Merge remote-tracking branch 'upstream/main'

.gitignore

@@ -41,33 +41,3 @@ settings.xml
 .classpath
 .classpath
 .classpath
-.metadata/.lock
-.metadata/.plugins/org.eclipse.core.resources/.projects/.org.eclipse.egit.core.cmp/.location
-.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/history.version
-.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.index
-.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.version
-.metadata/.plugins/org.eclipse.core.resources/.root/1.tree
-.metadata/.plugins/org.eclipse.core.resources/.safetable/org.eclipse.core.resources
-.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.core.resources.prefs
-.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.jdt.ui.prefs
-.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.m2e.discovery.prefs
-.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.ide.prefs
-.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.prefs
-.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.workbench.prefs
-.metadata/.plugins/org.eclipse.e4.workbench/workbench.xmi
-.metadata/.plugins/org.eclipse.egit.core/.org.eclipse.egit.core.cmp/.settings/org.eclipse.core.resources.prefs
-.metadata/.plugins/org.eclipse.jdt.core/assumedExternalFilesCache
-.metadata/.plugins/org.eclipse.jdt.core/externalFilesCache
-.metadata/.plugins/org.eclipse.jdt.core/javaLikeNames.txt
-.metadata/.plugins/org.eclipse.jdt.core/nonChainingJarsCache
-.metadata/.plugins/org.eclipse.jdt.core/variablesAndContainers.dat
-.metadata/.plugins/org.eclipse.jdt.ui/dialog_settings.xml
-.metadata/.plugins/org.eclipse.jdt.ui/OpenTypeHistory.xml
-.metadata/.plugins/org.eclipse.jdt.ui/QualifiedTypeNameHistory.xml
-.metadata/.plugins/org.eclipse.m2e.core/workspaceState.ser
-.metadata/.plugins/org.eclipse.m2e.logback/logback.2.1.100.20230106-1511.xml
-.metadata/.plugins/org.eclipse.oomph.setup/workspace.setup
-.metadata/.plugins/org.eclipse.tips.ide/dialog_settings.xml
-.metadata/.plugins/org.eclipse.ui.intro/introstate
-.metadata/.plugins/org.eclipse.ui.workbench/workingsets.xml
-.metadata/version.ini

src/Acquisition/FolderInputSystem.java

@@ -104,9 +104,13 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
 		boolean ans = super.prepareInputFile();
 		if (ans == false && ++currentFile < allFiles.size()) {
 			System.out.println("Failed to open sound file. Try again with file " + allFiles.get(currentFile).getName());
-
+			/*
+			 *  jumping striaght to the next file messes it up if it thinks the files
+			 *  are continuous, so we HAVE to stop and restart.  
+			 */
+//			return prepareInputFile();
 			PamController.getInstance().pamStop();
-			PamController.getInstance().startLater();
+			PamController.getInstance().startLater(false);
 		}
 		return ans;
 	}
@@ -648,7 +652,17 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
 			}
 			setFolderProgress();
 			//			sayEta();
-			ans = prepareInputFile();
+			/*
+			 * I think that here, we just need a check of the file. the prepareInputFile in 
+			 * this class will (on failure) move straight to the next file and also issue a 
+			 * stop/start, which is not good if it's trying a continuous file, where this is
+			 * being called, if false is returned it should manage moving onto the next file by 
+			 * itself if we use the super.prep .... 
+			 */
+			ans = super.prepareInputFile();
+			if (ans == false) {
+				return false;
+			}
 			currentFileStart = System.currentTimeMillis();
 			//			if (ans && audioFormat.getSampleRate() != currentSampleRate && currentFile > 0) {
 			//				acquisitionControl.getDaqProcess().setSampleRate(currentSampleRate = audioFormat.getSampleRate(), true);

src/Acquisition/filetypes/SUDFileType.java

@@ -22,7 +22,7 @@ public class SUDFileType extends SoundFileType {
 		if (isShown) {
 			return;
 		}
-		WarnOnce.showWarning("SoundTrap SUD Files", sudInfoText, WarnOnce.OK_OPTION);
+//		WarnOnce.showWarning("SoundTrap SUD Files", sudInfoText, WarnOnce.OK_OPTION);
 		isShown = true;		
 	}
 

src/Acquisition/pamAudio/SudAudioFile.java

@@ -48,9 +48,9 @@ public class SudAudioFile extends WavAudioFile {
 			}
 				// don't do anything and it will try the built in Audiosystem
 			catch (UnsupportedAudioFileException e) {
-				System.err.println("Could not open sud file: not a supported file " + soundFile.getName()); 
-
-				e.printStackTrace();
+				System.err.println("UnsupportedAudioFileException: Could not open sud file: not a supported file " + soundFile.getName()); 
+				System.err.println(e.getMessage());
+//				e.printStackTrace();
 			} catch (IOException e) {
 				System.err.println("Could not open sud file: IO Exception: " + soundFile.getName()); 
 

