module with that class and name. 
+	 */
+	public PamControlledUnit findControlledUnit(Class unitClass, String unitName) {
+		for (int i = 0; i < getNumControlledUnits(); i++) {
+			if (pamControlledUnits.get(i).getClass() == unitClass && (unitName == null ||
+					pamControlledUnits.get(i).getUnitName().equalsIgnoreCase(unitName))) {
+				return pamControlledUnits.get(i);
+			}
+		}
+		return null;
+	}
+	
+	/**
+	 * Get an Array list of PamControlledUnits of a particular class (exact matches only). 
+	 * @param unitClass PamControlledUnit class
+	 * @return List of current instances of this class. 
+	 */
+	public ArrayList<PamControlledUnit> findControlledUnits(Class unitClass) {
+		ArrayList<PamControlledUnit> foundUnits = new ArrayList<>();
+		for (int i = 0; i < getNumControlledUnits(); i++) {
+			if (pamControlledUnits.get(i).getClass() == unitClass) {
+				foundUnits.add(pamControlledUnits.get(i));
+			}
+		}
+		return foundUnits;
+	}
+
+	/**
+	 * Get an Array list of PamControlledUnits of a particular class (exact matches only). 
+	 * @param unitClass PamControlledUnit class
+	 * @return List of current instances of this class. 
+	 */
+	public ArrayList<PamControlledUnit> findControlledUnits(Class unitClass, boolean includeSubClasses) {
+		if (includeSubClasses == false) {
+			return findControlledUnits(unitClass);
+		}
+		ArrayList<PamControlledUnit> foundUnits = new ArrayList<>();
+		for (int i = 0; i < getNumControlledUnits(); i++) {
+			if (unitClass.isAssignableFrom(pamControlledUnits.get(i).getClass())) {
+				foundUnits.add(pamControlledUnits.get(i));
+			}
+		}
+		return foundUnits;
+	}
+	/**
+	 * Check whether a controlled unit exists based on it's name. 
+	 * @param the controlled unit name e.g. "my crazy click detector", not the default name. 
+	 */
+	public boolean isControlledUnit(String controlName) {
+		for (int i = 0; i < getNumControlledUnits(); i++) {
+			if (pamControlledUnits.get(i).getUnitName().equalsIgnoreCase(controlName)) {
+				return true;
+			}
+		}
+		return false;
+	}
+
+	/**
+	 * Gets called in pamStart and may / will attempt to store all
+	 * PAMGUARD settings via the database and binary storage modules. 
+	 */
+	public void saveSettings(long timeNow) {
+		PamControlledUnit pcu;
+		PamSettingsSource settingsSource;
+		for (int iU = 0; iU < pamControlledUnits.size(); iU++) {
+			pcu = pamControlledUnits.get(iU);
+			if (PamSettingsSource.class.isAssignableFrom(pcu.getClass())) {
+				settingsSource = (PamSettingsSource) pcu;
+				settingsSource.saveStartSettings(timeNow);
+			}
+		}
+		PamguardXMLWriter.getXMLWriter().writeStartSettings(timeNow);
+	}
+
+	/**
+	 * 
+	 * @return a list of PamControlledUnits which implements the 
+	 * PamSettingsSource interface
+	 * @see PamSettingsSource
+	 */
+	public ArrayList<PamSettingsSource> findSettingsSources() {
+		ArrayList<PamSettingsSource> settingsSources = new ArrayList<PamSettingsSource>();
+		PamControlledUnit pcu;
+		for (int iU = 0; iU < pamControlledUnits.size(); iU++) {
+			pcu = pamControlledUnits.get(iU);
+			if (PamSettingsSource.class.isAssignableFrom(pcu.getClass())) {
+				settingsSources.add((PamSettingsSource) pcu);
+			}
+		}
+		return settingsSources;
+	}
+
+	public ArrayList<PamDataBlock> getPlottableDataBlocks(GeneralProjector generalProjector) {
+
+		ArrayList<PamDataBlock> blockList = new ArrayList<PamDataBlock>();
+		PamProcess pP;
+		Class unitClass;
+		PanelOverlayDraw panelOverlayDraw;
+
+		for (int iU = 0; iU < pamControlledUnits.size(); iU++) {
+			for (int iP = 0; iP < pamControlledUnits.get(iU)
+					.getNumPamProcesses(); iP++) {
+				pP = pamControlledUnits.get(iU).getPamProcess(iP);
+				for (int j = 0; j < pP.getNumOutputDataBlocks(); j++) {
+					if(pP.getOutputDataBlock(j).canDraw(generalProjector)) {
+						blockList.add(pP.getOutputDataBlock(j));
+					}
+				}
+			}
+		}
+		return blockList;
+	}
+
+	public ArrayList<PamDataBlock> makeDataBlockList(Class classType, boolean includSubClasses) {
+
+		ArrayList<PamDataBlock> blockList = new ArrayList<PamDataBlock>();
+		PamProcess pP;
+		Class unitClass;
+
+		for (int iU = 0; iU < pamControlledUnits.size(); iU++) {
+			for (int iP = 0; iP < pamControlledUnits.get(iU)
+					.getNumPamProcesses(); iP++) {
+				pP = pamControlledUnits.get(iU).getPamProcess(iP);
+				for (int j = 0; j < pP.getNumOutputDataBlocks(); j++) {
+					//System.out.println("Comparing "+pP.getOutputDataBlock(j).getUnitClass().getCanonicalName()+" to "+classType.getCanonicalName());
+					if ((unitClass = pP.getOutputDataBlock(j).getUnitClass()) == classType) {
+						blockList.add(pP.getOutputDataBlock(j));
+					}
+					else if (includSubClasses) {
+						if (classType != null && classType.isAssignableFrom(unitClass)) {
+							blockList.add(pP.getOutputDataBlock(j));
+						}
+						//						while ((unitClass = unitClass.getSuperclass()) != null) {
+						//							if (unitClass == classType) {
+						//								blockList.add(pP.getOutputDataBlock(j));
+						//								break;
+						//							}
+						//						}
+					}
+				}
+			}
+		}
+
+		return blockList;
+	}
+
+	public void notifyModelChanged(int changeType) {
+		// also tell all PamControlledUnits since they may want to find their data source 
+		// it that was created after they were - i.e. dependencies have got all muddled
+		for (int i = 0; i < pamControlledUnits.size(); i++) {
+			pamControlledUnits.get(i).notifyModelChanged(changeType);
+		}
+	}
+
+	public Serializable getSettingsReference() {
+		ArrayList<UsedModuleInfo> usedModules = new ArrayList<UsedModuleInfo>();
+		for (int i = 0; i < pamControlledUnits.size(); i++) {
+			usedModules.add(new UsedModuleInfo(pamControlledUnits.get(i).getClass().getName(), 
+					pamControlledUnits.get(i).getUnitType(),
+					pamControlledUnits.get(i).getUnitName()));
+		}
+		return usedModules;
+	}
+
+	public void destroyModel() {
+
+		for (int i = 0; i < pamControlledUnits.size(); i++) {
+			pamControlledUnits.get(i).notifyModelChanged(PamController.DESTROY_EVERYTHING);
+		}
+		pamControlledUnits.clear();
+	}
+	
+	/**
+	 * Get the index of a PamControlledUnit
+	 * @param unit
+	 * @return
+	 */
+	public int getControlledUnitIndex(PamControlledUnit unit) {
+		return pamControlledUnits.indexOf(unit);
+	}
+
+	/**
+	 * Find the path to the binary store ....
+	 * @return path to the binary store. 
+	 */
+	public String findBinaryStorePath() {
+		BinaryStore binaryStore = (BinaryStore) findControlledUnit(BinaryStore.getBinaryUnitType());
+		if (binaryStore == null) {
+			return null;
+		}
+		String storeLoc = binaryStore.getBinaryStoreSettings().getStoreLocation();
+		if (storeLoc == null) {
+			return "";
+		}
+		if (storeLoc.endsWith(File.separator) == false) {
+			storeLoc += File.separator;
+		}
+		return storeLoc;
+	}
+	
+	/**
+	 * Get a list of all offline task groups in this configuration
+	 * @return task group list
+	 */
+	public ArrayList<OfflineTaskGroup> getAllOfflineTaskGroups() {
+		ArrayList<OfflineTaskGroup> tgs = new ArrayList<OfflineTaskGroup>();
+		for (PamControlledUnit unit : pamControlledUnits){
+			int numGroups = unit.getNumOfflineTaskGroups();
+			for (int iGp=0;iGp<numGroups;iGp++){
+				tgs.add( unit.getOfflineTaskGroup(iGp));
+				
+			}
+		}
+		return tgs;
+	}
+	
+	/**
+	 * Get a list of all offline tasks in the configuration
+	 * @return offline task list
+	 */
+	public ArrayList<OfflineTask> getAllOfflineTasks() {
+		ArrayList<OfflineTask> ots = new ArrayList<OfflineTask>();
+		ArrayList<OfflineTaskGroup> groups = getAllOfflineTaskGroups();
+		for (OfflineTaskGroup group : groups) {
+			int nTasks = group.getNTasks();
+			for (int i = 0; i < nTasks; i++) {
+				ots.add(group.getTask(i));
+			}
+		}
+		return ots;
+	}
+}

src/PamController/PamControlledUnit.java

@@ -141,6 +141,8 @@ public abstract class PamControlledUnit implements SettingsNameProvider {
 	
 	private ModuleStatusManager moduleStatusManager;
 	
+	private PamConfiguration pamConfiguration;
+	
 //	private ArrayList<OfflineTask> offlineTasks = new ArrayList<>();
 	
 	/**
@@ -155,8 +157,17 @@ public abstract class PamControlledUnit implements SettingsNameProvider {
 	 *            name of unit
 	 */
 	public PamControlledUnit(String unitType, String unitName) {
+		this(null, unitType, unitName);
+	}
+	
+	public PamControlledUnit(PamConfiguration pamConfiguration, String unitType, String unitName) {
 		this.unitType = unitType;
 		this.unitName = unitName;
+		this.pamConfiguration = pamConfiguration;
+		if (this.pamConfiguration == null) {
+			this.pamConfiguration = PamController.getInstance().getPamConfiguration();
+		}
+		
 		pamProcesses = new ArrayList<PamProcess>();
 		
 		isViewer = PamController.getInstance().getRunMode() == PamController.RUN_PAMVIEW;
@@ -497,6 +508,12 @@ public abstract class PamControlledUnit implements SettingsNameProvider {
 		return true;
 	}
 
+	/**
+	 * Get the GUI associated with this module. However, this may return null, so if you want a frame
+	 * to use for a dialog, better to use PamController.getGuiFrame() which handles null automatically. 
+	 * @return
+	 */
+	@Deprecated
 	public PamView getPamView() {
 		return pamView;
 	}
@@ -674,11 +691,11 @@ public abstract class PamControlledUnit implements SettingsNameProvider {
 	 * @param offlineTaskGroup
 	 */
 	public void addOfflineTaskGroup(OfflineTaskGroup offlineTaskGroup) {
-		if (isViewer){
+//		if (isViewer){
 			offlineTaskGroups.add(offlineTaskGroup);
-		}else{
+//		}else{
-			System.out.println("OfflineTaskGroup cannot be added as is not viewer mode");
+//			System.out.println("OfflineTaskGroup cannot be added as is not viewer mode");
-		}
+//		}
 		
 	}
 	
@@ -864,4 +881,34 @@ public abstract class PamControlledUnit implements SettingsNameProvider {
 		return instanceIndex;
 	}
 
+	/**
+	 * The PamConfiguration holds the master list of modules which form part of a
+	 * configuration. It should be accessed to find list of datablocks, etc. rather than 
+	 * doing everything through PAMController whenever possible.  
+	 * @return the pamConfiguration
+	 */
+	public PamConfiguration getPamConfiguration() {
+		if (pamConfiguration == null) {
+			pamConfiguration = PamController.getInstance().getPamConfiguration();
+		}
+		return pamConfiguration;
+	}
+	
+	/**
+	 * Is this module in the main configuration. If it isn't then it's probably a dummy config
+	 * used in the batch processor or for importing  / exporting configs, so it should be stopped from 
+	 * doing too much !
+	 * @return
+	 */
+	public boolean isInMainConfiguration() {
+		return pamConfiguration == PamController.getInstance().getPamConfiguration();
+	}
+
+	/**
+	 * @param pamConfiguration the pamConfiguration to set
+	 */
+	public void setPamConfiguration(PamConfiguration pamConfiguration) {
+		this.pamConfiguration = pamConfiguration;
+	}
+
 }

src/PamController/PamController.java

@@ -34,6 +34,9 @@ import javax.swing.SwingUtilities;
 import javax.swing.Timer;
 import javax.swing.ToolTipManager;
 
