From e70ae9616cb7b51ed6ecff4abc8fbe18633c33f3 Mon Sep 17 00:00:00 2001
From: douggillespie <dg50@st-andrews.ac.uk>
Date: Mon, 10 Jan 2022 10:20:58 +0000
Subject: [PATCH 1/4] Revert "Delete .gitignore"

This reverts commit c537dacbd9db4d69fec07ae391bfdd9b34c94e6f.
---
 .gitignore | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 .gitignore

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 00000000..c836fce5
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,24 @@
+# Compiled class file
+*.class
+
+# Log file
+*.log
+
+# BlueJ files
+*.ctxt
+
+# Mobile Tools for Java (J2ME)
+.mtj.tmp/
+
+# Package Files #
+*.jar
+*.war
+*.nar
+*.ear
+*.zip
+*.tar.gz
+*.rar
+
+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*
+/target/

From aa7e9e452b29011205859952560095a99f44e870 Mon Sep 17 00:00:00 2001
From: douggillespie <dg50@st-andrews.ac.uk>
Date: Mon, 10 Jan 2022 10:21:12 +0000
Subject: [PATCH 2/4] Revert "Delete .classpath"

This reverts commit 582ea3cbe2c7461a37863476893acfd0765c3799.
---
 .classpath | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 .classpath

diff --git a/.classpath b/.classpath
new file mode 100644
index 00000000..fe69133f
--- /dev/null
+++ b/.classpath
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry including="**/*.java" kind="src" output="target/classes" path="src">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<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/AdoptOpenJDK 16">
+		<attributes>
+			<attribute name="module" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

From 32dd401dd9c163e630f8940ec54dcb082390f55f Mon Sep 17 00:00:00 2001
From: douggillespie <dg50@st-andrews.ac.uk>
Date: Mon, 10 Jan 2022 10:21:26 +0000
Subject: [PATCH 3/4] Revert "Delete pom.xml"

This reverts commit bb667b7c3b33252ec86675a04bacd17a4bbfb00a.
---
 pom.xml | 823 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 823 insertions(+)
 create mode 100644 pom.xml

diff --git a/pom.xml b/pom.xml
new file mode 100644
index 00000000..98f428a9
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,823 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" 
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>org.pamguard</groupId>
+  <artifactId>PamguardBeta</artifactId>
+  <version>2.02.02</version>
+  <name>Pamguard Java12+</name>
+  <description>Pamguard for Java 12+, using Maven to control dependcies</description>
+	<url>www.pamguard.org</url>
+	<organization>
+		<name>Sea Mammal Research Unit, University of St. Andrews</name>
+		<url>http://www.smru.st-andrews.ac.uk</url>
+	</organization>
+
+
+    <properties>
+        <javafx.version>16</javafx.version>
+        <maven.compiler.source>11</maven.compiler.source>
+        <maven.compiler.target>11</maven.compiler.target>
+    </properties>
+
+  <build>
+    <sourceDirectory>src</sourceDirectory>
+    <resources>
+      <resource>
+        <directory>src</directory>
+        <excludes>
+          <exclude>**/*.java</exclude> <!--  don't include any source files -->
+          <exclude>jars/*.*</exclude> <!--  don't include files in the jars folder -->
+        </excludes>
+      </resource>
+    </resources>
+    <plugins>
+      <plugin>
+      
+      <!-- original maven compiler definition - uses the JRE's javac compiler, not the one Eclipse uses 
+        <artifactId>maven-compiler-plugin</artifactId>
+        <version>3.8.0</version>
+        <configuration>
+          <release>13</release>
+        </configuration>
+      -->
+
+		<!--  attempt to use the Eclipse JDT compiler, so that the errors match when building
+		https://stackoverflow.com/questions/38070326/java-generics-compiler-error-not-shown-in-eclipse
+		https://wiki.eclipse.org/JDT/FAQ#Can_I_use_JDT_outside_Eclipse_to_compile_Java_code.3F
+		https://wiki.eclipse.org/Tycho/FAQ#Can_I_use_the_Tycho_compiler_support_in_non-OSGi_projects.2C_too.3F
+		-->      
+		<groupId>org.apache.maven.plugins</groupId>
+		<artifactId>maven-compiler-plugin</artifactId>
+        <version>3.8.1</version>
+		<configuration>
+		
+			<!--  set compiler to use Java version 11 API https://docs.oracle.com/javase/9/tools/javac.htm#JSWOR627 -->
+			<release>11</release>
+			<compilerId>jdt</compilerId>
+            <compilerArguments>