src/Acquisition/pamAudio/SudAudioFileReader.java

@@ -46,7 +46,8 @@ public class SudAudioFileReader {
 		try {
 			sudAudioInputStream = SudAudioInputStream.openInputStream(file, sudParams, false); 
 		} catch (Exception e) {
-			e.printStackTrace();
+			String msg = String.format("Corrupt sud file %s: %s", file.getName(), e.getMessage());
+			throw new UnsupportedAudioFileException(msg);
 		} 
 		return sudAudioInputStream;
 	}

src/GPS/GPSControl.java

@@ -245,6 +245,31 @@ public class GPSControl extends PamControlledUnit implements PamSettings, Positi
 	public GpsDataUnit getShipPosition(long timeMilliseconds) {
 		return getGpsDataBlock().getClosestUnitMillis(timeMilliseconds);
 	}
+	/**
+	 * Do we want this string ? It will be either RMC or GGA and may want wildcarding
+	 * @param stringId
+	 * @return
+	 */
+	public boolean wantString(String stringId) {
+		if (stringId == null || stringId.length() < 6) {
+			return false;
+		}
+		if (gpsControl.gpsParameters.allowWildcard) {
+			String lastBit = stringId.substring(3, 6);
+			switch (gpsControl.gpsParameters.mainString) {
+			case GPSParameters.READ_RMC:
+				return lastBit.equals("RMC");
+			case GPSParameters.READ_GGA:
+				return lastBit.equals("GGA");
+			default:
+				return false;
+			}
+		}
+		else {
+			String wantedString = gpsControl.getWantedString();
+			return stringId.equals(wantedString);
+		}
+	}
 	
 	/**
 	 * Get the name of the string we're wanting. 

src/GPS/GPSParameters.java

@@ -59,6 +59,8 @@ public class GPSParameters implements Serializable, Cloneable, ManagedParameters
 	public String rmcInitials = "GP";
 	public String ggaInitials = "GP";
 	
+	public boolean allowWildcard = true;
+	
 	/**
 	 * Attempt to read true heading information
 	 */

src/GPS/GPSParametersDialog.java

@@ -149,9 +149,9 @@ public class GPSParametersDialog extends PamDialog {
 		}
 	}
 	public static GPSParameters showDialog(Frame parentFrame, GPSParameters gpsParameters) {
-		if (parentFrame != lastFrame || gpsParametersDialog == null) {
+//		if (parentFrame != lastFrame || gpsParametersDialog == null) {
 			gpsParametersDialog = new GPSParametersDialog(parentFrame);
-		}
+//		}
 		gpsParametersDialog.gpsParameters = gpsParameters.clone();
 		gpsParametersDialog.setParams();
 		gpsParametersDialog.setVisible(true);		
@@ -335,6 +335,7 @@ public class GPSParametersDialog extends PamDialog {
 		JRadioButton ggaString;
 		JTextField rmcInitials;
 		JTextField ggaInitials;
+		JCheckBox allowWildcard;
 		public MainStringPanel() {
 			super();
 			setBorder(new TitledBorder("Main Nav' data string"));
@@ -345,8 +346,16 @@ public class GPSParametersDialog extends PamDialog {
 			
 			ButtonGroup buttonGroup = new ButtonGroup();
 
+			c.gridx = 0;
+			c.gridy++;
+			c.gridwidth = 5;
+			this.add(allowWildcard = new JCheckBox("Allow any string initials"), c);
+			allowWildcard.setToolTipText("Use RMC or GGA data from any source independent of the string initials (e.g. GP, GN, etc.)");
+			c.gridy ++;
+			c.gridwidth = 1;
+			c.gridx=0;
 			addComponent(this, new JLabel("RMC String"), c);
-			c.gridx++;
+			c.gridx ++;
 			addComponent(this, rmcString = new JRadioButton(""), c);
 			c.gridx++;
 			addComponent(this, rmcInitials = new JTextField(2), c);
@@ -355,6 +364,7 @@ public class GPSParametersDialog extends PamDialog {
 			
 			c.gridx = 0;
 			c.gridy ++;
+			c.gridwidth = 1;
 			addComponent(this, new JLabel("GGA String"), c);
 			c.gridx++;
 			addComponent(this, ggaString = new JRadioButton(""), c);
@@ -363,6 +373,7 @@ public class GPSParametersDialog extends PamDialog {
 			c.gridx++;
 			addComponent(this, new JLabel(" GGA"), c);
 			