+import com.jcraft.jsch.ConfigRepository.Config;
+import com.sun.xml.bind.v2.TODO;
+
 import Acquisition.AcquisitionProcess;
 
 //import com.sun.org.apache.xerces.internal.dom.DocumentImpl;
@@ -67,7 +70,6 @@ import PamController.soundMedium.GlobalMediumManager;
 import PamDetection.PamDetection;
 import PamDetection.RawDataUnit;
 import PamModel.PamModel;
-import PamModel.PamModelInterface;
 import PamModel.PamModelSettings;
 import PamModel.PamModuleInfo;
 import PamModel.SMRUEnable;
@@ -144,11 +146,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 	 */
 	private PamModel pamModelInterface;
 
-	/**
+	private PamConfiguration pamConfiguration;
-	 * List of the current controlled units (PAMGuard modules)
-	 */
-	private ArrayList<PamControlledUnit> pamControlledUnits;
-
 	/**
 	 * The current PAM status
 	 */
@@ -236,6 +234,8 @@ public class PamController implements PamControllerInterface, PamSettings {
 
 		uniqueController = this;
 		
+		pamConfiguration = new PamConfiguration();
+
 		this.runMode = runMode;
 
 		if (runMode == PamController.RUN_PAMVIEW) {
@@ -353,10 +353,6 @@ public class PamController implements PamControllerInterface, PamSettings {
 	 */
 	public void setupPamguard() {
 
-
-		// create the array list to hold multiple views
-		pamControlledUnits = new ArrayList<PamControlledUnit>();
-
 		/**
 		 * Set Locale to English so that formated writes to text fields
 		 * in dialogs use . and not , for the decimal. 
@@ -661,9 +657,10 @@ public class PamController implements PamControllerInterface, PamSettings {
 	//	}
 
 	void setupProcesses() {
-		for (int i = 0; i < pamControlledUnits.size(); i++) {
+//		for (int i = 0; i < pamControlledUnits.size(); i++) {
-			pamControlledUnits.get(i).setupControlledUnit();
+//			pamControlledUnits.get(i).setupControlledUnit();
-		}
+//		}
+		pamConfiguration.setupProcesses();
 	}
 
 	/**
@@ -675,12 +672,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 	 * without corrupting or losing data. 
 	 */
 	public boolean canClose() {
-		for (int i = 0; i < pamControlledUnits.size(); i++) {
+		return pamConfiguration.canClose();
-			if (pamControlledUnits.get(i).canClose() == false) {
-				return false;
-			}
-		}
-		return true;
 	}
 
 
@@ -694,9 +686,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 
 		getUidManager().runShutDownOps();
 		
-		for (int i = 0; i < pamControlledUnits.size(); i++) {
+		pamConfiguration.pamClose();
-			pamControlledUnits.get(i).pamClose();
-		}
 	}
 
 	/**
@@ -716,6 +706,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 	 * it to be easy to override this for specific modules / processes / data blocks. 
 	 */
 	public void saveViewerData() {
+		ArrayList<PamControlledUnit> pamControlledUnits = pamConfiguration.getPamControlledUnits();
 		for (int i = 0; i < pamControlledUnits.size(); i++) {
 			pamControlledUnits.get(i).saveViewerData();
 		}
@@ -728,7 +719,8 @@ public class PamController implements PamControllerInterface, PamSettings {
 
 	@Override
 	public void addControlledUnit(PamControlledUnit controlledUnit) {
-		pamControlledUnits.add(controlledUnit);
+		
+		pamConfiguration.addControlledUnit(controlledUnit);
 
 		guiFrameManager.addControlledUnit(controlledUnit);
 
@@ -854,8 +846,8 @@ public class PamController implements PamControllerInterface, PamSettings {
 
 		guiFrameManager.removeControlledUnit(controlledUnit);
 
-		while (pamControlledUnits.contains(controlledUnit)) {
+		boolean removed = pamConfiguration.removeControlledUnt(controlledUnit);
-			pamControlledUnits.remove(controlledUnit);
+		if (removed) {
 			notifyModelChanged(PamControllerInterface.REMOVE_CONTROLLEDUNIT);
 		}
 		//		getMainFrame().revalidate(); //handled inside the GUIFrameManager by notify model changed. The controller should have 
@@ -871,7 +863,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 		int[] newOrder = ModuleOrderDialog.showDialog(this, parentFrame); 
 		if (newOrder != null) {
 			// re-order the modules according the new list.
-			reOrderModules(newOrder);
+			pamConfiguration.reOrderModules(newOrder);
 
 			notifyModelChanged(PamControllerInterface.REORDER_CONTROLLEDUNITS);
 
@@ -881,22 +873,22 @@ public class PamController implements PamControllerInterface, PamSettings {
 		return false;
 	}
 
-	private boolean reOrderModules(int[] newOrder) {
+//	private boolean reOrderModules(int[] newOrder) {
-
+//
-		if (pamControlledUnits.size() != newOrder.length) return false;
+//		if (pamControlledUnits.size() != newOrder.length) return false;
-
+//
-		ArrayList<PamControlledUnit> newList = new ArrayList<PamControlledUnit>();
+//		ArrayList<PamControlledUnit> newList = new ArrayList<PamControlledUnit>();
-
+//
-		for (int i = 0; i < newOrder.length; i++) {
+//		for (int i = 0; i < newOrder.length; i++) {
-
+//
-			newList.add(pamControlledUnits.get(newOrder[i]));
+//			newList.add(pamControlledUnits.get(newOrder[i]));
-
+//
-		}
+//		}
-
+//
-		pamControlledUnits = newList;
+//		pamControlledUnits = newList;
-
+//
-		return true;
+//		return true;
-	}
+//	}
 
 	/**
 	 * Swaps the positions of two modules in the main list of modules and 
@@ -922,20 +914,12 @@ public class PamController implements PamControllerInterface, PamSettings {
 
 	@Override
 	public PamControlledUnit getControlledUnit(int iUnit) {
-		if (iUnit < getNumControlledUnits()) {
+		return pamConfiguration.getControlledUnit(iUnit);
-			return pamControlledUnits.get(iUnit);
-		}
-		return null;
 	}
 
 	@Override
 	public PamControlledUnit findControlledUnit(String unitType) {
-		for (int i = 0; i < getNumControlledUnits(); i++) {
+		return pamConfiguration.findControlledUnit(unitType);
-			if (pamControlledUnits.get(i).getUnitType().equalsIgnoreCase(unitType)) {
-				return pamControlledUnits.get(i);
-			}
-		}
-		return null;
 	}
 
 	/**
@@ -944,17 +928,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 	 * @return list of units. 
 	 */
 	public ArrayList<PamControlledUnit> findControlledUnits(String unitType) {
-		ArrayList<PamControlledUnit> l = new ArrayList<PamControlledUnit>();
+		return pamConfiguration.findControlledUnits(unitType);
-		int n = getNumControlledUnits();
-		PamControlledUnit pcu;
-		for (int i = 0; i < n; i++) {
-			pcu = getControlledUnit(i);
-			if (pcu.getUnitType().equals(unitType)) {
-				l.add(pcu);
-			}
-		}
-
-		return l;
 	}
 	/**
 	 * Get a list of PamControlledUnit units of a given type and name, allowing for nulls. 
@@ -963,32 +937,12 @@ public class PamController implements PamControllerInterface, PamSettings {
 	 * @return list of units. 
 	 */
 	public ArrayList<PamControlledUnit> findControlledUnits(String unitType, String unitName) {
-		ArrayList<PamControlledUnit> l = new ArrayList<PamControlledUnit>();
+		return pamConfiguration.findControlledUnits(unitType, unitName);
-		int n = getNumControlledUnits();
-		PamControlledUnit pcu;
-		for (int i = 0; i < n; i++) {
-			pcu = getControlledUnit(i);
-			if (unitType != null && !unitType.equals(pcu.getUnitType())) {
-				continue;
-			}
-			if (unitName != null && !unitName.equals(pcu.getUnitName())) {
-				continue;
-			}
-			l.add(pcu);
-		}
-
-		return l;
 	}
 
 	@Override
 	public PamControlledUnit findControlledUnit(String unitType, String unitName) {
-		for (int i = 0; i < getNumControlledUnits(); i++) {
+		return pamConfiguration.findControlledUnit(unitType, unitName);
-			if (pamControlledUnits.get(i).getUnitType().equalsIgnoreCase(unitType) &&
-					pamControlledUnits.get(i).getUnitName().equalsIgnoreCase(unitName)) {
-				return pamControlledUnits.get(i);
-			}
-		}
-		return null;
 	}
 
 	/**
@@ -1000,13 +954,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 	 * @return Existing module with that class and name. 
 	 */
 	public PamControlledUnit findControlledUnit(Class unitClass, String unitName) {
-		for (int i = 0; i < getNumControlledUnits(); i++) {
+		return pamConfiguration.findControlledUnit(unitClass, unitName);
-			if (pamControlledUnits.get(i).getClass() == unitClass && (unitName == null ||
-					pamControlledUnits.get(i).getUnitName().equalsIgnoreCase(unitName))) {
-				return pamControlledUnits.get(i);
-			}
-		}
-		return null;
 	}
 
 	/**
@@ -1015,13 +963,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 	 * @return List of current instances of this class. 
 	 */
 	public ArrayList<PamControlledUnit> findControlledUnits(Class unitClass) {
-		ArrayList<PamControlledUnit> foundUnits = new ArrayList<>();
+		return pamConfiguration.findControlledUnits(unitClass);
-		for (int i = 0; i < getNumControlledUnits(); i++) {
-			if (pamControlledUnits.get(i).getClass() == unitClass) {
-				foundUnits.add(pamControlledUnits.get(i));
-			}
-		}
-		return foundUnits;
 	}
 	
 	/**
@@ -1030,16 +972,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 	 * @return List of current instances of this class. 
 	 */
 	public ArrayList<PamControlledUnit> findControlledUnits(Class unitClass, boolean includeSubClasses) {
-		if (includeSubClasses == false) {
+		return pamConfiguration.findControlledUnits(unitClass, includeSubClasses);
-			return findControlledUnits(unitClass);
-		}
-		ArrayList<PamControlledUnit> foundUnits = new ArrayList<>();
-		for (int i = 0; i < getNumControlledUnits(); i++) {
-			if (unitClass.isAssignableFrom(pamControlledUnits.get(i).getClass())) {
-				foundUnits.add(pamControlledUnits.get(i));
-			}
-		}
-		return foundUnits;
 	}
 
 	/**
@@ -1047,28 +980,19 @@ public class PamController implements PamControllerInterface, PamSettings {
 	 * @param the controlled unit name e.g. "my crazy click detector", not the default name. 
 	 */
 	public boolean isControlledUnit(String controlName) {
-		for (int i = 0; i < getNumControlledUnits(); i++) {
+		return pamConfiguration.isControlledUnit(controlName);
-			if (pamControlledUnits.get(i).getUnitName().equalsIgnoreCase(controlName)) {
-				return true;
-			}
-		}
-		return false;
 	}
 
 	@Override
 	public int getNumControlledUnits() {
-		if (pamControlledUnits == null) {
+		return pamConfiguration.getNumControlledUnits();
-			return 0;
-		}
-		return pamControlledUnits.size();
 	}
 
 	static public PamController getInstance() {
 		return uniqueController;
 	}
 
-	@Override
+	public PamModel getModelInterface() {
-	public PamModelInterface getModelInterface() {
 		return pamModelInterface;
 	}
 
@@ -1186,6 +1110,8 @@ public class PamController implements PamControllerInterface, PamSettings {
 
 		manualStop = false;
 		
+		ArrayList<PamControlledUnit> pamControlledUnits = pamConfiguration.getPamControlledUnits();
+
 		PamCalendar.setSessionStartTime(startTime);
 		setPamStatus(PAM_RUNNING);
 		long t1 = System.currentTimeMillis();
@@ -1283,6 +1209,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 		// actually stopped
 //		statusCheckThread = new Thread(new StatusTimer());
 //		statusCheckThread.start();
+		ArrayList<PamControlledUnit> pamControlledUnits = pamConfiguration.getPamControlledUnits();
 
