Updated POM

working POM for build with Tethys. Note though that it's failing to get
rid of all signature files in the \META-INF\ folder, so the two files
META-INF\ECLIPSE_.SF and META-INF\ECLIPSE_.RSA must be removed before
the jar file can be used.

.classpath

@@ -6,8 +6,9 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/jre">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
 		<attributes>
+			<attribute name="module" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
@@ -16,7 +17,5 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry combineaccessrules="false" kind="src" path="/nilusxmlgenerator"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/TethysJavaClient"/>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>

dependency-reduced-pom.xml

@@ -17,6 +17,7 @@
       <resource>
         <directory>src</directory>
         <excludes>
+          <exclude>META-INF/*.SF,META-INF/*.DSA,META-INF/*.RSA</exclude>
           <exclude>**/*.java</exclude>
           <exclude>jars/*.*</exclude>
         </excludes>
@@ -196,6 +197,10 @@
   <properties>
     <maven.compiler.target>11</maven.compiler.target>
     <maven.compiler.source>11</maven.compiler.source>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <javafx.version>16</javafx.version>
+    <jaxb.runtime.version>2.4.0-b180830.0438</jaxb.runtime.version>
+    <jaxb.xjc.version>2.4.0-b180830.0438</jaxb.xjc.version>
+    <jaxb.api.version>2.4.0-b180830.0359</jaxb.api.version>
   </properties>
 </project>

src/PamController/PamguardVersionInfo.java

@@ -24,19 +24,19 @@ public class PamguardVersionInfo {
 	 * PAMGuard can work with. 
 	 */
 	static public final String minJavaVersion = "11.0.0";
-	static public final String maxJavaVersion = "19.99.99";
+	static public final String maxJavaVersion = "21.99.99";
 	
 
 	/**
 	 * Version number, major version.minorversion.sub-release.
 	 * Note: can't go higher than sub-release 'f'
 	 */
-	static public final String version = "2.02.09c";
+	static public final String version = "2.02.09f";
 	
 	/**
 	 * Release date
 	 */
-	static public final String date = "10 November 2023";
+	static public final String date = "18 December 2023";
 	
 //	/**
 //	 * Release type - Beta or Core

src/help/utilities/tethys/docs/tethys_overview.html

@@ -37,15 +37,29 @@ img {
 		experimental efforts based on a common attribute. This resulting
 		database can then be queried based on time, space, or any desired
 		attribute and the results can be integrated with external datasets
-		such as NASA’s Ocean Color, lunar illumination, etc. in a consistent
+		such as NASA's Ocean Color, lunar illumination, etc. in a consistent
 		manner. While Tethys is designed primarily for acoustic metadata from
 		marine mammals, the design is general enough to permit use in other
 		areas as well.
 		
 	</p>
-	<br>
+	<p>PAMGuard is compatible with Tethys 3.0, released early in 2024. </p>
-	<br>
+	<p>The Tethys database is not a replacement for the existing 
-	<p class="nextLink">
+	
+	<a href="../../generalDatabaseHelp/docs/database_database.html">PAMGuard Database.</a> 
+	Where the PAMGuard database only contains data from a single instrument or cruise, the Tethys
+	database contains data from many cruises and projects and can be used to hold a summary of all data 
+	from a lab or organisation.
+	</p>
+	
+	<p>Before using the module in PAMGuard, you should install the Tethys Server, which runs under 
+	Windows. <a href="https://tethys.sdsu.edu/install/">
+	Instructions for installing the Tethys Server can be found here.</a></p>
+		
+	
+	<br><br>
+	
+	
 		<a href="tethys_configure.html">Next: Configuring the Tethys
 			Module</a>
 	</p>

src/pamguard/Pamguard.java

@@ -717,6 +717,47 @@ public class Pamguard {
 			}
 		}
 	}
+	/*
+	 * Some bits that need added to Maven POM. 
+	 * 
+<!-- From NilusXMLGenerator POM at https://bitbucket.org/tethysacousticmetadata/nilusxmlgenerator/src/master/-->
+    <dependency>
+        <groupId>org.eclipse.persistence</groupId>
+        <artifactId>org.eclipse.persistence.moxy</artifactId>
+        <version>2.5.0</version>
+    </dependency>
+	<dependency>
+	    <groupId>javax.xml.bind</groupId>
+	    <artifactId>jaxb-api</artifactId>
+	    <version>2.4.0-b180830.0359</version> 
+	</dependency>
+	<dependency>
+	    <groupId>org.glassfish.jaxb</groupId>
+	    <artifactId>jaxb-runtime</artifactId>
+	    <version>2.4.0-b180830.0438</version> 
+	</dependency>
+	<dependency>
+        <groupId>org.glassfish.jaxb</groupId>
+        <artifactId>jaxb-xjc</artifactId>
+        <version>2.4.0-b180830.0438</version>
+    </dependency>
+	 
+	 <!-- Also not in Maven, so you may need to copy the javaclient and nilus folders from 
+e.g. C:\Users\dg50\source\repos\**your projectfolder**\repo\tethys\org
+to C:\Users\dg50\.m2\repository\tethys\org
+
+ 	<dependency>
+	    <groupId>tethys.org</groupId>
+	    <artifactId>nilus</artifactId>
+	    <version>3.0</version>
+	</dependency>
+
+ 	<dependency>
+	    <groupId>tethys.org</groupId>
+	    <artifactId>javaclient</artifactId>
+	    <version>3.0</version>
+	</dependency>-->
+	 */
 
 
 }

src/whistlesAndMoans/StubRemover.java

@@ -82,7 +82,13 @@ public class StubRemover {
 	private int searchStubSize(List<SliceData> sliceData, int currentSlice, int peakInd, int searchDir, int diagGap, int currentSize) {
 		int nSlice = sliceData.size();
 		int nextSliceInd = currentSlice + searchDir;
-		if (nextSliceInd < 0 || nextSliceInd >= nSlice-1) {
+		/**
+		 * This function is only every used to throw away very small stubs, so there is no need to get the full size 
+		 * of every one. It's OK to return as soon as the size is bigger than the minimum required to make
+		 * something worth keeping. This reduces the time spent tracing down every little alley which was 
+		 * severely impacting performance for larger whistles. 
+		 */
+		if (nextSliceInd < 0 || nextSliceInd >= nSlice-1 || currentSize > whistleControl.getWhistleToneParameters().minPixels) {
 			return currentSize;
 		}
 		SliceData nextSlice = sliceData.get(nextSliceInd);