+			allowWildcard.addActionListener(this);			
 			rmcString.addActionListener(this);
 			ggaString.addActionListener(this);
 			buttonGroup.add(rmcString);
@@ -374,10 +385,12 @@ public class GPSParametersDialog extends PamDialog {
 			ggaString.setSelected(gpsParameters.mainString == GPSParameters.READ_GGA);
 			rmcInitials.setText(gpsParameters.rmcInitials);
 			ggaInitials.setText(gpsParameters.ggaInitials);
+			allowWildcard.setSelected(gpsParameters.allowWildcard);
 			enableControls();
 		}
 		
 		public boolean getParams() {
+			gpsParameters.allowWildcard = allowWildcard.isSelected();
 			if (ggaString.isSelected()) {
 				gpsParameters.mainString = GPSParameters.READ_GGA;
 			}
@@ -385,12 +398,12 @@ public class GPSParametersDialog extends PamDialog {
 				gpsParameters.mainString = GPSParameters.READ_RMC;
 			}
 			gpsParameters.rmcInitials = rmcInitials.getText();
-			if (gpsParameters.rmcInitials.length() != 2) {
-				return false;
+			if (gpsParameters.rmcInitials.length() != 2 && !gpsParameters.allowWildcard) {
+				return showWarning("Expecting a two character identifier for RMC strings");
 			}
 			gpsParameters.ggaInitials = ggaInitials.getText();
-			if (gpsParameters.ggaInitials.length() != 2) {
-				return false;
+			if (gpsParameters.ggaInitials.length() != 2 && !gpsParameters.allowWildcard) {
+				return showWarning("Expecting a two character identifier for GGA strings");
 			}
 			return true;
 		}
@@ -400,8 +413,9 @@ public class GPSParametersDialog extends PamDialog {
 		}
 		
 		private void enableControls() {
-			rmcInitials.setEnabled(rmcString.isSelected());
-			ggaInitials.setEnabled(ggaString.isSelected());
+			boolean wild = allowWildcard.isSelected();
+			rmcInitials.setEnabled(rmcString.isSelected() & !wild);
+			ggaInitials.setEnabled(ggaString.isSelected() & !wild);
 		}
 		
 		

src/GPS/ProcessNmeaData.java

@@ -57,7 +57,7 @@ public class ProcessNmeaData extends PamProcess {
 
 	private GpsLogger gpsLogger;
 
-	private String wantedString = "$GPRMC";
+//	private String wantedString = "$GPRMC";
 
 	private GpsDataUnit previousUnit = null;
 	
@@ -161,7 +161,7 @@ public class ProcessNmeaData extends PamProcess {
 	@Override
 	public void noteNewSettings() {
 		findNMEADataBlock();
-		setWantedString();
+//		setWantedString();
 		double minRate = Math.max(.2, 1./gpsController.gpsParameters.readInterval);
 		processCheck.getOutputCounter().setMinRate(minRate);
 	}
@@ -179,7 +179,8 @@ public class ProcessNmeaData extends PamProcess {
 		StringBuffer nmeaString = nmeaData.getCharData();
 		String stringId = NMEADataBlock.getSubString(nmeaString, 0);
 
-		if (stringId.equalsIgnoreCase(wantedString)) {
+//		if (stringId.equalsIgnoreCase(wantedString)) {
+		if (gpsController.wantString(stringId)) {
 			gpsData = new GpsData(nmeaString, gpsController.gpsParameters.mainString); // GpsData constructor which
 			// unpacks the string.
 			if (gpsData.isDataOk()) {
@@ -316,13 +317,13 @@ public class ProcessNmeaData extends PamProcess {
 		super.clearOldData();
 	}
 
-	public String getWantedString() {
-		return wantedString;
-	}
-	
-	public void setWantedString() {
-		wantedString = gpsController.getWantedString();
-	}
+//	public String getWantedString() {
+//		return wantedString;
+//	}
+//	
+//	public void setWantedString() {
+//		wantedString = gpsController.getWantedString();
+//	}
 
 	public GPSControl getGpsController() {
 		return gpsController;

src/GPS/UpdateClockDialog.java

@@ -221,9 +221,8 @@ public class UpdateClockDialog extends JDialog implements ActionListener, PamObs
 //		NMEADataBlock nmeaDataBlock = (NMEADataBlock) o;
 		NMEADataUnit nmeaDataUnit = (NMEADataUnit) arg;
 		StringBuffer nmeaData = nmeaDataUnit.getCharData();
-		String wantedString = gpsControl.getWantedString();
 		String stringId = NMEADataBlock.getSubString(nmeaData, 0);
-		if (wantedString.equals(stringId) == false) {
+		if (gpsControl.wantString(stringId) == false) {
 			return;
 		}
 		if (gpsControl.gpsParameters.mainString == GPSParameters.READ_GGA) {
@@ -232,6 +231,8 @@ public class UpdateClockDialog extends JDialog implements ActionListener, PamObs
 			newRMCData(nmeaData);
 		}
 	}
+	
+	
 	@Override
 	public void updateData(PamObservable observable, PamDataUnit pamDataUnit) {
 		// TODO Auto-generated method stub

src/Localiser/detectionGroupLocaliser/TMGroupLocInfo.java

@@ -810,6 +810,9 @@ public class TMGroupLocInfo implements GroupLocInfo {
 		 for (int i = 0; i < nSubDetections; i++) {
 			 
 			 localisation = getParentDetection().getSubDetection(i).getLocalisation();
+			 if (localisation == null) {
+				 continue;
+			 }
 			 angles = localisation.getAngles();
 			 angleErrors = localisation.getAngleErrors();
 			 