 		// tell all controlled units to stop
 		for (int iU = 0; iU < pamControlledUnits.size(); iU++) {
@@ -1358,6 +1285,8 @@ public class PamController implements PamControllerInterface, PamSettings {
 		 * it is necessary to make sure that all internal datablock 
 		 * buffers have had time to empty.
 		 */
+		ArrayList<PamControlledUnit> pamControlledUnits = pamConfiguration.getPamControlledUnits();
+		
 		if (PamModel.getPamModel().isMultiThread()) {
 			for (int iU = 0; iU < pamControlledUnits.size(); iU++) {
 				pamControlledUnits.get(iU).flushDataBlockBuffers(2000);
@@ -1475,6 +1404,8 @@ public class PamController implements PamControllerInterface, PamSettings {
 //		}
 //		Debug.out.println("   Are we finished? " + areWeFinished);
 //		return areWeFinished;
+		ArrayList<PamControlledUnit> pamControlledUnits = pamConfiguration.getPamControlledUnits();
+		
 		boolean running = false;
 		for (PamControlledUnit aUnit : pamControlledUnits) {
 			int numProcesses = aUnit.getNumPamProcesses();
@@ -1497,16 +1428,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 	 * PAMGUARD settings via the database and binary storage modules. 
 	 */
 	private void saveSettings(long timeNow) {
-		PamControlledUnit pcu;
+		pamConfiguration.saveSettings(timeNow);
-		PamSettingsSource settingsSource;
-		for (int iU = 0; iU < pamControlledUnits.size(); iU++) {
-			pcu = pamControlledUnits.get(iU);
-			if (PamSettingsSource.class.isAssignableFrom(pcu.getClass())) {
-				settingsSource = (PamSettingsSource) pcu;
-				settingsSource.saveStartSettings(timeNow);
-			}
-		}
-		PamguardXMLWriter.getXMLWriter().writeStartSettings(timeNow);
 	}
 
 	/**
@@ -1523,18 +1445,20 @@ public class PamController implements PamControllerInterface, PamSettings {
 	 * @return path to the binary store. 
 	 */
 	public String findBinaryStorePath() {
-		BinaryStore binaryControl = BinaryStore.findBinaryStoreControl();
+//		TODO get rid of the singleton binary store control and do from the Config.class 
-		if (binaryControl == null) {
+//		BinaryStore binaryControl = BinaryStore.findBinaryStoreControl();
-			return null;
+//		if (binaryControl == null) {
-		}
+//			return null;
-		String storeLoc = binaryControl.getBinaryStoreSettings().getStoreLocation();
+//		}
-		if (storeLoc == null) {
+//		String storeLoc = binaryControl.getBinaryStoreSettings().getStoreLocation();
-			return "";
+//		if (storeLoc == null) {
-		}
+//			return "";
-		if (storeLoc.endsWith(File.separator) == false) {
+//		}
-			storeLoc += File.separator;
+//		if (storeLoc.endsWith(File.separator) == false) {
-		}
+//			storeLoc += File.separator;
-		return storeLoc;
+//		}
+//		return storeLoc;
+		return pamConfiguration.findBinaryStorePath();
 	}
 
 	/**
@@ -1544,15 +1468,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 	 * @see PamSettingsSource
 	 */
 	public ArrayList<PamSettingsSource> findSettingsSources() {
-		ArrayList<PamSettingsSource> settingsSources = new ArrayList<PamSettingsSource>();
+		return pamConfiguration.findSettingsSources();
-		PamControlledUnit pcu;
-		for (int iU = 0; iU < pamControlledUnits.size(); iU++) {
-			pcu = pamControlledUnits.get(iU);
-			if (PamSettingsSource.class.isAssignableFrom(pcu.getClass())) {
-				settingsSources.add((PamSettingsSource) pcu);
-			}
-		}
-		return settingsSources;
 	}
 
 	@Override
@@ -1581,37 +1497,37 @@ public class PamController implements PamControllerInterface, PamSettings {
 	 */
 	@Override
 	public ArrayList<PamDataBlock> getFFTDataBlocks() {
-		return makeDataBlockList(FFTDataUnit.class, true);
+		return pamConfiguration.getFFTDataBlocks();
 	}
 
 	@Override
 	public PamDataBlock getFFTDataBlock(int id) {
-		return getDataBlock(FFTDataUnit.class, id);
+		return pamConfiguration.getDataBlock(FFTDataUnit.class, id);
 	}
 
 	@Override
 	public PamDataBlock getFFTDataBlock(String name) {
-		return getDataBlock(FFTDataUnit.class, name);
+		return pamConfiguration.getDataBlock(FFTDataUnit.class, name);
 	}
 
 	@Override
 	public ArrayList<PamDataBlock> getRawDataBlocks() {
-		return makeDataBlockList(RawDataUnit.class, true);
+		return pamConfiguration.makeDataBlockList(RawDataUnit.class, true);
 	}
 
 	@Override
 	public PamRawDataBlock getRawDataBlock(int id) {
-		return (PamRawDataBlock) getDataBlock(RawDataUnit.class, id);
+		return (PamRawDataBlock) pamConfiguration.getDataBlock(RawDataUnit.class, id);
 	}
 
 	@Override
 	public PamRawDataBlock getRawDataBlock(String name) {
-		return (PamRawDataBlock) getDataBlock(RawDataUnit.class, name);
+		return pamConfiguration.getRawDataBlock(name);
 	}
 
 	@Override
 	public ArrayList<PamDataBlock> getDetectorDataBlocks() {
-		return makeDataBlockList(PamDetection.class, true);
+		return pamConfiguration.getDetectorDataBlocks();
 	}
 
 	@Override
@@ -1649,33 +1565,16 @@ public class PamController implements PamControllerInterface, PamSettings {
 	 * true.
 	 */
 	public ArrayList<PamDataBlock> getDataBlocks(Class blockType, boolean includeSubClasses) {
-		return makeDataBlockList(blockType, includeSubClasses);
+		return pamConfiguration.getDataBlocks(blockType, includeSubClasses);
 	}
 
 	@Override
 	public ArrayList<PamDataBlock> getDataBlocks() {
-		return makeDataBlockList(PamDataUnit.class, true);
+		return pamConfiguration.getDataBlocks();
 	}
 
 	public ArrayList<PamDataBlock> getPlottableDataBlocks(GeneralProjector generalProjector) {
-
+		return pamConfiguration.getPlottableDataBlocks(generalProjector);
-		ArrayList<PamDataBlock> blockList = new ArrayList<PamDataBlock>();
-		PamProcess pP;
-		Class unitClass;
-		PanelOverlayDraw panelOverlayDraw;
-
-		for (int iU = 0; iU < pamControlledUnits.size(); iU++) {
-			for (int iP = 0; iP < pamControlledUnits.get(iU)
-					.getNumPamProcesses(); iP++) {
-				pP = pamControlledUnits.get(iU).getPamProcess(iP);
-				for (int j = 0; j < pP.getNumOutputDataBlocks(); j++) {
-					if(pP.getOutputDataBlock(j).canDraw(generalProjector)) {
-						blockList.add(pP.getOutputDataBlock(j));
-					}
-				}
-			}
-		}
-		return blockList;
 	}
 
 	/**
@@ -1702,38 +1601,9 @@ public class PamController implements PamControllerInterface, PamSettings {
 	//				}
 	//			}
 	//		}
-	private ArrayList<PamDataBlock> makeDataBlockList(Class classType, boolean includSubClasses) {
+//	private ArrayList<PamDataBlock> makeDataBlockList(Class classType, boolean includSubClasses) {
-
+//		return pamConfiguration.makeDataBlockList(classType, includSubClasses);
-		ArrayList<PamDataBlock> blockList = new ArrayList<PamDataBlock>();
+//	}
-		PamProcess pP;
-		Class unitClass;
-
-		for (int iU = 0; iU < pamControlledUnits.size(); iU++) {
-			for (int iP = 0; iP < pamControlledUnits.get(iU)
-					.getNumPamProcesses(); iP++) {
-				pP = pamControlledUnits.get(iU).getPamProcess(iP);
-				for (int j = 0; j < pP.getNumOutputDataBlocks(); j++) {
-					//System.out.println("Comparing "+pP.getOutputDataBlock(j).getUnitClass().getCanonicalName()+" to "+classType.getCanonicalName());
-					if ((unitClass = pP.getOutputDataBlock(j).getUnitClass()) == classType) {
-						blockList.add(pP.getOutputDataBlock(j));
-					}
-					else if (includSubClasses) {
-						if (classType != null && classType.isAssignableFrom(unitClass)) {
-							blockList.add(pP.getOutputDataBlock(j));
-						}
-						//						while ((unitClass = unitClass.getSuperclass()) != null) {
-						//							if (unitClass == classType) {
-						//								blockList.add(pP.getOutputDataBlock(j));
-						//								break;
-						//							}
-						//						}
-					}
-				}
-			}
-		}
-
-		return blockList;
-	}
 
 	/** 
 	 * Find a block of a given type with the id number, or null if the number
@@ -1745,10 +1615,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 	 */
 	@Override
 	public PamDataBlock getDataBlock(Class blockType, int id) {
-
+		return pamConfiguration.getDataBlock(blockType, id);
-		ArrayList<PamDataBlock> blocks = getDataBlocks(blockType, true);
-		if (id >= 0 && id < blocks.size()) return blocks.get(id);
-		return null;
 	}
 
 	/** 
@@ -1760,23 +1627,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 	 */
 	@Override
 	public PamDataBlock getDataBlock(Class blockType, String name) {
-		if (name == null) return null;
+		return pamConfiguration.getDataBlock(blockType, name);
-		ArrayList<PamDataBlock> blocks = getDataBlocks(blockType, true);
-		for (PamDataBlock dataBlock:blocks) {
-			if (name.equals(dataBlock.getLongDataName())) { // check for a long name match first 
-				return dataBlock;
-			}
-			if (dataBlock instanceof FFTDataBlock) {
-				FFTDataBlock fb = (FFTDataBlock) dataBlock;
-				if (name.equals(fb.getOldLongDataName())) {
-					return dataBlock;
-				}
-			}
-			if (name.equals(dataBlock.toString())) {
-				return dataBlock;
-			}
-		}
-		return null;
 	}
 
 	/**
@@ -1785,20 +1636,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 	 * @return block
 	 */
 	public PamDataBlock getDataBlockByLongName(String longName) {
-		if (longName == null) return null;
+		return pamConfiguration.getDataBlockByLongName(longName);
-		ArrayList<PamDataBlock> allBlocks = getDataBlocks();
-		for (PamDataBlock dataBlock:allBlocks) {
-			if (longName.equals(dataBlock.getLongDataName())) {
-				return dataBlock;
-			}
-			if (dataBlock instanceof FFTDataBlock) {
-				FFTDataBlock fb = (FFTDataBlock) dataBlock;
-				if (longName.equals(fb.getOldLongDataName())) {
-					return dataBlock;
-				}
-			}
-		}
-		return null;
 	}
 
 	/**
@@ -1885,11 +1723,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 
 		MasterReferencePoint.notifyModelChanged(changeType);
 
-		// also tell all PamControlledUnits since they may want to find their data source 
+		pamConfiguration.notifyModelChanged(changeType);
-		// it that was created after they were - i.e. dependencies have got all muddled
-		for (int i = 0; i < pamControlledUnits.size(); i++) {
-			pamControlledUnits.get(i).notifyModelChanged(changeType);
-		}
 
 		PamSettingManager.getInstance().notifyModelChanged(changeType);
 
@@ -1960,6 +1794,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 	private void changedThreading() {
 		PamProcess pamProcess;
 		int nP;
+		ArrayList<PamControlledUnit> pamControlledUnits = pamConfiguration.getPamControlledUnits();
 		for (int i = 0; i < pamControlledUnits.size(); i++) {
 			nP = pamControlledUnits.get(i).getNumPamProcesses();
 			for (int iP = 0; iP < nP; iP++) {
@@ -1993,13 +1828,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 
 	@Override
 	public Serializable getSettingsReference() {
-		ArrayList<UsedModuleInfo> usedModules = new ArrayList<UsedModuleInfo>();
+		return pamConfiguration.getSettingsReference();
-		for (int i = 0; i < pamControlledUnits.size(); i++) {
-			usedModules.add(new UsedModuleInfo(pamControlledUnits.get(i).getClass().getName(), 
-					pamControlledUnits.get(i).getUnitType(),
-					pamControlledUnits.get(i).getUnitName()));
-		}
-		return usedModules;
 	}
 