+               <properties>.settings/org.eclipse.jdt.core.prefs</properties> <!--  make sure to use same params as what Eclipse uses -->
+            </compilerArguments>
+		</configuration>
+		
+		<dependencies>
+			<!-- https://mvnrepository.com/artifact/org.eclipse.tycho/tycho-compiler-jdt -->
+			<dependency>
+			    <groupId>org.eclipse.tycho</groupId>
+			    <artifactId>tycho-compiler-jdt</artifactId>
+			    <version>1.5.1</version>
+			</dependency>
+		</dependencies>		 	
+		
+      </plugin>
+      
+      <plugin>
+      	<groupId>org.openjfx</groupId>
+		<artifactId>javafx-maven-plugin</artifactId>
+		<version>0.0.6</version>
+		<configuration>
+        	<source>16</source>
+        	<target>16</target>
+        	<release>16</release>
+        </configuration>
+	  </plugin>
+	  
+	  <!--  Maven Shade plugin - for creating the uberjar / fatjar -->
+	  <!--  see http://maven.apache.org/plugins/maven-shade-plugin/index.html for details -->
+      <plugin>
+      	<groupId>org.apache.maven.plugins</groupId>
+      	<artifactId>maven-shade-plugin</artifactId>
+      	<version>3.2.1</version>
+		<configuration>
+			<transformers>
+				<transformer
+					implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
+			</transformers>
+		</configuration>
+        <executions>
+          <execution>
+            <phase>package</phase>
+            <goals>
+              <goal>shade</goal>
+            </goals>
+            <configuration>
+              <transformers>
+                <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+                  <manifestEntries>
+                    <Main-Class>pamguard.Pamguard</Main-Class>
+                    <Class-Path>.</Class-Path> <!--  this is from the orig ant build file -->
+                    <SplashScreen-Image>Resources/pgBlankSplash.png</SplashScreen-Image> <!--  this is from the orig ant build file -->
+                  </manifestEntries>
+                </transformer>
+ 				<transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
+              </transformers>
+              <filters>
+                <filter>
+                  <artifact>*:*</artifact>
+                  <excludes>
+                    <exclude>META-INF/*.SF</exclude> <!--  get rid of manifests from library jars - also done in orig ant build file -->
+                    <exclude>META-INF/*.DSA</exclude>
+                    <exclude>META-INF/*.RSA</exclude>
+                  </excludes>
+                </filter>
+              </filters>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+
+	  <!--  The Maven-JDEPS plugin, to analyze necessary JDK dependencies.  See
+	  		this site for details: https://maven.apache.org/plugins/maven-jdeps-plugin/index.html -->	
+      <plugin>
+        <groupId>com.github.marschall</groupId>
+        <artifactId>jdeps-maven-plugin</artifactId>
+        <version>0.5.1</version>
+      </plugin>
+
+	  <!-- The Maven dependency plugin, which can copy all dependencies into a temp folder for jdeps analysis -->      
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-dependency-plugin</artifactId>
+        <version>3.1.1</version>
+        <executions>
+          <execution>
+            <id>copy-dependencies</id>
+            <phase>package</phase>
+            <goals>
+              <goal>copy-dependencies</goal>
+            </goals>
+            <configuration>
+              <outputDirectory>${project.build.directory}/tempDependencies</outputDirectory>
+              <overWriteReleases>false</overWriteReleases>
+              <overWriteSnapshots>false</overWriteSnapshots>
+              <overWriteIfNewer>true</overWriteIfNewer>
+            </configuration>
+          </execution>
+          
+          <!--  this deletes all the dependencies in the local repository and downloads them again.  
+          Run a Maven > Update after doing this in order to properly reset the dependencies.  Also, you
+          will need to add the 3 jar files (x3, JasioHost and jave) back into the local repository after
+          running this command -->
+          
+    	<!-- I'm not sure why, but every time I try to run the shade:shade build to create a
+		fatjar it first runs this, which deletes all of the dependencies and completely fails.