@@ -879,6 +882,10 @@ public class TMGroupLocInfo implements GroupLocInfo {
 			 totalVectors += nVectors;
 		 }
 		 
+		 if (totalVectors == 0) {
+			 return;
+		 }
+		 
 		 //now create the separate arrays for different ambiguities. 
 		 /**
 		  * 

src/Map/GebcoMapFile.java

@@ -11,8 +11,10 @@ import java.util.Vector;
 import javax.swing.JFileChooser;
 import javax.swing.JOptionPane;
 
+import PamController.PamController;
 import PamUtils.LatLong;
 import PamUtils.PamFileChooser;
+import PamView.dialog.warn.WarnOnce;
 
 public class GebcoMapFile implements MapFileManager {
 	
@@ -109,10 +111,19 @@ public class GebcoMapFile implements MapFileManager {
 		int pointCount;
 		int depth;
 		MapContour mapContour;
+		boolean error = false;
 		try {
+			int iLine = 0;
 			while((line = reader.readLine())!=null){
+				iLine++;
 				line = line.trim();
 				spaceIndex = line.indexOf(' ');
+				if (spaceIndex < 0) {
+					String msg = String.format("Error in map file at line %d \"%s\"", iLine, line);
+					WarnOnce.showNamedWarning("Gebco Map File Warning", PamController.getMainFrame(), gebcoFile.getName(), msg, WarnOnce.WARNING_MESSAGE);
+					error = true;
+					break;
+				}
 				num1 = line.substring(0,spaceIndex).trim();
 				num2 = line.substring(spaceIndex).trim();
 				depth = Integer.valueOf(num1);
@@ -143,11 +154,22 @@ public class GebcoMapFile implements MapFileManager {
 		}
 		catch (NumberFormatException nex) {
 			nex.printStackTrace();
-			return false;
+			error = true;
+		}
+		catch (IndexOutOfBoundsException iex) {
+			iex.printStackTrace();
+			error = true;
+		}
+		if (reader != null) {
+			try {
+				reader.close();
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
 		}
 		Collections.sort(mapContours);
 		Collections.sort(availableContours);
-		return true;
+		return !error;
 	}
 	
 	

src/PamController/PamSettingManager.java

@@ -520,9 +520,15 @@ public class PamSettingManager {
 		if (initializationComplete == false) {
 			// if PAMGAURD hasn't finished loading, then don't save the settings
 			// or the file will get wrecked (bug tracker 2269579)			
+			String msg = "There was an error loading settings from this configuration, so the configuration"
+					+ " may be incomplete. <p>Do you want to save anyway ? <p>"
+					+ " If you have added new modules, the answer is probably \"Yes\"";
+			int ans = WarnOnce.showWarning("Confuguration file warning", msg, WarnOnce.YES_NO_OPTION);
+			if (ans == WarnOnce.CANCEL_OPTION) {
 				System.out.println("Settings have not yet loaded. Don't save file");
 				return false;
 			}
+		}
 
 		saveGlobalSettings();
 		//		saveSettingToDatabase();

src/PamController/PamguardVersionInfo.java

@@ -31,12 +31,12 @@ public class PamguardVersionInfo {
 	 * Version number, major version.minorversion.sub-release.
 	 * Note: can't go higher than sub-release 'f'
 	 */
-	static public final String version = "2.02.07f";
+	static public final String version = "2.02.08a";
 	
 	/**
 	 * Release date
 	 */
-	static public final String date = "4 April 2023";
+	static public final String date = "30 May 2023";
 	
 //	/**
 //	 * Release type - Beta or Core

src/PamController/settings/SettingsImport.java

@@ -1,5 +1,6 @@
 package PamController.settings;
 
+import java.io.ByteArrayInputStream;
 import java.io.EOFException;
 import java.io.File;
 import java.io.FileInputStream;
@@ -14,6 +15,7 @@ import PamController.PamController;
 import PamController.PamSettingManager;
 import PamController.PamSettings;
 import PamController.PamSettingsGroup;
+import PamModel.PamModel;
 import PamModel.PamModuleInfo;
 import PamModel.SMRUEnable;
 import PamView.dialog.PamFileBrowser;
@@ -226,7 +228,13 @@ public class SettingsImport {
 				ownerClass = Class.forName(aSet.getOwnerClassName());
 			} catch (ClassNotFoundException e) {
 				// TODO Auto-generated catch block
-				e.printStackTrace();
+//				e.printStackTrace();
+				// this is happening since the ownerclassname is not set correctly in psfx files
+				// so we have to deserialise the data to find the class. 
+//				ownerClass = getClassFromData(aSet.getSerialisedByteArray());
+//				ownerClass = PamModuleInfo.findModuleClass(aSet.getUnitType());
+			}
+			if (ownerClass == null) {
 				continue;
 			}
 			if (PamControlledUnit.class.isAssignableFrom(ownerClass)) {
@@ -264,6 +272,17 @@ public class SettingsImport {
 		return groupedSettings;
 	}
 	