 	@Override
@@ -2041,10 +1870,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 
 		// also tell all PamControlledUnits since they may want to find their data source 
 		// it that was created after they were - i.e. dependencies have got all muddled
-		for (int i = 0; i < pamControlledUnits.size(); i++) {
+		pamConfiguration.destroyModel();
-			pamControlledUnits.get(i).notifyModelChanged(DESTROY_EVERYTHING);
-		}
-		pamControlledUnits = null;
 
 		PamSettingManager.getInstance().reset();
 
@@ -2369,6 +2195,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 	public void loadOldSettings(PamSettingsGroup settingsGroup) {
 		loadOldSettings(settingsGroup, true);
 	}
+	
 	/**
 	 * Called to load a specific set of PAMGUARD settings in 
 	 * viewer mode, which were previously loaded in from a 
@@ -2473,7 +2300,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 				continue;
 			}
 			aUnit = findControlledUnit(moduleClass, aModuleInfo.unitName);
-			currentPos = pamControlledUnits.indexOf(aUnit);
+			currentPos = pamConfiguration.getControlledUnitIndex(aUnit);
 			if (currentPos >= 0) {
 				temp = orderLUT[nFound];
 				orderLUT[nFound] = currentPos;
@@ -2839,4 +2666,12 @@ public class PamController implements PamControllerInterface, PamSettings {
 		return this.globalMediumManager;
 	}
 
+	/**
+	 * Gt the main PAMGuard configuration (list of connected modules). 
+	 * @return the pamConfiguration
+	 */
+	public PamConfiguration getPamConfiguration() {
+		return pamConfiguration;
+	}
+
 }

src/PamController/PamControllerInterface.java

@@ -25,7 +25,7 @@ import java.util.ArrayList;
 
 import javax.swing.JFrame;
 
-import PamModel.PamModelInterface;
+import PamModel.PamModel;
 import PamModel.PamModuleInfo;
 import PamView.GuiFrameManager;
 import PamView.PamViewInterface;
@@ -102,7 +102,7 @@ public interface PamControllerInterface {
 	 * 
 	 * @return Reference to the PamGuard model
 	 */
-	public PamModelInterface getModelInterface();
+	public PamModel getModelInterface();
 
 	/**
 	 * Instruction to the controller (probably from a menu command inthe view)

src/PamController/PamSettingManager.java

@@ -293,7 +293,7 @@ public class PamSettingManager {
 	 * call this for at least one set of settings. Often the PamSettings
 	 * is implemented by the class that extends PamControlledunit, but
 	 * it's also possible to have multiple sub modules, processes or displays
-	 * implemnt PamSettings so that different settings for different bits of
+	 * implement PamSettings so that different settings for different bits of
 	 * a PamControlledUnit are stored separately.
 	 * @see PamSettings
 	 * @see PamControlledUnit

src/PamModel/PamModel.java

@@ -74,7 +74,7 @@ import PamUtils.FileFinder;
  * PamController.
  * 
  */
-final public class PamModel implements PamModelInterface, PamSettings {
+final public class PamModel implements PamSettings {
 
 	private PamController pamController;
 
@@ -982,7 +982,6 @@ final public class PamModel implements PamModelInterface, PamSettings {
 
 	}
 
-	@Override
 	public boolean modelSettings(JFrame frame) {
 		PamModelSettings newSettings = ThreadingDialog.showDialog(frame, pamModelSettings);
 		if (newSettings != null) {

src/PamModel/PamModelInterface.java

@@ -29,6 +29,7 @@ import javax.swing.JFrame;
  *         order that the PamController and the PamView can interface with the
  *         model.
  */
+@Deprecated
 public interface PamModelInterface {
 
 	/**

src/PamModel/PamModuleInfo.java

@@ -10,6 +10,7 @@ import javax.swing.JMenu;
 import javax.swing.JMenuItem;
 import javax.swing.JOptionPane;
 
+import PamController.PamConfiguration;
 import PamController.PamControlledUnit;
 import PamController.PamController;
 import PamController.PamControllerInterface;
@@ -34,6 +35,9 @@ public class PamModuleInfo implements PamDependent{
 	private Class moduleClass;
 	private String toolTipText;
 	
+	private static final Class[] constrParams1 = {PamConfiguration.class, String.class};
+	private static final Class[] constrParams2 = {String.class};
+	
 	/**
 	 * A list of possible GUI types the module can have. These are received from flags in PAMGuiManager();
 	 */
@@ -209,7 +213,7 @@ public class PamModuleInfo implements PamDependent{
 			  dependencyManager.checkDependency(parentFrame, moduleInfo, true);
 			}
 			// create a new PamControlledUnit and add it to PamGuard ...
-			PamControllerInterface pamController = PamController.getInstance();
+			PamController pamController = PamController.getInstance();
 		
 			pamController.addModule(parentFrame, moduleInfo);
 		}
@@ -221,29 +225,42 @@ public class PamModuleInfo implements PamDependent{
 	}
 
 	public PamControlledUnit create(String unitName) {
+		return create(null, unitName);
+	}
+	
+	public PamControlledUnit create(PamConfiguration pamConfiguration, String unitName) {
 		
 		PamControlledUnit newUnit = null;
-		Class[] paramList = new Class[1];
+//		Class[] paramList = new Class[1];
-		paramList[0] = unitName.getClass();
+//		paramList[0] = unitName.getClass();
+		boolean error = false;
 		try {
-			Constructor constructor = moduleClass.getConstructor(paramList);
+			Constructor constructor = moduleClass.getConstructor(constrParams1);
-//			Debug.out.println("unitName:"+ unitName);
+			newUnit = (PamControlledUnit) constructor.newInstance(pamConfiguration, unitName);
-			newUnit = (PamControlledUnit) constructor.newInstance(unitName);
 			newUnit.setPamModuleInfo(this);
 		}
 		catch (Exception Ex) {
-			String title = "Error loading module";
+		}
-			String msg = "There was an error trying to load " + unitName + ".<p>" +
+		if (newUnit == null) {
-					"If this is a core Pamguard module, please copy the error message text and email to " +
+			try {
-					"support@pamguard.org.<p>" +
+				Constructor constructor = moduleClass.getConstructor(constrParams2);
-					"If this is a plug-in, the error may have been caused by an incompatibility between " +
+				newUnit = (PamControlledUnit) constructor.newInstance(unitName);
-					"it and this version of PAMGuard, or a problem with the code.  Please check the developer's website for help.<p>" +
+				newUnit.setPamModuleInfo(this);
-					"This module will not be loaded.";
+			}
-			String help = null;
+			catch (Exception Ex) {
-			int ans = WarnOnce.showWarning(title, msg, WarnOnce.WARNING_MESSAGE, help, Ex);
+				String title = "Error loading module";
-			System.err.println("Exception while loading " +	Ex.getMessage());
+				String msg = "There was an error trying to load " + unitName + ".<p>" +
-			Ex.printStackTrace();
+						"If this is a core Pamguard module, please copy the error message text and email to " +
-			return null;
+						"support@pamguard.org.<p>" +
+						"If this is a plug-in, the error may have been caused by an incompatibility between " +
+						"it and this version of PAMGuard, or a problem with the code.  Please check the developer's website for help.<p>" +
+						"This module will not be loaded.";
+				String help = null;
+				int ans = WarnOnce.showWarning(title, msg, WarnOnce.WARNING_MESSAGE, help, Ex);
+				System.err.println("Exception while loading " +	Ex.getMessage());
+				Ex.printStackTrace();
+				return null;
+			}
 		}
 
 		setNInstances(nInstances + 1);
@@ -251,6 +268,18 @@ public class PamModuleInfo implements PamDependent{
 		return newUnit;
 	}
 	
+	private Constructor findConstructor() throws NoSuchMethodException, SecurityException {
+		Constructor constructor = null;
+		try {
+			constructor = moduleClass.getConstructor(constrParams1);
+			return constructor;
+		} catch (NoSuchMethodException | SecurityException e1) {
+		}
+
+		constructor = moduleClass.getConstructor(constrParams2);
+		return constructor;
+	}
+	
 	private void moduleRemoved(PamControlledUnit controlledUnit) {
 
 		setNInstances(nInstances - 1);
@@ -376,7 +405,7 @@ public class PamModuleInfo implements PamDependent{
 		}
 
 		public void actionPerformed(ActionEvent e) {
-			int ans = JOptionPane.showConfirmDialog(pamControlledUnit.getPamView().getGuiFrame(),
+			int ans = JOptionPane.showConfirmDialog(pamControlledUnit.getGuiFrame(),
 					"Do you really want to remove the module " 
 					+ pamControlledUnit.getUnitName());
 			if (ans == JOptionPane.YES_OPTION) {

src/PamView/PamGui.java

@@ -87,7 +87,6 @@ import PamController.PamguardVersionInfo;
 import PamController.settings.SettingsImport;
 import PamModel.CommonPluginInterface;
 import PamModel.PamModel;
-import PamModel.PamModelInterface;
 import PamModel.PamModuleInfo;
 import PamModel.PamPluginInterface;
 import PamModel.AboutPluginDisplay;
@@ -133,12 +132,15 @@ public class PamGui extends PamView implements WindowListener, PamSettings {
 	 * Outer layered pane which allows things to be added the GUI. 
 	 */
 	private JLayeredPane layeredPane;
+	private PamController pamController;
 
-	public PamGui(PamControllerInterface pamControllerInterface, 
+	public PamGui(PamController pamControllerInterface, 
-			PamModelInterface pamModelInterface, int frameNumber)
+			PamModel pamModelInterface, int frameNumber)
 	{
 		super(pamControllerInterface, pamModelInterface, frameNumber);
 		
+		this.pamController = pamControllerInterface;
+
 		startMenuEnabler = new MenuItemEnabler();
 		stopMenuEnabler = new MenuItemEnabler();
 		stopMenuEnabler.enableItems(false);
@@ -1198,7 +1200,7 @@ public class PamGui extends PamView implements WindowListener, PamSettings {
 
 	class menuShowObjectDiagram implements ActionListener {
 		public void actionPerformed(ActionEvent ev){
-			PamObjectViewer.Show(getGuiFrame());
+			PamObjectViewer.Show(getGuiFrame(), pamController.getPamConfiguration());
 		}
 	}
 

src/PamView/PamMenu.java

@@ -26,7 +26,7 @@ import javax.swing.JMenu;
 import javax.swing.JMenuBar;
 import javax.swing.JMenuItem;
 
-import PamModel.PamModelInterface;
+import PamModel.PamModel;
 
 /**
  * @author dgillespie
@@ -39,7 +39,7 @@ import PamModel.PamModelInterface;
  * 
  */
 public class PamMenu {
-	static public JMenuBar createBasicMenu(PamModelInterface pamModelInterface,
+	static public JMenuBar createBasicMenu(PamModel pamModelInterface,
 			ActionListener actionListener) {
 
 		JMenuBar menuBar = new JMenuBar();
@@ -52,7 +52,7 @@ public class PamMenu {
 		return menuBar;
 	}
 
-	static public JMenu fileMenu(PamModelInterface pamModelInterface,
+	static public JMenu fileMenu(PamModel pamModelInterface,
 			ActionListener actionListener) {
 		JMenuItem menuItem;
 		JMenu menu = new JMenu("File");
@@ -64,7 +64,7 @@ public class PamMenu {
 		return menu;
 	}
 
-	static public JMenu loggingMenu(PamModelInterface pamModelInterface,
+	static public JMenu loggingMenu(PamModel pamModelInterface,
 			ActionListener actionListener) {
 		JMenuItem menuItem;
 		JMenu menu = new JMenu("Logging");
@@ -76,7 +76,7 @@ public class PamMenu {
 		return menu;
 	}
 
-	static public JMenu detectionMenu(PamModelInterface pamModelInterface,
+	static public JMenu detectionMenu(PamModel pamModelInterface,
 			ActionListener actionListener) {
 		JMenu menu = new JMenu("Detection");
 		JMenuItem menuItem;
@@ -108,7 +108,7 @@ public class PamMenu {
 		return menu;
 	}
 