+		I think it has something to do with the lifecycle mapping, but that's beyond my Maven
+		abilities right now.
+		I can't even remember why I added this in the first place, so I'm going to comment
+		it out 
+          <execution>
+            <id>purge-local-dependencies</id>
+            <phase>process-sources</phase>
+            <goals>
+              <goal>purge-local-repository</goal>
+            </goals>
+            <configuration>
+            </configuration>
+          </execution>
+          -->
+        </executions>
+      </plugin>
+      
+ 
+    </plugins>
+    <pluginManagement>
+    	<plugins>
+    		<!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself.-->
+    		<plugin>
+    			<groupId>org.eclipse.m2e</groupId>
+    			<artifactId>lifecycle-mapping</artifactId>
+    			<version>1.0.0</version>
+    			<configuration>
+    				<lifecycleMappingMetadata>
+    					<pluginExecutions>
+    						<pluginExecution>
+    							<pluginExecutionFilter>
+    								<groupId>
+    									org.apache.maven.plugins
+    								</groupId>
+    								<artifactId>
+    									maven-dependency-plugin
+    								</artifactId>
+    								<versionRange>
+    									[3.1.1,)
+    								</versionRange>
+    								<goals>
+    									<goal>
+    										purge-local-repository
+    									</goal>
+    								</goals>
+    							</pluginExecutionFilter>
+    							<action>
+    								<ignore></ignore>
+    							</action>
+    						</pluginExecution>
+    					</pluginExecutions>
+    				</lifecycleMappingMetadata>
+    			</configuration>
+    		</plugin>
+    	</plugins>
+    </pluginManagement>
+  </build>
+ 
+ <reporting>
+    <plugins>
+      <plugin>
+        <groupId>com.github.marschall</groupId>
+        <artifactId>jdeps-maven-plugin</artifactId>
+        <version>0.5.1</version>
+      </plugin>
+    </plugins>
+  </reporting>
+  
+  
+  <!--  ************************* Extra Repositories ************************************* -->
+	  <repositories>
+	  
+		<!--  Project repo to hold the custom jar files that are not available in Maven.  Do
+		this so that we don't have to do the extra step of manually installing jar files in the local repo -->
+		<repository>
+			<id>repo</id>
+			<releases>
+				<enabled>true</enabled>
+				<checksumPolicy>ignore</checksumPolicy>
+			</releases>
+			<snapshots>
+				<enabled>false</enabled>
+			</snapshots>
+			<url>file://${project.basedir}/repo</url>
+		</repository>
+		
+	  	<!-- Repo for Jamie's code -->
+	  	<!-- IMPORTANT: SOMEHOW THIS REPO INTERFERES WITH THE
+	  		JAVAFX DEPENDENCIES.  Don't understand how, but it
+	  		does.  If Maven is not downloading the JavaFX dependencies
+	  		and is instead throwing errors, try commenting out this
+	  		repository.  Let Maven download the JavaFX files, and
+	  		then uncomment this repo again.