+	private Class getClassFromData(byte[] data) {
+		try {
+			ObjectInputStream ois = new ObjectInputStream(new ByteArrayInputStream(data));
+			Object obj = ois.readObject();
+			return obj.getClass();
+		} catch (Exception e) {
+			return null;
+		}
+		
+	}
+
 	private SettingsImportGroup findGroup(ArrayList<SettingsImportGroup> groupedSettings, String unitName) {
 		for (SettingsImportGroup iG:groupedSettings) {
 			if (iG.getMainSettings().getUnitName().equals(unitName)) {

src/PamModel/PamModel.java

@@ -45,14 +45,10 @@ import fftManager.FFTDataUnit;
 import fftManager.PamFFTControl;
 import group3dlocaliser.Group3DLocaliserControl;
 import meygenturbine.MeygenTurbine;
-import networkTransfer.receive.BuoyStatusDataUnit;
-import networkTransfer.receive.NetworkReceiver;
 import printscreen.PrintScreenControl;
 import rockBlock.RockBlockControl;
 import turbineops.TurbineOperationControl;
 import GPS.GpsDataUnit;
-import Map.MapController;
-import Map.gridbaselayer.GridbaseControl;
 import NMEA.NMEADataUnit;
 import PamController.PamControlledUnitSettings;
 import PamController.PamController;
@@ -66,7 +62,6 @@ import PamguardMVC.PamDataBlock;
 import analogarraysensor.ArraySensorControl;
 import backupmanager.BackupManager;
 import beamformer.continuous.BeamFormerControl;
-import beamformer.localiser.BeamFormLocaliserControl;
 import bearinglocaliser.BearingLocaliserControl;
 import binaryFileStorage.SecondaryBinaryStore;
 import cepstrum.CepstrumControl;
@@ -1083,7 +1078,6 @@ final public class PamModel implements PamModelInterface, PamSettings {
 		 * PamModel !
 		 */
 
-
 		// Load up whatever default classloader was used to create this class.  Must use the same classloader
 		// for all plugins, or else we will not be able to create proper dependencies between them or be able
 		// to save properties in the psf file.  Found this problem because ipiDemo requires the
@@ -1150,30 +1144,11 @@ final public class PamModel implements PamModelInterface, PamSettings {
 					    // to add that URL to the default classloader path.
 					    URL newURL = jarList.get(i).toURI().toURL();
 					    
-					    // original method
-//					    Method method = URLClassLoader.class.getDeclaredMethod("addURL", URL.class);
-//					    method.setAccessible(true);
-//					    method.invoke(cl, newURL);
-					    
-					    // first fix attempt - create a brand new URLClassLoader. As expected, we get a ClassCastException when trying
-					    // to load the parameters so we can't save params using this method
-//					    URL[] newURLArray = new URL[1];
-//					    newURLArray[0] = newURL;
-//						cl = new URLClassLoader(newURLArray);
 						
 					    // second attempt - custom class loader with the system app loader specified as the parent.  Loads controlled unit, but
 					    // as before it doesn't load the parameters
 					    classLoader.addURL(newURL);
 
-					    // third attempt
-//					    Class<?> genericClass = cl.getClass();
-//					    Method method = genericClass.getSuperclass().getDeclaredMethod("addURL", new Class[] {URL.class});
-//					    method.setAccessible(true);
-//					    method.invoke(cl, new Object[] {newURL});
-
-					    
-					    
-					    
 					    // Save the name of the class to the global pluginBeingLoaded variable, and load the class.
 					    this.setPluginBeingLoaded(className);
 //						Class c = cl.loadClass(className);
@@ -1254,9 +1229,8 @@ final public class PamModel implements PamModelInterface, PamSettings {
 										"for help.<p>" +
 										"This plug-in will not be available for loading";
 								String help = null;
-								int ans = WarnOnce.showWarning(PamController.getMainFrame(), title, msg, WarnOnce.WARNING_MESSAGE, help, e1);
+								int ans = WarnOnce.showWarning(PamController.getInstance().getGuiFrameManager().getFrame(0), title, msg, WarnOnce.WARNING_MESSAGE, help, e1);
 								System.err.println("Exception while loading " +	className);
-								System.err.println(e1.getMessage());								
 								continue;
 							}
 						}						
@@ -1269,7 +1243,7 @@ final public class PamModel implements PamModelInterface, PamSettings {
 							"for help.<p>" +
 							"This plug-in will not be available for loading";
 					String help = null;
-					int ans = WarnOnce.showWarning(PamController.getMainFrame(), title, msg, WarnOnce.WARNING_MESSAGE, help, ex);
+					int ans = WarnOnce.showWarning(PamController.getInstance().getGuiFrameManager().getFrame(0), title, msg, WarnOnce.WARNING_MESSAGE, help, ex);
 					System.err.println("Exception while loading " +	jarList.get(i).getName());
 					continue;
 				}
@@ -1294,7 +1268,7 @@ final public class PamModel implements PamModelInterface, PamSettings {
 						