-	static public JMenu displayMenu(PamModelInterface pamModelInterface,
+	static public JMenu displayMenu(PamModel pamModelInterface,
 			ActionListener actionListener) {
 		JMenu menu = new JMenu("Display");
 		JMenuItem menuItem;

src/PamView/PamObjectViewer.java

@@ -42,6 +42,7 @@ import javax.swing.Timer;
 import javax.swing.WindowConstants;
 
 import PamController.NewModuleDialog;
+import PamController.PamConfiguration;
 import PamController.PamControlledUnit;
 import PamController.PamControlledUnitSettings;
 import PamController.PamController;
@@ -114,9 +115,11 @@ public class PamObjectViewer implements PamViewInterface, ComponentListener,
 	
 	private Stroke arrowStroke, instantArrowStroke;
 
+	private PamConfiguration pamConfiguration;
+
 	// Font controllerFont, processFont, datablockFont;
 
-	private PamObjectViewer(JFrame frame) {
+	private PamObjectViewer(Frame frame) {
 		
 		arrowStroke = new BasicStroke(1.5f);
 		instantArrowStroke = new BasicStroke(1.5f);
@@ -125,23 +128,27 @@ public class PamObjectViewer implements PamViewInterface, ComponentListener,
 
 		objectFrame = new ObjectFrame(frame);
 
-		MakeDiagram();
+//		MakeDiagram();
 
 		PamController.getInstance().addView(this);
 
 		PamSettingManager.getInstance().registerSettings(this);
 	}
 
-	static public PamObjectViewer getObjectViewer(JFrame frame) {
+	static public PamObjectViewer getObjectViewer(Frame frame) {
 		if (singleInstance == null) {
 			singleInstance = new PamObjectViewer(frame);
 		}
 		return singleInstance;
 	}
 
-	static public void Show(JFrame frame) {
+	static public void Show(Frame frame, PamConfiguration pamConfiguration) {
+
+		getObjectViewer(frame).setConfiguration(pamConfiguration);
 		getObjectViewer(frame).objectFrame.setVisible(true);
 		
+		singleInstance.MakeDiagram();
+		
 		// Go through all of the processes/datablocks in every view and update button/tooltip text.
 		// Mostly done for the FFT Engine process because it includes the FFT size in the
 		// process name, and without this code the name would get set the first time you open
@@ -164,6 +171,10 @@ public class PamObjectViewer implements PamViewInterface, ComponentListener,
 		}
 	}
 
+	private void setConfiguration(PamConfiguration pamConfiguration) {
+		this.pamConfiguration = pamConfiguration;
+	}
+
 	void MakeDiagram() {
 
 		if (pamObjectViewerSettings.viewStyle == PamObjectViewerSettings.VIEWBYPROCESS) {
@@ -180,12 +191,16 @@ public class PamObjectViewer implements PamViewInterface, ComponentListener,
 	private void makeControllerDiagram() {
 
 		clearDiagram();
-		PamControllerInterface pamController = PamController.getInstance();
+		
+		if (pamConfiguration == null) {
+			return;
+		}
+		
 		PamControlledUnit pamControlledUnit;
 		PamControllerView pamControllerView;
 		controllerList = new ArrayList<PamControllerView>();
-		for (int iUnit = 0; iUnit < pamController.getNumControlledUnits(); iUnit++) {
+		for (int iUnit = 0; iUnit < pamConfiguration.getNumControlledUnits(); iUnit++) {
-			pamControlledUnit = pamController.getControlledUnit(iUnit);
+			pamControlledUnit = pamConfiguration.getControlledUnit(iUnit);
 			if (pamControlledUnit.getNumPamProcesses() == 0
 					&& pamObjectViewerSettings.showProcesslessModules == false) {
 				continue;
@@ -198,25 +213,6 @@ public class PamObjectViewer implements PamViewInterface, ComponentListener,
 
 	}
 
-	// private void makeProcesslessModules() {
-	// PamControllerInterface pamController = PamController.getInstance();
-	// PamControlledUnit pamControlledUnit;
-	// PamControllerView pamControllerView;
-	// if (controllerList == null)
-	// controllerList = new ArrayList<PamControllerView>();
-	// for (int iUnit = 0; iUnit < pamController.getNumControlledUnits();
-	// iUnit++) {
-	// pamControlledUnit = pamController.getControlledUnit(iUnit);
-	// if (pamControlledUnit.getNumPamProcesses() > 0) {
-	// continue;
-	// }
-	// pamControllerView = new PamControllerView(pamControlledUnit);
-	// controllerList.add(pamControllerView);
-	// layoutPanel.add(pamControllerView);
-	// pamControllerView.addComponentListener(this);
-	// }
-	//		
-	// }
 	private void layoutControllerDiagram() {
 		if (controllerList == null) {
 			return;
@@ -285,11 +281,10 @@ public class PamObjectViewer implements PamViewInterface, ComponentListener,
 		int x = xStart;
 		int y = yStart;
 
-		PamControllerInterface pamController = PamController.getInstance();
 		PamControlledUnit pamControlledUnit;
 		PamProcess pamProcess;
-		for (int iUnit = 0; iUnit < pamController.getNumControlledUnits(); iUnit++) {
+		for (int iUnit = 0; iUnit < pamConfiguration.getNumControlledUnits(); iUnit++) {
-			pamControlledUnit = pamController.getControlledUnit(iUnit);
+			pamControlledUnit = pamConfiguration.getControlledUnit(iUnit);
 			for (int iP = 0; iP < pamControlledUnit.getNumPamProcesses(); iP++) {
 				pamProcess = pamControlledUnit.getPamProcess(iP);
 				pamProcessView = new PamProcessView(pamControlledUnit,
@@ -417,7 +412,7 @@ public class PamObjectViewer implements PamViewInterface, ComponentListener,
 
 	class ObjectFrame extends JFrame implements ActionListener {
 
-		ObjectFrame(JFrame frame) {
+		ObjectFrame(Frame frame) {
 			setTitle("Pamguard Data Model");
 
 			// fixed case of Resources 17/8/08 DG.
@@ -599,6 +594,9 @@ public class PamObjectViewer implements PamViewInterface, ComponentListener,
 			int bestYGap;
 			Rectangle sourceBounds, destBounds;
 			hasInstant = false;
+			if (controllerList == null) {
+				return;
+			}
 			for (int i = 0; i < controllerList.size(); i++) {
 				pamControllerView = controllerList.get(i);
 				pamControlledUnit = pamControllerView.pamControlledUnit;

src/PamView/PamView.java

@@ -24,7 +24,7 @@ import javax.swing.JFrame;
 
 import PamController.PamControlledUnit;
 import PamController.PamControllerInterface;
-import PamModel.PamModelInterface;
+import PamModel.PamModel;
 import javafx.application.Platform;
 
 /**
@@ -36,7 +36,7 @@ abstract public class PamView implements PamViewInterface {
 
 	protected PamControllerInterface pamControllerInterface;
 
-	protected PamModelInterface pamModelInterface;
+	protected PamModel pamModelInterface;
 
 	/** 
 	 * Frame for main window associated with this view (i.e a PamGUI).
@@ -47,7 +47,7 @@ abstract public class PamView implements PamViewInterface {
 		
 
 	public PamView(PamControllerInterface pamControllerInterface,
-			PamModelInterface pamModelInterface, int frameNumber) {
+			PamModel pamModelInterface, int frameNumber) {
 		this.pamControllerInterface = pamControllerInterface;
 		this.pamModelInterface = pamModelInterface;
 		this.frameNumber = frameNumber;

src/PamView/component/DataBlockTableView.java

@@ -11,6 +11,7 @@ import javax.swing.JComponent;
 import javax.swing.JMenuItem;
 import javax.swing.JPopupMenu;
 import javax.swing.JScrollPane;
+import javax.swing.JTable;
 import javax.swing.ListSelectionModel;
 import javax.swing.SwingUtilities;
 import javax.swing.table.AbstractTableModel;
@@ -128,6 +129,14 @@ public abstract class DataBlockTableView<T extends PamDataUnit> {
 		}
 	}
 	
+	/**
+	 * Get table. Allows adding of more menu handlers, etc. 
+	 * @return the table object. 
+	 */
+	public JTable getTable() {
+		return testTable;
+	}
+	
 	/**
 	 * Set allowing of multiple row selection. 
 	 * @param allow
@@ -228,7 +237,7 @@ public abstract class DataBlockTableView<T extends PamDataUnit> {
 	 * @param tableRow
 	 * @return data unit for the table row. 
 	 */
-	private final T getDataUnit(int tableRow) {
+	protected final T getDataUnit(int tableRow) {
 		synchronized (copySynch) {
 			int rowIndex = getDataIndexForRow(tableRow);
 			if (rowIndex < 0) return null;
@@ -377,7 +386,7 @@ public abstract class DataBlockTableView<T extends PamDataUnit> {
 	 * so consider changing the row selection
 	 * @param e
 	 */
-	private void checkRowSelection(MouseEvent e) {
+	protected void checkRowSelection(MouseEvent e) {
 		int tableRow = testTable.rowAtPoint(e.getPoint());
 		int currentRow = testTable.getSelectedRow();
 		if (tableRow != currentRow) {
@@ -389,6 +398,16 @@ public abstract class DataBlockTableView<T extends PamDataUnit> {
 		}
 	}
 
+	/**
+	 * Put the getColumnName function out here, so that subclasses can 
+	 * more easily override it than if it's buried in the table model 
+	 * @param column
+	 * @return colum name
+	 */
+	public String getColumnName(int column) {
+		return getColumnNames()[column];
+	}
+
 	private class ViewScrollObserver implements PamScrollObserver {
 
 		@Override
@@ -448,7 +467,7 @@ public abstract class DataBlockTableView<T extends PamDataUnit> {
 		 */
 		@Override
 		public String getColumnName(int column) {
-			return getColumnNames()[column];
+			return DataBlockTableView.this.getColumnName(column);
 		}
 
 		/* (non-Javadoc)

src/PamView/dialog/GroupedSourcePanel.java

@@ -154,9 +154,13 @@ public class GroupedSourcePanel extends SourcePanel {
 	
 	public void setChannelGroups(int[] channelGroups) {
 		if (channelGroups == null) return;
-		for (int i = 0; i < Math.min(channelGroups.length, PamConstants.MAX_CHANNELS); i++) {
+		for (int i = 0; i < Math.min(channelGroups.length, PamConstants.MAX_CHANNELS); i++) {			try {
 			groupList[i].setSelectedIndex(channelGroups[i]);
 		}
+		catch (Exception e) {
+			
+		}
+		}
 	}
 
 	public static void addComponent(JPanel panel, Component p, GridBagConstraints constraints){

src/SoundRecorder/RecorderTabPanel.java

@@ -343,7 +343,7 @@ public class RecorderTabPanel implements PamTabPanel, RecorderView {
 		class SettingsButtonListener implements ActionListener {
 
 			public void actionPerformed(ActionEvent e) {
-				recorderControl.recordSettingsDialog(recorderControl.getPamView().getGuiFrame());
+				recorderControl.recordSettingsDialog(recorderControl.getGuiFrame());
 			}
 			
 		}

src/Spectrogram/SpectrogramDisplay.java

@@ -107,6 +107,7 @@ import PamView.GeneralProjector;
 import PamView.ColourArray.ColourArrayType;
 import PamView.dialog.PamLabel;
 import PamView.PamColors;
+import PamView.PamView;
 import PamView.hidingpanel.HidingDialogPanel;
 import PamView.panel.CornerLayout;
 import PamView.panel.CornerLayoutContraint;
@@ -275,11 +276,13 @@ InternalFrameListener, DisplayPanelContainer, SpectrogramParametersUser, PamSett
 		//		}
 		if (spectrogramParameters == null) {
 			this.spectrogramParameters = new SpectrogramParameters();
-			//			setSettings(); // force up the dialog. 
+			PamView view = userDisplayControl.getPamView();
-			SpectrogramParameters newParams = SpectrogramParamsDialog
+			if (view != null) {
-					.showDialog(userDisplayControl.getPamView().getGuiFrame(), spectrogramPanels, spectrogramParameters);
+				SpectrogramParameters newParams = SpectrogramParamsDialog
-			if (newParams != null) {
+						.showDialog(userDisplayControl.getGuiFrame(), spectrogramPanels, spectrogramParameters);
-				this.spectrogramParameters = newParams;
+				if (newParams != null) {
+					this.spectrogramParameters = newParams;
+				}
 			}
 		}
 