+	  		Same thing seems to be occurring if I try to update the postgresql library. -->
+		<repository>
+			<snapshots>
+				<enabled>false</enabled>
+			</snapshots>
+	        <id>central</id>
+            <name>a0u0ltozdsehx-artifactory-primary-0-releases</name>
+            <url>https://jmachund.jfrog.io/artifactory/jpam2</url>
+		</repository> 
+		
+	    <!-- Repo for netCDF -->
+	    <repository>
+	        <snapshots>
+	            <enabled>false</enabled>
+	        </snapshots>
+	        <id>unidata-all</id>
+	        <name>Unidata netCDF</name>
+	        <url>https://artifacts.unidata.ucar.edu/repository/unidata-all/</url>
+	    </repository>
+	    
+	    <!--  -->
+	    <repository>
+	        <snapshots>
+	            <enabled>false</enabled>
+	        </snapshots>
+	        <id>geomajas</id>
+	        <name>geomajas</name>
+	        <url>http://maven.geomajas.org/</url>
+	    </repository>
+	    
+	    <!-- Repo for Renjin Script Engine -->
+	    <repository>
+	        <snapshots>
+	            <enabled>false</enabled>
+	        </snapshots>
+	        <id>bedatadriven</id>
+	        <name>bedatadriven_renjin</name>
+	        <url>https://nexus.bedatadriven.com/content/groups/public/</url>
+	    </repository>
+	    
+	    
+	    <repository>
+	        <snapshots>
+	            <enabled>false</enabled>
+	        </snapshots>
+	        <id>talan</id>
+	        <name>talan</name>
+	        <url>https://nexus.talanlabs.com/content/repositories/releases/</url>
+	    </repository>
+	    
+	</repositories>
+
+
+  <!--  ************************* Dependencies ************************************* -->
+  <dependencies>
+
+	<!--jpam project - utilities -->
+	<dependency>
+		<groupId>org.jamdev</groupId>
+		<artifactId>jpamutils</artifactId>
+		<version>0.0.55</version>
+	</dependency>
+
+	<!--jpam project - Deep learning java library -->
+	<dependency>
+		<groupId>org.jamdev</groupId>
+		<artifactId>jdl4pam</artifactId>
+		<version>0.0.91</version>
+	</dependency>
+
+	<!-- https://mvnrepository.com/artifact/gov.nist.math/jama -->
+  	<dependency>
+  		<groupId>gov.nist.math</groupId>
+  		<artifactId>jama</artifactId>
+  		<version>1.0.3</version>
+  	</dependency>
+  	
+	<!-- https://mvnrepository.com/artifact/org.openjfx/javafx-controls -->
+	<!--  IMPORTANT - IF MAVEN IS NOT DOWNLOADING THE JAVAFX FILES AND
+		INSTEAD THROWING AN ERROR, IT MIGHT BE BECAUSE THERE IS AN
+		INTERFERENCE WITH JAMIE'S REPOSITORY.  I'm not sure why this happens,
+		but it does.  To fix, comment out the repository (in
+		the <repositories> section above, let Maven download the JavaFX
+		files, and then uncomment the repository again.    -->
+	<dependency>
+           <groupId>org.openjfx</groupId>
+           <artifactId>javafx-controls</artifactId>
+           <version>${javafx.version}</version>
+	</dependency>
+
+	<!-- https://mvnrepository.com/artifact/org.openjfx/javafx-swing -->
+	<!--  IMPORTANT - IF MAVEN IS NOT DOWNLOADING THE JAVAFX FILES AND
+		INSTEAD THROWING AN ERROR, IT MIGHT BE BECAUSE THERE IS AN
+		INTERFERENCE WITH JAMIE'S REPOSITORY.  I'm not sure why this happens,
+		but it does.  To fix, comment out the repository (in
+		the <repositories> section above, let Maven download the JavaFX
+		files, and then uncomment the repository again.    -->
+	<dependency>
+		<groupId>org.openjfx</groupId>
+		<artifactId>javafx-swing</artifactId>
+           <version>${javafx.version}</version>
+	</dependency>
+		
+	<!-- https://mvnrepository.com/artifact/org.openjfx/javafx-media -->
+	<!--  IMPORTANT - IF MAVEN IS NOT DOWNLOADING THE JAVAFX FILES AND
+		INSTEAD THROWING AN ERROR, IT MIGHT BE BECAUSE THERE IS AN
+		INTERFERENCE WITH JAMIE'S REPOSITORY.  I'm not sure why this happens,