 						// instantiate the plugin control class using the custom class loader
 						try {
-							File classFile = new File(pf.getJarFile());		
+//							File classFile = new File(pf.getJarFile());		
 							//URLClassLoader cl = new URLClassLoader(new URL[]{classFile.toURI().toURL()});
 //							mi = PamModuleInfo.registerControlledUnit(pf.getClassName(), pf.getDescription(),cl);
 							mi = PamModuleInfo.registerControlledUnit(pf.getClassName(), pf.getDescription(),classLoader);
@@ -1360,7 +1334,7 @@ final public class PamModel implements PamModelInterface, PamSettings {
 								"for help.<p>" +
 								"This plug-in will not be available for loading";
 						String help = null;
-						int ans = WarnOnce.showWarning(PamController.getMainFrame(), title, msg, WarnOnce.WARNING_MESSAGE, help, e1);
+						int ans = WarnOnce.showWarning(PamController.getInstance().getGuiFrameManager().getFrame(0), title, msg, WarnOnce.WARNING_MESSAGE, help, e1);
 						System.err.println("Exception while loading " +	pf.getDefaultName());
 						pluginList.remove(pf);
 						continue;

src/PamModel/PamModuleInfo.java

@@ -283,6 +283,7 @@ public class PamModuleInfo implements PamDependent{
 	}
 	
 
+	
 	public static JMenu getModulesMenu(Frame parentFrame) {
 
 		ArrayList<ModulesMenuGroup> moduleGroupsList = new ArrayList<ModulesMenuGroup>();

src/PamView/dialog/warn/WarnOnce.java

@@ -24,6 +24,7 @@ import javafx.scene.control.Alert.AlertType;
 public class WarnOnce implements PamSettings {
 
 	public static final int OK_CANCEL_OPTION = JOptionPane.OK_CANCEL_OPTION;
+	public static final int YES_NO_OPTION = JOptionPane.YES_NO_OPTION;
 	public static final int WARNING_MESSAGE = JOptionPane.DEFAULT_OPTION;
 	public static final int OK_OPTION = JOptionPane.OK_OPTION;
 	public static final int CANCEL_OPTION = JOptionPane.CANCEL_OPTION;

src/PamView/dialog/warn/WarnOnceDialog.java

@@ -92,12 +92,17 @@ public class WarnOnceDialog extends PamDialog {
 		}
 		
 		// if the message type is OK_OPTION, hide the cancel button
-		if (messageType == WarnOnce.OK_OPTION) {
+		if (messageType == WarnOnce.YES_NO_OPTION) {
+			getOkButton().setText("Yes");
+			getCancelButton().setText("No");
+		}
+		else if (messageType == WarnOnce.OK_OPTION) {
 			getCancelButton().setVisible(false);
 		} else {
 			getCancelButton().setVisible(true);
 		}
 		
+		
 		// change the button text to custom text, if needed
 		if (okButtonText!=null) {
 			getOkButton().setText(okButtonText);

src/PamguardMVC/PamDataBlock.java

@@ -844,6 +844,30 @@ public class PamDataBlock<Tunit extends PamDataUnit> extends PamObservable {
 		return unitsInInterval;
 	}
 	
+	/**
+	 * Do data exist which cover the given time range ?  
+	 * @param startMillis
+	 * @param endMillis
+	 * @return true if data exist covering that time range. 
+	 */
+	public boolean hasDataRange(long startMillis, long endMillis) {
+		PamDataUnit first = null, last = null;
+		synchronized (synchronizationLock) {
+			first = getFirstUnit();
+			last = getLastUnit();
+		}
+		if (first == null || last == null) {
+			return false;
+		}
+		if (first.getTimeMilliseconds() > startMillis) {
+			return false;
+		}
+		if (last.getEndTimeInMilliseconds() < endMillis) {
+			return false;
+		}
+		return true;
+	}
+
 	// recursive search for the correct unit
 	// private Tunit searchFirstUnitAfter(int i1, int i2, long timems) {
 	// /*
@@ -1014,6 +1038,9 @@ public class PamDataBlock<Tunit extends PamDataUnit> extends PamObservable {
 	 * @return true if we need to reload offline data.
 	 */
 	public boolean needViewerDataLoad(OfflineDataLoadInfo offlineDataLoadInfo) {
+		if (pamDataUnits.size() == 0) {
+			return true;
+		}
 		if (offlineDataLoadInfo.getStartMillis() == currentViewDataStart
 				&& offlineDataLoadInfo.getEndMillis() == currentViewDataEnd) {
 			return false;