@@ -1184,7 +1187,7 @@ InternalFrameListener, DisplayPanelContainer, SpectrogramParametersUser, PamSett
 		//		SpectrogramParameters newParams = SpectrogramParamsDialog
 		//				.showDialog(userDisplayControl.getPamView().getGuiFrame(), this.getOverlayMarker(), spectrogramParameters);
 		SpectrogramParameters newParams = SpectrogramParamsDialog
-				.showDialog(userDisplayControl.getPamView().getGuiFrame(), spectrogramPanels, spectrogramParameters);
+				.showDialog(userDisplayControl.getGuiFrame(), spectrogramPanels, spectrogramParameters);
 
 
 		if (newParams == null) return;

src/alarm/AlarmOfflineTask.java

@@ -62,7 +62,7 @@ public class AlarmOfflineTask extends OfflineTask<PamDataUnit> {
 
 	@Override
 	public boolean callSettings() {
-		Frame frame = alarmControl.getPamView().getGuiFrame();
+		Frame frame = alarmControl.getGuiFrame();
 		boolean ok = alarmControl.showAlarmDialog(frame);
 		if (ok) {
 			setParentDataBlock(alarmProcess.getSourceDataBlock());

src/autecPhones/AutecPhonesControl.java

@@ -22,7 +22,7 @@ public class AutecPhonesControl extends PamControlledUnit {
 	}
 
 	public Frame getGuiFrame() {
-		return super.getPamView().getGuiFrame();
+		return super.getGuiFrame();
 	}
 	class AutecProcess extends PamProcess {
 

src/binaryFileStorage/BinaryStore.java

@@ -923,7 +923,7 @@ PamSettingsSource, DataOutputStore {
 		protected void process(List<BinaryMapMakeProgress> chunks) {
 			if (PamGUIManager.isSwing()) {
 				if (binaryMapDialog == null) {
-					binaryMapDialog = BinaryMapMakingDialog.showDialog(getPamView().getGuiFrame());
+					binaryMapDialog = BinaryMapMakingDialog.showDialog(PamController.getMainFrame());
 				}
 				super.process(chunks);
 				for (int i = 0; i < chunks.size(); i++) {
@@ -2370,7 +2370,7 @@ PamSettingsSource, DataOutputStore {
 	 * Get the unit type for the binary store. 
 	 * @return the binary store unit type. 
 	 */
-	private static String getBinaryUnitType() {
+	public static String getBinaryUnitType() {
 		return defUnitType;
 	}
 

src/clickDetector/ClickBTDisplay.java

@@ -2771,7 +2771,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
 
 			BTDisplayParameters newParameters = 
 					ClickDisplayDialog.showDialog(clickControl, 
-							clickControl.getPamView().getGuiFrame(), btDisplayParameters);
+							clickControl.getGuiFrame(), btDisplayParameters);
 			if (newParameters != null){
 				btDisplayParameters = newParameters.clone();
 				if (getVScaleManager() != null) {

src/clickDetector/ClickControl.java

@@ -44,6 +44,7 @@ import binaryFileStorage.BinaryStore;
 import Filters.FilterDialog;
 import Filters.FilterParams;
 import Localiser.detectionGroupLocaliser.GroupDetection;
+import PamController.PamConfiguration;
 import PamController.PamControlledUnit;
 import PamController.PamControlledUnitGUI;
 import PamController.PamControlledUnitSettings;
@@ -97,6 +98,7 @@ import dataPlotsFX.data.TDDataProviderRegisterFX;
 import detectionPlotFX.data.DDPlotRegister;
 import detectionPlotFX.rawDDPlot.ClickDDPlotProvider;
 import fftManager.fftorganiser.FFTDataOrganiser;
+import offlineProcessing.OfflineTaskGroup;
 
 /**
  * Main Controller for click detection.
@@ -207,9 +209,22 @@ public class ClickControl extends PamControlledUnit implements PamSettings {
 
 	public static final String UNITTYPE = "Click Detector";
 
+	/**
+	 * Old style constructor which only gets a name
+	 * @param name
+	 */
 	public ClickControl(String name) {
+		this(null, name);
+	}
 	
-		super(UNITTYPE, name);
+	/**
+	 * New style constructor which get a configuraiton and a name. 
+	 * @param pamConfiguration
+	 * @param name
+	 */
+	public ClickControl(PamConfiguration pamConfiguration, String name) {
+
+		super(pamConfiguration, UNITTYPE, name);
 
 		sortDataBlockPrefix();
 
@@ -220,7 +235,6 @@ public class ClickControl extends PamControlledUnit implements PamSettings {
 		//		}
 		clickControl = this;
 
-
 		angleVetoes = new AngleVetoes(this);
 
 		offlineToolbar = new OfflineToolbar(this);
@@ -288,6 +302,9 @@ public class ClickControl extends PamControlledUnit implements PamSettings {
 			roccaControl = (RoccaControl) PamController.getInstance().findControlledUnit(RoccaControl.unitType);
 
 		}
+		else {
+			ClicksOffline.getOfflineTaskGroup(this);
+		}
 
 		if (PamGUIManager.isSwing()) {
 
@@ -988,6 +1005,19 @@ public class ClickControl extends PamControlledUnit implements PamSettings {
 		return clicksOffline;
 	}
 
+//	/**
+//	 * @return the number of offlineTaskGroups
+//	 */
+//	public int getNumOfflineTaskGroups() {
+//		return 1;
+//	}
+//	
+//	/**
+//	 * @return the iTH offlineTaskGroup
+//	 */
+//	public OfflineTaskGroup getOfflineTaskGroup(int i) {
+//		return offlineTaskGroups.get(i);
+//	}
 
 	/**
 	 * @return the latestOfflineEvent
@@ -1187,7 +1217,8 @@ public class ClickControl extends PamControlledUnit implements PamSettings {
 	 * @return
 	 */
 	public PamRawDataBlock findRawDataBlock() {
-		return (PamController.getInstance().getRawDataBlock(clickParameters.getRawDataSource()));
+		return getPamConfiguration().getRawDataBlock(clickParameters.getRawDataSource());
+//		return (PamController.getInstance().getRawDataBlock(clickParameters.getRawDataSource()));
 	}
 
 

src/clickDetector/ClickDetector.java

@@ -403,7 +403,7 @@ public class ClickDetector extends PamProcess {
 			// try to connect automatically to the acquisition module ...
 			// ArrayList<PamDataBlock> rawBlocks =
 			// PamController.getInstance().getDataBlocks(RawDataUnit.class, false);
-			AcquisitionControl daq = (AcquisitionControl) PamController.getInstance()
+			AcquisitionControl daq = (AcquisitionControl) clickControl.getPamConfiguration()
 					.findControlledUnit(AcquisitionControl.unitType);
 			if (daq != null) {
 				rawDataSource = daq.getRawDataBlock();

src/clickDetector/ClickSpectrum.java

@@ -841,7 +841,7 @@ public class ClickSpectrum extends ClickDisplay implements PamObserver , PamSett
 		pt.x += 10;
 		pt.y += 20;
 		ClickSpectrumParams newParams = ClickSpectrumDialog.showDialog(
-				clickControl.getPamView().getGuiFrame(), pt, this, clickSpectrumParams);
+				clickControl.getGuiFrame(), pt, this, clickSpectrumParams);
 		if (newParams != null) {
 			if (newParams.plotCepstrum) {
 				newParams.logScale = false;
@@ -859,7 +859,7 @@ public class ClickSpectrum extends ClickDisplay implements PamObserver , PamSett
 		pt.x += 10;
 		pt.y += 20;
 		ClickSpectrumTemplateParams newTempParams = ClickSpectrumTemplateEditDialog.showDialog(
-				clickControl.getPamView().getGuiFrame(), pt, this, clickTemplateParams,clickControl);
+				clickControl.getGuiFrame(), pt, this, clickTemplateParams,clickControl);
 		if (newTempParams!=null){
 			clickTemplateParams = newTempParams.clone();
 			sortWestAxis();
@@ -873,7 +873,7 @@ public class ClickSpectrum extends ClickDisplay implements PamObserver , PamSett
 		pt.x += 10;
 		pt.y += 20;
 		ClickSpectrumTemplateParams newTempParams = ClickSpectrumTemplateDialog.showDialog(
-				clickControl.getPamView().getGuiFrame(), pt, this, clickTemplateParams);
+				clickControl.getGuiFrame(), pt, this, clickTemplateParams);
 		if (newTempParams!=null){
 			clickTemplateParams = newTempParams.clone();
 			sortWestAxis();

src/clickDetector/ClickWaveform.java

@@ -765,7 +765,7 @@ public class ClickWaveform extends ClickDisplay implements PamObserver {
 		@Override
 		public void actionPerformed(ActionEvent arg0) {
 
-			ClickParameters newParams = WaveDisplayDialog.showDialog(clickControl.getPamView().getGuiFrame(),
+			ClickParameters newParams = WaveDisplayDialog.showDialog(clickControl.getGuiFrame(),
 					clickWaveform, clickControl.clickParameters);
 			if (newParams != null) {
 				clickControl.clickParameters = newParams.clone();

src/clickDetector/IDI_Display.java

@@ -975,7 +975,7 @@ public class IDI_Display extends ClickDisplay implements PamObserver, PamSetting
 			pt.y -= 10;
 			pt.x += 10;
 			IDI_DisplayParams newParams = IDI_DisplayDialog.showDialog(
-					clickControl.getPamView().getGuiFrame(), pt, idiParams);
+					clickControl.getGuiFrame(), pt, idiParams);
 			if (newParams != null) {
 				idiParams = newParams.clone();
                 setParameters();

src/clickDetector/WignerPlot.java

@@ -248,7 +248,7 @@ public class WignerPlot extends ClickDisplay implements PamSettings {
 			pt.y -= 10;
 			pt.x += 10;
 			WignerPlotOptions newoptions = WignerPlotdialog.showDialog(
-					clickControl.getPamView().getGuiFrame(), pt, wignerPlotOptions);
+					clickControl.getGuiFrame(), pt, wignerPlotOptions);
 			if (newoptions != null) {
 				wignerPlotOptions = newoptions.clone();
 				clickedOnClick(lastClick);

src/clickDetector/offlineFuncs/ClickDelayTask.java

@@ -123,7 +123,7 @@ public class ClickDelayTask extends OfflineTask<ClickDetection> {
 //			clickControl.getClickParameters().setDelayMeasurementParams(0, newParams.clone());
 //			return true;
 //		}
-		ClickParameters newParams = ClickDelayDialog.showDialog(clickControl.getPamView().getGuiFrame(), clickControl);
+		ClickParameters newParams = ClickDelayDialog.showDialog(clickControl.getGuiFrame(), clickControl);
 		if (newParams != null) {
 			clickControl.setClickParameters(newParams);
 			return true;

src/clickDetector/offlineFuncs/ClickReClassifyTask.java

@@ -75,7 +75,7 @@ public class ClickReClassifyTask extends OfflineTask<ClickDetection> {
 
 	@Override
 	public boolean callSettings() {
-		return clickControl.classificationDialog(clickControl.getPamView().getGuiFrame());
+		return clickControl.classificationDialog(clickControl.getGuiFrame());
 	}
 
 

src/clickDetector/offlineFuncs/ClicksOffline.java

@@ -62,8 +62,6 @@ public class ClicksOffline {
 
 	private OLProcessDialog clickOfflineDialog;
 	
-	private OfflineTaskGroup offlineTaskGroup;
-	
 	public static final String ClickTypeLookupName = "OfflineRCEvents";
 
 	/**
@@ -545,8 +543,8 @@ public class ClicksOffline {
 	 */
 	public void reAnalyseClicks() {
 		if (clickOfflineDialog == null) {
-			clickOfflineDialog = new OLProcessDialog(clickControl.getPamView().getGuiFrame(), 
+			clickOfflineDialog = new OLProcessDialog(clickControl.getGuiFrame(), 
-					getOfflineTaskGroup(), "Click Reprocessing");
+					getOfflineTaskGroup(clickControl), "Click Reprocessing");
 		}
 		clickOfflineDialog.setVisible(true);
 	}
@@ -576,8 +574,9 @@ public class ClicksOffline {
 	 * Get / Create an offline task group for click re-processing. 
 	 * @return offline task group. Create if necessary
 	 */
-	private OfflineTaskGroup getOfflineTaskGroup() {
+	public static OfflineTaskGroup getOfflineTaskGroup(ClickControl clickControl) {
-		offlineTaskGroup = new OfflineTaskGroup(clickControl, "Click Reprocessing");
+		
+		OfflineTaskGroup offlineTaskGroup = new OfflineTaskGroup(clickControl, "Click Reprocessing");
 		