+		but it does.  To fix, comment out the repository (in
+		the <repositories> section above, let Maven download the JavaFX
+		files, and then uncomment the repository again.    -->
+	<dependency>
+		<groupId>org.openjfx</groupId>
+		<artifactId>javafx-media</artifactId>
+           <version>${javafx.version}</version>
+	</dependency>
+
+	<!-- https://mvnrepository.com/artifact/org.openjfx/javafx-web -->
+	<!--  IMPORTANT - IF MAVEN IS NOT DOWNLOADING THE JAVAFX FILES AND
+		INSTEAD THROWING AN ERROR, IT MIGHT BE BECAUSE THERE IS AN
+		INTERFERENCE WITH JAMIE'S REPOSITORY.  I'm not sure why this happens,
+		but it does.  To fix, comment out the repository (in
+		the <repositories> section above, let Maven download the JavaFX
+		files, and then uncomment the repository again.    -->
+	<dependency>
+		<groupId>org.openjfx</groupId>
+		<artifactId>javafx-web</artifactId>
+           <version>${javafx.version}</version>
+	</dependency>
+	
+	<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-compress -->
+	<dependency>
+	    <groupId>org.apache.commons</groupId>
+	    <artifactId>commons-compress</artifactId>
+	    <version>1.19</version>
+	</dependency>
+
+	<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-csv -->
+  	<dependency>
+  		<groupId>org.apache.commons</groupId>
+  		<artifactId>commons-csv</artifactId>
+  		<version>1.7</version>
+  	</dependency>
+  	
+  	<!-- https://mvnrepository.com/artifact/commons-io/commons-io -->
+  	<dependency>
+  		<groupId>commons-io</groupId>
+  		<artifactId>commons-io</artifactId>
+  		<version>2.6</version>
+  	</dependency>
+  	
+  	<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-lang3 -->
+  	<dependency>
+  		<groupId>org.apache.commons</groupId>
+  		<artifactId>commons-lang3</artifactId>
+  		<version>3.9</version>
+  	</dependency>
+  	
+  	<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-math3 -->
+  	<dependency>
+  		<groupId>org.apache.commons</groupId>
+  		<artifactId>commons-math3</artifactId>
+  		<version>3.6.1</version>
+  	</dependency>
+  	
+	<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-math -->
+	<dependency>
+	    <groupId>org.apache.commons</groupId>
+	    <artifactId>commons-math</artifactId>
+	    <version>2.2</version>
+	</dependency>
+	
+	<!-- https://mvnrepository.com/artifact/commons-net/commons-net -->
+  	<dependency>
+  		<groupId>commons-net</groupId>
+  		<artifactId>commons-net</artifactId>
+  		<version>3.6</version>
+  	</dependency>
+  	
+  	<!-- https://mvnrepository.com/artifact/org.controlsfx/controlsfx -->
+  	<dependency>
+  		<groupId>org.controlsfx</groupId>
+  		<artifactId>controlsfx</artifactId>
+  		<version>11.0.0</version>
+  		<exclusions>
+  			<exclusion>
+  				<groupId>org.openjfx</groupId>
+  				<artifactId>javafx-base</artifactId>
+  			</exclusion>
+  			<exclusion>
+  				<groupId>org.openjfx</groupId>
+  				<artifactId>javafx-controls</artifactId>
+  			</exclusion>
+  			<exclusion>
+  				<groupId>org.openjfx</groupId>
+  				<artifactId>javafx-graphics</artifactId>
+  			</exclusion>
+  			<exclusion>
+  				<groupId>org.openjfx</groupId>
+  				<artifactId>javafx-media</artifactId>
+  			</exclusion>
+  			<exclusion>
+  				<groupId>org.openjfx</groupId>
+  				<artifactId>javafx-web</artifactId>
+  			</exclusion>
+  		</exclusions>
+  	</dependency>
+  	
+	<!-- https://search.maven.org/artifact/org.kordamp.ikonli/ikonli-javafx/12.2.0/jar -->
+	<!-- Icon symbol pack to replace FontAwesome.  This is the core library, and the
+	     actual symbol packs need to be added separately (see below) -->
+	<dependency>
+		<groupId>org.kordamp.ikonli</groupId>
+		<artifactId>ikonli-javafx</artifactId>
+		<version>12.2.0</version>