src/PamguardMVC/dataOffline/OfflineDataLoading.java

@@ -527,7 +527,10 @@ public class OfflineDataLoading<T extends PamDataUnit> {
 	public void notifyOfflineObservers(T pamDataUnit) {
 		if (requestingObservers != null) {
 			for (int i = 0; i < requestingObservers.size(); i++) {
-				requestingObservers.get(i).addData(pamDataBlock, pamDataUnit);
+				PamObserver obs = requestingObservers.get(i);
+				if (obs != null) {
+					obs.addData(pamDataBlock, pamDataUnit);
+				}
 			}
 		}
 

src/analogarraysensor/AnalogArraySensorDataUnit.java

@@ -60,7 +60,7 @@ public class AnalogArraySensorDataUnit extends PamDataUnit implements Array.sens
 	}
 
 	private Double getFieldVal(int iVal) {
-		if (sensorData == null || sensorData.length <= iVal) {
+		if (sensorData == null || sensorData.length <= iVal || iVal < 0) {
 			return null;
 		}
 		AnalogSensorData sensDat = sensorData[iVal];

src/analoginput/swing/AnalogDiagnosticsDisplay.java

@@ -225,7 +225,8 @@ public class AnalogDiagnosticsDisplay extends UserDisplayComponentAdapter implem
 				}
 				break;
 			case 4:
-				if (allItemData[rowIndex] != null) {
+				ItemAllData data = allItemData[rowIndex];
+				if (data != null) {
 					return allItemData[rowIndex].getIntValue();
 				}
 				break;

src/bearinglocaliser/offline/BLOfflineTask.java

@@ -4,6 +4,7 @@ import java.util.ListIterator;
 
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
+import PamguardMVC.dataOffline.OfflineDataLoadInfo;
 import bearinglocaliser.BearingLocaliserControl;
 import bearinglocaliser.BearingProcess;
 import dataMap.OfflineDataMapPoint;
@@ -28,6 +29,9 @@ public class BLOfflineTask extends OfflineTask {
 
 	@Override
 	public String getName() {
+		if (bearingLocaliserControl == null) {
+			return null;
+		}
 		return bearingLocaliserControl.getUnitName();
 	}
 
@@ -67,15 +71,21 @@ public class BLOfflineTask extends OfflineTask {
 		if (rawOrFFTBlock == null) {
 			return;
 		}
-		ListIterator it = rawOrFFTBlock.getListIterator(dataUnit.getTimeMilliseconds(), rawOrFFTBlock.getChannelMap(), 
-				PamDataBlock.MATCH_BEFORE, PamDataBlock.POSITION_BEFORE);
-		if (it == null || it.hasNext() == false) {
 		long dataStart = dataUnit.getTimeMilliseconds();
 		long dataEnd = dataUnit.getEndTimeInMilliseconds();
-			if (dataEnd-dataStart <= 0) {
-				dataEnd = dataStart + 1000;
-			}
-			rawOrFFTBlock.loadViewerData(dataStart, dataEnd, null);
+		boolean haveData = rawOrFFTBlock.hasDataRange(dataStart, dataEnd);
+		if (haveData == false) {
+//		ListIterator it = rawOrFFTBlock.getListIterator(dataUnit.getTimeMilliseconds(), rawOrFFTBlock.getChannelMap(), 
+//				PamDataBlock.MATCH_BEFORE, PamDataBlock.POSITION_BEFORE);
+//		if (it == null || it.hasNext() == false) {
+//			if (dataEnd-dataStart <= 0) {
+//				dataEnd = dataStart + 1000;
+//			}
+			OfflineDataLoadInfo offlineLoadInfo = new OfflineDataLoadInfo(dataStart, dataEnd);
+			offlineLoadInfo.setLoadKeepLayers(2);
+			rawOrFFTBlock.getOfflineData(offlineLoadInfo);
+//			System.out.printf("Loaded some FFT data I hope\n");
+//			rawOrFFTBlock.loadViewerData(dataStart, dataEnd, null);
 		}
 		
 	}

src/dataMap/ScrollingDataPanel.java

@@ -391,6 +391,9 @@ public class ScrollingDataPanel extends PamBorderPanel {
 	public void scrollToData(PamDataBlock dataBlock) {
 		long startTime = dataBlock.getCurrentViewDataStart();
 		int val = (int) ((startTime - getScreenStartMillis())/1000 - getScreenSeconds()/5)  ;
+		val += hScrollBar.getValue();
+//		System.out.printf("Scroll bar %d to %d set %d\n", hScrollBar.getMinimum(), 
+//				hScrollBar.getMaximum(), val);
 		hScrollBar.setValue(val);
 	}
 

src/fftManager/fftorganiser/FFTDataOrganiser.java

@@ -4,6 +4,7 @@ import java.util.Arrays;
 import java.util.List;
 import java.util.ListIterator;
 