 		/**
 		 * These tasks are not registered - gets too complicated since some of them 
@@ -607,7 +606,7 @@ public class ClicksOffline {
 	}
 
 	public void labelClicks(OverlayMark overlayMark, List<PamDataUnit> dataList) {
-		Window win = clickControl.getPamView().getGuiFrame();
+		Window win = clickControl.getGuiFrame();
 		OfflineEventDataUnit event = LabelClicksDialog.showDialog(win, clickControl, overlayMark, dataList);
 		if (event != null) {
 			notifyEventChanges(event);
@@ -625,7 +624,7 @@ public class ClicksOffline {
 	}
 
 	public void newEvent(OverlayMark overlayMark, List<PamDataUnit> markedClicks) {
-		Window win = clickControl.getPamView().getGuiFrame();
+		Window win = clickControl.getGuiFrame();
 		OfflineEventDataBlock offlineEventDataBlock = clickControl.getClickDetector().getOfflineEventDataBlock();
 		if (markedClicks == null) {
 			return;
@@ -692,7 +691,7 @@ public class ClicksOffline {
 	}
 
 	public void labelClick(OverlayMark overlayMark, PamDataUnit singleClick) {
-		Window win = clickControl.getPamView().getGuiFrame();
+		Window win = clickControl.getGuiFrame();
 		OfflineEventDataUnit event = LabelClicksDialog.showDialog(win, clickControl, overlayMark, singleClick);
 		if (event != null) {
 			notifyEventChanges(event);

src/clickDetector/offlineFuncs/EchoDetectionTask.java

@@ -90,7 +90,7 @@ public class EchoDetectionTask extends OfflineTask<ClickDetection> {
 		if (echoDetectionSystem == null) {
 			return false;
 		}
-		return EchoDialog.showDialog(clickControl.getPamView().getGuiFrame(), echoDetectionSystem);
+		return EchoDialog.showDialog(clickControl.getGuiFrame(), echoDetectionSystem);
 	}
 
 	/* (non-Javadoc)

src/clickTrainDetector/offline/ClickTrainOfflineProcess.java

@@ -84,7 +84,7 @@ public class ClickTrainOfflineProcess {
 		
 		//if null open the dialog- also create a new offlineTask group if the datablock has changed. 
 		if (clickTrainDialog == null) {
-			clickTrainDialog = new CTProcessDialog(this.clickTrainControl.getPamView().getGuiFrame(), 
+			clickTrainDialog = new CTProcessDialog(this.clickTrainControl.getGuiFrame(), 
 					clickTrainOfflineGroup, "Click Train Detection");
 			//batchLocaliseDialog.setModalityType(Dialog.ModalityType.MODELESS);
 		}

src/dbht/DbHtControl.java

@@ -122,7 +122,7 @@ public class DbHtControl extends PamControlledUnit implements PamSettings {
 			offlineTaskGroup.addTask(task);
 		}
 		if (olProcessDialog == null) {
-			olProcessDialog = new OLProcessDialog(getPamView().getGuiFrame(), offlineTaskGroup, "dBHt Data Export");
+			olProcessDialog = new OLProcessDialog(getGuiFrame(), offlineTaskGroup, "dBHt Data Export");
 		}
 		olProcessDialog.setVisible(true);
 	}

src/difar/DifarControl.java

@@ -455,7 +455,7 @@ public class DifarControl extends PamControlledUnit implements PamSettings {
 //			offlineTaskGroup.addTask(task);
 		}
 		OLProcessDialog olProcessDialog;
-		olProcessDialog = new OLProcessDialog(getPamView().getGuiFrame(), offlineTaskGroup, "DIFAR Data Export");
+		olProcessDialog = new OLProcessDialog(getGuiFrame(), offlineTaskGroup, "DIFAR Data Export");
 		olProcessDialog.setVisible(true);
 	}
 	

src/fftManager/PamFFTControl.java

@@ -37,6 +37,7 @@ import fftManager.layoutFX.FFTGuiFX;
 //import fftManager.layoutFX.FFTGuiFX;
 import fftManager.newSpectrogram.SpectrogramPlotProvider;
 import spectrogramNoiseReduction.SpectrogramNoiseProcess;
+import PamController.PamConfiguration;
 import PamController.PamControlledUnit;
 import PamController.PamControlledUnitGUI;
 import PamController.PamControlledUnitSettings;
@@ -70,7 +71,11 @@ public class PamFFTControl extends PamControlledUnit implements PamSettings {
 	private PamControlledGUISwing fftGUISwing;
 
 	public PamFFTControl(String unitName) {
-		super("FFT Engine", unitName);
+		this(null, unitName);
+	}
+	
+	public PamFFTControl(PamConfiguration pamConfiguration, String unitName) {
+		super(pamConfiguration, "FFT Engine", unitName);
 
 		PamRawDataBlock rawDataBlock = PamController.getInstance().
 		getRawDataBlock(fftParameters.dataSource);

src/fftManager/PamFFTProcess.java

@@ -144,10 +144,10 @@ public class PamFFTProcess extends PamProcess {
 		 * name has not been set, so if there isn't a name, use the number !
 		 */
 		if (fftParameters.dataSourceName != null) {
-			rawDataBlock = (PamRawDataBlock) PamController.getInstance().getDataBlock(RawDataUnit.class, fftParameters.dataSourceName);
+			rawDataBlock = (PamRawDataBlock) fftControl.getPamConfiguration().getDataBlock(RawDataUnit.class, fftParameters.dataSourceName);
 		}
 		else {
-			rawDataBlock = PamController.getInstance().getRawDataBlock(fftParameters.dataSource);
+			rawDataBlock = fftControl.getPamConfiguration().getRawDataBlock(fftParameters.dataSource);
 			if (rawDataBlock != null) {
 				fftParameters.dataSourceName = rawDataBlock.getDataName();
 			}

src/generalDatabase/DBControl.java

@@ -32,6 +32,7 @@ import offlineProcessing.OLProcessDialog;
 import offlineProcessing.OfflineTaskGroup;
 import warnings.PamWarning;
 import warnings.WarningSystem;
+import PamController.PamConfiguration;
 import PamController.PamControlledUnit;
 import PamController.PamControlledUnitGUI;
 import PamController.PamControlledUnitSettings;
@@ -109,8 +110,8 @@ PamSettingsSource {
 
 	private int lastErrorCount;
 
-	public DBControl(String unitName, int settingsStore, boolean openImmediately) {
+	public DBControl(PamConfiguration pamconfiguration, String unitName, int settingsStore, boolean openImmediately) {
-		super(dbUnitType, unitName);
+		super(pamconfiguration, dbUnitType, unitName);
 		THIS = this;
 
 		databaseWarning = new PamWarning(getUnitName(), "Database error", 2);
@@ -157,6 +158,9 @@ PamSettingsSource {
 
 		//		selectDatabase(null);
 
+		if (isInMainConfiguration() == false) {
+			openImmediately = false;
+		}
 		if (databaseSystem == null){
 			selectSystem(dbParameters.getDatabaseSystem(), openImmediately);
 		}
@@ -529,7 +533,7 @@ PamSettingsSource {
 				//				offlineTaskGroup.addTask(task);
 			}
 			if (olProcessDialog == null) {
-				olProcessDialog = new OLProcessDialog(getPamView().getGuiFrame(), offlineTaskGroup, 
+				olProcessDialog = new OLProcessDialog(getGuiFrame(), offlineTaskGroup, 
 						dataBlock.getDataName() + " Export");
 			}
 			olProcessDialog.setVisible(true);

src/generalDatabase/DBControlSettings.java

@@ -18,7 +18,7 @@ public class DBControlSettings extends DBControl {
 
 	public DBControlSettings(String unitName) {
 
-		super(unitName, PamSettingManager.LIST_DATABASESTUFF, false);
+		super(null, unitName, PamSettingManager.LIST_DATABASESTUFF, false);
 
 		//		logSettings = new LogSettings(this);
 

src/generalDatabase/DBControlUnit.java

@@ -20,6 +20,7 @@ import pamViewFX.pamTask.PamTaskUpdate;
 import PamController.AWTScheduler;
 import PamController.DataOutputStore;
 import PamController.OfflineDataStore;
+import PamController.PamConfiguration;
 import PamController.PamControlledUnit;
 import PamController.PamController;
 import PamController.PamControllerInterface;
@@ -51,7 +52,10 @@ public class DBControlUnit extends DBControl implements DataOutputStore {
 	private BackupInformation backupInformation;
 
 	public DBControlUnit(String unitName) {
-		super(unitName, whichStore(), true);
+		this(null, unitName);
+	}
+	public DBControlUnit(PamConfiguration pamConfiguration, String unitName) {
+		super(pamConfiguration, unitName, whichStore(), true);
 		THIS = this;
 		setFullTablesCheck(true);
 		//		int runMode = PamController.getInstance().getRunMode();

src/matchedTemplateClassifer/offline/MTOfflineProcess.java

@@ -70,7 +70,7 @@ public class MTOfflineProcess {
 		
 		//if null open the dialog- also create a new offlineTask group if the datablock has changed. 
 		if (mtOfflineDialog == null) {
-			mtOfflineDialog = new OLProcessDialog(this.mtContorl.getPamView().getGuiFrame(), 
+			mtOfflineDialog = new OLProcessDialog(this.mtContorl.getGuiFrame(), 
 					mtOfflineGroup, "Match Template Classifier");
 			//batchLocaliseDialog.setModalityType(Dialog.ModalityType.MODELESS);
 		}

src/noiseBandMonitor/NoiseBandProcess.java

@@ -62,7 +62,7 @@ public class NoiseBandProcess extends PamProcess {
 
 	public void setupProcess() {
 		super.setupProcess();
-		PamDataBlock sourceData = PamController.getInstance().getDataBlock(RawDataUnit.class, noiseBandControl.noiseBandSettings.rawDataSource);
+		PamDataBlock sourceData = noiseBandControl.getPamConfiguration().getDataBlock(RawDataUnit.class, noiseBandControl.noiseBandSettings.rawDataSource);
 		if (sourceData == null) {
 			return;
 		}

src/noiseMonitor/NoiseProcess.java

@@ -129,7 +129,7 @@ public class NoiseProcess extends PamProcess {
 	}
 
 	private void findDataSource() {
-		PamDataBlock source = PamController.getInstance().getDataBlock(FFTDataUnit.class, 
+		PamDataBlock source = noiseControl.getPamConfiguration().getDataBlock(FFTDataUnit.class, 
 				noiseControl.noiseSettings.dataSource);
 		daqProcess = null;
 		

src/noiseMonitor/NoiseTabPanel.java

@@ -1189,7 +1189,7 @@ private void setAxisLabels() {
 		if (mouseMenu == null) {
 			mouseMenu = new JPopupMenu();
 			JMenuItem menuItem = new JMenuItem("Display Options ...");
-			menuItem.addActionListener(new DisplayOptions(pamControlledUnit.getPamView().getGuiFrame()));
+			menuItem.addActionListener(new DisplayOptions(pamControlledUnit.getGuiFrame()));
 			mouseMenu.add(menuItem);
 
 		}

src/noiseOneBand/OneBandControl.java

@@ -126,7 +126,7 @@ public class OneBandControl extends PamControlledUnit implements PamSettings {
 			offlineTaskGroup.addTask(task);
 		}
 		if (olProcessDialog == null) {
-			olProcessDialog = new OLProcessDialog(getPamView().getGuiFrame(), offlineTaskGroup, "Noise Data Export");
+			olProcessDialog = new OLProcessDialog(getGuiFrame(), offlineTaskGroup, "Noise Data Export");
 		}
 		olProcessDialog.setVisible(true);
 	}

src/radardisplay/RadarDisplay.java

@@ -123,7 +123,7 @@ public class RadarDisplay extends UserFramePlots implements PamObserver, PamSett
 		if (this.radarParameters == null) {
 			this.radarParameters = new RadarParameters();
 			RadarParameters newParams = RadarParametersDialog.showDialog(RadarDisplay.this,
-					userDisplayControl.getPamView().getGuiFrame(), this.radarParameters, radarProjector);
+					userDisplayControl.getGuiFrame(), this.radarParameters, radarProjector);
 			if (newParams != null) {
 				this.radarParameters = newParams.clone();
 			}
@@ -697,7 +697,7 @@ public class RadarDisplay extends UserFramePlots implements PamObserver, PamSett
 		public void actionPerformed(ActionEvent e) {
 