+import PamController.PamController;
 import PamController.SettingsNameProvider;
 import PamDetection.RawDataUnit;
 import PamUtils.PamUtils;
@@ -143,6 +144,11 @@ public class FFTDataOrganiser {
 		if (rawOrFFTData == null) {
 			return null;
 		}
+		
+//		if (PamController.getInstance().getRunMode() == PamController.RUN_PAMVIEW) {
+//			checkOfflineDataLoad(rawOrFFTData, pamDataUnit.getTimeMilliseconds(), pamDataUnit.getEndTimeInMilliseconds());
+//		}
+		
 		switch (inputType) {
 		case FFTData:
 			return createFromFFTData(pamDataUnit, sampleRate, channelMap);
@@ -157,6 +163,52 @@ public class FFTDataOrganiser {
 		}
 	}
 
+	/**
+	 * Called when running offline to try to ensure required raw or fft data are in memory. 
+	 * @param sourceData
+	 * @param timeMilliseconds
+	 * @param endTimeInMilliseconds
+	 */
+	private boolean checkOfflineDataLoad(PamDataBlock sourceData, long startMilliseconds, long endMilliseconds) {
+		if (sourceData == null) {
+			return false;
+		}
+		boolean needData = needOfflineDataLoad(sourceData, startMilliseconds, endMilliseconds);
+		if (needData) {
+			sourceData.loadViewerData(startMilliseconds, endMilliseconds, null);
+		}
+		return needOfflineDataLoad(sourceData, startMilliseconds, endMilliseconds);		
+	}
+	
+	/**
+	 * Test to see if we still need to load offline data. 
+	 * @param sourceData
+	 * @param startMilliseconds
+	 * @param endMilliseconds
+	 * @return
+	 */
+	private boolean needOfflineDataLoad(PamDataBlock sourceData, long startMilliseconds, long endMilliseconds) {
+		if (sourceData == null) {
+			return false;
+		}
+		synchronized (sourceData.getSynchLock()) {
+			PamDataUnit first = sourceData.getFirstUnit();
+			PamDataUnit last = sourceData.getLastUnit();
+			if (first == null || last == null) {
+				return true;
+			}
+			if (first.getTimeMilliseconds() > startMilliseconds) {
+				return true;
+			}
+			if (last.getEndTimeInMilliseconds() < endMilliseconds) {
+				return true;
+			}
+		}
+		return false;
+	}
+	
+	
+
 	/**
 	 * Get FFT data units matching in time from the source 
 	 * @param pamDataUnit data unit we need FFT data for (can be anything, just needs it's times)

src/fileOfflineData/OfflineFileList.java

@@ -3,6 +3,8 @@ package fileOfflineData;
 import java.io.File;
 import java.io.FileFilter;
 import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
 
 /**
  * Make a list of files with the given file filter. 
@@ -30,6 +32,21 @@ public class OfflineFileList {
 		return files.size();
 	}
 	
+	public void sortByFileName() {
+		if (files == null || files.size() == 0) {
+			return;
+		}
+		Collections.sort(files, new Comparator<File>() {
+
+			@Override
+			public int compare(File file1, File file2) {
+				String n1 = file1.getName();
+				String n2 = file2.getName();
+				return n1.compareTo(n2);
+			}
+		});
+	}
+
 	private void addFiles(File current) {
 		if (current.exists() == false) {
 			return;

src/group3dlocaliser/dialog/GroupLocSettingPaneFX.java

@@ -173,6 +173,9 @@ public class GroupLocSettingPaneFX extends SettingsPane<Group3DParams>{
 			algoOptsButton.setDisable(true);
 			return;
 		}
+		// also enable / disable the more options button ...
+		algoOptsButton.setDisable(localiserAlgorithm.hasParams() == false);
+		
 		/**
 		 * Need to immediately tell the algorithm which input we're using so that it can 
 		 * show the correct settings...
@@ -209,9 +212,6 @@ public class GroupLocSettingPaneFX extends SettingsPane<Group3DParams>{
 		}
 		algorithmSourcePane = newPane;
 				
-		// also enable / disable the more options button ...
-		algoOptsButton.setDisable(localiserAlgorithm.hasParams() == false);
-		
 		
 		repackDialog();
 	}

src/help/mapping/NMEA/docs/ConfiguringGPS.html

@@ -36,7 +36,10 @@ From the Detection Menu, select <strong><em>GPS>GPS Options</em></strong>
 <p>
 On very rare occasions, if the GPS data have been multiplexed through some other instruments, the first 
 two characters of the string identifier are changed. If this is the case, it may also be necessary to set these
-so that the GPS module can identify the appropriate data. 
+so that the GPS module can identify the appropriate data. As an alternative, select the "Allow and string initials" option
+which will use any valid RMC or GGA string. Note however, that with a complex NMEA system there may be more than one GPS and 
+it is better to select only strings from the most accurate</p>
+
 
 <h3>Read Options</h3>
 <p>Three options for reading and storing GPS data are available.</p>

src/modbustcp/brainbox/BBED549.java

@@ -140,7 +140,7 @@ public class BBED549 {
 	public static double hexToEngineering(int range, int data) {
 		/**
 		 * convert integer data to engineering units. 
-		 * @param range range on device, asumed the same for all channels. 
+		 * @param range range on device, assumed the same for all channels. 
 		 * @param data data array
 		 * @return
 		 */