 			RadarParameters newParams = RadarParametersDialog.showDialog(RadarDisplay.this,
-					userDisplayControl.getPamView().getGuiFrame(), radarParameters, radarProjector);
+					userDisplayControl.getGuiFrame(), radarParameters, radarProjector);
 			if (newParams != null) {
 				radarParameters = newParams.clone();
 				newSettings();

src/rawDeepLearningClassifier/offline/DLOfflineProcess.java

@@ -56,7 +56,7 @@ public class DLOfflineProcess {
 		
 		//if null open the dialog- also create a new offlineTask group if the datablock has changed. 
 		if (mtOfflineDialog == null) {
-			mtOfflineDialog = new OLProcessDialog(this.dlControl.getPamView().getGuiFrame(), 
+			mtOfflineDialog = new OLProcessDialog(this.dlControl.getGuiFrame(), 
 					dlOfflineGroup, "Deep Learning Classifier");
 			//batchLocaliseDialog.setModalityType(Dialog.ModalityType.MODELESS);
 		}

src/spectrogramNoiseReduction/SpectrogramNoiseControl.java

@@ -6,6 +6,7 @@ import java.awt.event.ActionListener;
 import java.io.Serializable;
 import javax.swing.JMenuItem;
 
+import PamController.PamConfiguration;
 import PamController.PamControlledUnit;
 import PamController.PamControlledUnitSettings;
 import PamController.PamControllerInterface;
@@ -22,7 +23,10 @@ public class SpectrogramNoiseControl extends PamControlledUnit implements PamSet
 	protected SpectrogramNoiseProcess spectrogramNoiseProcess;
 	
 	public SpectrogramNoiseControl(String unitName) {
-		super("Spectrogram Noise Reduction", unitName);
+		this(null, unitName);
+	}
+	public SpectrogramNoiseControl(PamConfiguration pamConfiguration, String unitName) {
+		super(pamConfiguration, "Spectrogram Noise Reduction", unitName);
 		
 		spectrogramNoiseProcess = new SpectrogramNoiseProcess(this);
 		addPamProcess(spectrogramNoiseProcess);

src/spectrogramNoiseReduction/SpectrogramNoiseProcess.java

@@ -15,6 +15,7 @@ import spectrogramNoiseReduction.threshold.ThresholdParams;
 
 import fftManager.FFTDataBlock;
 import fftManager.FFTDataUnit;
+import PamController.PamConfiguration;
 import PamController.PamControlledUnit;
 import PamController.PamController;
 import PamUtils.complex.ComplexArray;
@@ -64,7 +65,11 @@ public class SpectrogramNoiseProcess extends PamProcess {
 	@Override
 	public void setupProcess() {
 		super.setupProcess();
-		sourceData = (FFTDataBlock) PamController.getInstance().getDataBlock(FFTDataUnit.class, 
+		
+		PamConfiguration mainConfig = PamController.getInstance().getPamConfiguration();
+		PamConfiguration localConfig = getPamControlledUnit().getPamConfiguration();
+		
+		sourceData = (FFTDataBlock) getPamControlledUnit().getPamConfiguration().getDataBlock(FFTDataUnit.class, 
 				getNoiseSettings().dataSource);
 		setParentDataBlock(sourceData);
 		

src/targetMotionModule/TargetMotionLocaliser.java

@@ -64,7 +64,7 @@ public class TargetMotionLocaliser<T extends PamDataUnit> extends AbstractLocali
 
 //	public boolean showTMDialog(T dataUnit) {
 //		if (targetMotionMainPanel == null) {
-////targetMotionDialog = new TargetMotionMainPanel<T>(pamControlledUnit.getPamView().getGuiFrame(), this);
+////targetMotionDialog = new TargetMotionMainPanel<T>(pamControlledUnit.getGuiFrame(), this);
 //		}
 //		targetMotionMainPanel.updateCurrentControlPanel();
 //		return true;

src/targetMotionModule/offline/TMOfflineFunctions.java

@@ -54,7 +54,7 @@ public class TMOfflineFunctions {
 		//when we change datablock the taks group is going to stay the same- need to make sure it changes
 		
 		if (batchLocaliseDialog == null || currentDataBlock!=targetMotionControl.getCurrentDataBlock()) {
-			batchLocaliseDialog = new TMOLProcessDialog(targetMotionControl.getPamView().getGuiFrame(), 
+			batchLocaliseDialog = new TMOLProcessDialog(targetMotionControl.getGuiFrame(), 
 					getOfflineTaskGroup(), "Batch Localise");
 			//batchLocaliseDialog.setModalityType(Dialog.ModalityType.MODELESS);
 		}

src/targetMotionOld/TargetMotionLocaliser.java

@@ -153,7 +153,7 @@ public class TargetMotionLocaliser<T extends GroupDetection> extends AbstractLoc
 
 	public boolean showTMDialog(T dataUnit) {
 		if (targetMotionDialog == null) {
-			targetMotionDialog = new TargetMotionDialog<T>(pamControlledUnit.getPamView().getGuiFrame(), this);
+			targetMotionDialog = new TargetMotionDialog<T>(pamControlledUnit.getGuiFrame(), this);
 		}
 		targetMotionDialog.updateEventList();
 		targetMotionDialog.setDataUnit(dataUnit);

src/videoRangePanel/VRControl.java

@@ -1,6 +1,7 @@
 package videoRangePanel;
 
 import java.util.List;
+import java.awt.Frame;
 import java.awt.Point;
 import java.io.File;
 import java.io.Serializable;
@@ -361,9 +362,9 @@ public class VRControl extends PamControlledUnit implements PamSettings {
 	 * @param frame
 	 * @param tab- the tab to open the settings dialog on. 
 	 */
-	public void settingsButtonAWT(JFrame frame, int tab) {
+	public void settingsButtonAWT(Frame frame, int tab) {
 		if (frame == null) {
-			frame = getPamView().getGuiFrame();
+			frame = getGuiFrame();
 		}
 		VRParameters newParams = VRParametersDialog.showDialog(frame, this, tab);
 		if (newParams != null) {

src/videoRangePanel/importTideData/TideManager.java

@@ -105,7 +105,7 @@ public class TideManager extends  DataImport<String>   {
 //		}
 //		else dir=null;
 //			
-//		String newFile=PamFileBrowser.fileBrowser(vrControl.getPamView().getGuiFrame(),dir,PamFileBrowser.OPEN_FILE,"txt");
+//		String newFile=PamFileBrowser.fileBrowser(vrControl.getGuiFrame(),dir,PamFileBrowser.OPEN_FILE,"txt");
 //		
 //		return newFile;
 //	}

src/videoRangePanel/layoutAWT/VRSidePanel.java

@@ -179,7 +179,7 @@ public class VRSidePanel implements PamSidePanel {
 			}
 			
 			if (vrControl.getVRParams().currentImageFile==null) {
-				PamDialog.showWarning(vrControl.getPamView().getGuiFrame(), "No image found", "The folder selected did not contain any compatible images");
+				PamDialog.showWarning(vrControl.getGuiFrame(), "No image found", "The folder selected did not contain any compatible images");
 				return;
 			}
 			vrControl.loadFile(vrControl.getVRParams().currentImageFile);

src/videoRangePanel/layoutFX/VRDisplayFX.java

@@ -221,7 +221,7 @@ public class VRDisplayFX extends PamBorderPane implements VRPane {
 		}
 
 		if (vrControl.getVRParams().currentImageFile==null) {
-			PamDialog.showWarning(vrControl.getPamView().getGuiFrame(), "No image found", "The folder selected did not contain any compatible images");
+			PamDialog.showWarning(vrControl.getGuiFrame(), "No image found", "The folder selected did not contain any compatible images");
 			return;
 		}
 		//go back up a few levels to load file as update flags etc need to be triggerred. 

src/whistlesAndMoans/WhistleMoanControl.java

@@ -19,6 +19,7 @@ import detectionPlotFX.whistleDDPlot.WhistleDDPlotProvider;
 import spectrogramNoiseReduction.SpectrogramNoiseProcess;
 import whistlesAndMoans.layoutFX.WhistleMoanGUIFX;
 import whistlesAndMoans.plots.WhistlePlotProvider;
+import PamController.PamConfiguration;
 import PamController.PamControlledUnit;
 import PamController.PamControlledUnitGUI;
 import PamController.PamControlledUnitSettings;
@@ -55,7 +56,10 @@ public class WhistleMoanControl extends PamControlledUnit implements PamSettings
 	public static final String UNITTYPE = "WhistlesMoans";
 
 	public WhistleMoanControl(String unitName) {
-		super(UNITTYPE, unitName);
+		this(null, unitName);
+	}
+	public WhistleMoanControl(PamConfiguration pamConfiguration, String unitName) {
+		super(pamConfiguration, UNITTYPE, unitName);
 
 		spectrogramNoiseProcess = new SpectrogramNoiseProcess(this);
 		addPamProcess(spectrogramNoiseProcess);

src/whistlesAndMoans/WhistleToneConnectProcess.java

@@ -201,36 +201,20 @@ public class WhistleToneConnectProcess extends PamProcess {
 	@Override
 	public void setupProcess() {
 		super.setupProcess();
+		
 		SpectrogramNoiseProcess snp = whistleMoanControl.getSpectrogramNoiseProcess();
 		setParentDataBlock(snp.getOutputDataBlock());
 		if (whistleMoanControl.whistleToneParameters.getDataSource() == null) {
 			return;
 		}
-		//		sourceData = (FFTDataBlock) PamController.getInstance().getDataBlock(FFTDataUnit.class, 
+
-		//				whistleMoanControl.whistleToneParameters.getDataSource());
-		//		snp.setParentDataBlock(sourceData);
 		sourceData = (FFTDataBlock) getParentDataBlock(); // our source should always be the output of the SpectrogramNoiseProcess
 		SpectrogramNoiseSettings specnoiseSettings = whistleMoanControl.whistleToneParameters.getSpecNoiseSettings();
 		specnoiseSettings.dataSource = whistleMoanControl.whistleToneParameters.getDataSource();
 		snp.setNoiseSettings(specnoiseSettings);
 
 		chanOrSeqMap = whistleMoanControl.whistleToneParameters.getChanOrSeqBitmap();	// the channelMap in WhistleToneParameters object may be a sequence map or a channel map, depending on source
-		//		if (sourceData != null) {
+
-		////			chanOrSeqMap = getParentDataBlock().getChannelMap() & 
-		//			chanOrSeqMap = getParentDataBlock().getSequenceMap() & // use the sequence bitmap instead of the channel bitmap, in case this is beamformer output 
-		//					whistleMoanControl.whistleToneParameters.getChanOrSeqBitmap();
-		//			outputData.sortOutputMaps(getParentDataBlock().getChannelMap(), getParentDataBlock().getSequenceMapObject(), chanOrSeqMap);
-		//			outputData.setFftHop(sourceData.getFftHop());
-		//			outputData.setFftLength(sourceData.getFftLength());
-		//			
-		//			// 2017/11/30 set the whistleLocations channelMap properly
-		//			whistleLocations.sortOutputMaps(getParentDataBlock().getChannelMap(), getParentDataBlock().getSequenceMapObject(), chanOrSeqMap);
-		//			
-		//			//			smoothingChannelProcessList = new SmoothingChannelProcess[PamUtils.getHighestChannel(chanOrSeqMap)+1];
-		//			//			for (int i = 0; i < PamUtils.getHighestChannel(chanOrSeqMap)+1; i++) {
-		//			//				smoothingChannelProcessList[i] = new SmoothingChannelProcess();
-		//			//			}
-		//		}
 		// set the localisation information in the two output datablocks. If the source is using sequence numbers, then we cannot localise
 		boolean mayBearings = whistleMoanControl.whistleToneParameters.mayHaveBearings();
 		boolean mayRange = whistleMoanControl.whistleToneParameters.mayHaveRange();