+	</dependency> 
+	
+	<!-- Ikonli FontAwesome5 font pack https://kordamp.org/ikonli/cheat-sheet-fontawesome5.html -->
+	<!--
+	<dependency>
+	    <groupId>org.kordamp.ikonli</groupId>
+		<artifactId>ikonli-fontawesome5-pack</artifactId>
+		<version>12.2.0</version>
+	</dependency>
+	 -->
+	 
+	<!-- Ikonli MaterialDesign2 (Latest) font pack https://kordamp.org/ikonli/cheat-sheet-materialdesign2.html -->
+	<dependency>
+	    <groupId>org.kordamp.ikonli</groupId>
+	    <artifactId>ikonli-materialdesign2-pack</artifactId>
+	    <version>12.2.0</version>
+	</dependency>
+	 
+	<!-- https://mvnrepository.com/artifact/net.sf.geographiclib/GeographicLib-Java -->
+	<dependency>
+		<groupId>net.sf.geographiclib</groupId>
+		<artifactId>GeographicLib-Java</artifactId>
+		<version>1.50</version>
+	</dependency>
+	
+	<!-- https://mvnrepository.com/artifact/org.jogamp.gluegen/gluegen -->
+	<dependency>
+		<groupId>org.jogamp.gluegen</groupId>
+		<artifactId>gluegen-rt-main</artifactId>
+		<version>2.3.2</version>
+	</dependency>
+	
+	<!-- https://mvnrepository.com/artifact/java3d/j3dutils -->
+	
+	<!-- https://mvnrepository.com/artifact/java3d/j3dcore -->
+
+	<!-- https://mvnrepository.com/artifact/com.healthmarketscience.jackcess/jackcess -->
+	<dependency>
+		<groupId>com.healthmarketscience.jackcess</groupId>
+		<artifactId>jackcess</artifactId>
+		<version>3.0.1</version>
+	</dependency>
+	
+	<!-- https://mvnrepository.com/artifact/com.fasterxml.jackson.core/jackson-databind -->
+	<dependency>
+		<groupId>com.fasterxml.jackson.core</groupId>
+		<artifactId>jackson-databind</artifactId>
+		<version>2.10.1</version>
+	</dependency>
+	
+	<!-- https://mvnrepository.com/artifact/org.jogamp.jogl/jogl-all-main -->
+	<dependency>
+		<groupId>org.jogamp.jogl</groupId>
+		<artifactId>jogl-all-main</artifactId>
+		<version>2.3.2</version>
+	</dependency>
+	
+	<!-- NOT SURE IF WE NEED THE JAXB LIBRARIES HERE - NO ERRORS WHEN REMOVED
+	<dependency>
+	    <groupId>javax.xml.bind</groupId>
+	    <artifactId>jaxb-api</artifactId>
+	    <version>2.3.1</version>
+	</dependency>
+    <dependency>
+	    <groupId>org.glassfish.jaxb</groupId>
+	    <artifactId>jaxb-core</artifactId>
+	    <version>2.3.0.1</version>
+	</dependency>
+    <dependency>
+	    <groupId>com.sun.xml.bind</groupId>
+ 	   <artifactId>jaxb-impl</artifactId>
+    	<version>2.3.2</version>
+	</dependency>
+	 -->
+	 
+	 <!-- https://mvnrepository.com/artifact/org.jflac/jflac-codec -->
+	<dependency>
+	    <groupId>org.jflac</groupId>
+	    <artifactId>jflac-codec</artifactId>
+	    <version>1.5.2</version>
+	</dependency>
+	
+	<!-- https://mvnrepository.com/artifact/javax.help/javahelp -->
+	<dependency>
+	    <groupId>javax.help</groupId>
+	    <artifactId>javahelp</artifactId>
+	    <version>2.0.05</version>
+	</dependency>
+	
+	<!-- https://mvnrepository.com/artifact/net.java.dev.jna/jna -->
+	<dependency>
+	    <groupId>net.java.dev.jna</groupId>
+	    <artifactId>jna</artifactId>
+	    <version>5.5.0</version>
+	</dependency>
+	
+		<!-- https://mvnrepository.com/artifact/net.java.dev.jna/jna-platform -->
+	<dependency>
+		<groupId>net.java.dev.jna</groupId>
+		<artifactId>jna-platform</artifactId>
+		<version>5.5.0</version>
+	</dependency>
+	
+	<!-- https://mvnrepository.com/artifact/com.jcraft/jsch -->
+	<dependency>
+	    <groupId>com.jcraft</groupId>
+	    <artifactId>jsch</artifactId>
+	    <version>0.1.55</version>
+	</dependency>
+	 
+	<!-- https://mvnrepository.com/artifact/com.fazecast/jSerialComm -->
+	<dependency>
+	    <groupId>com.fazecast</groupId>
+	    <artifactId>jSerialComm</artifactId>
+	    <version>2.5.3</version>
+	</dependency>
+
+	<!-- https://mvnrepository.com/artifact/edu.emory.mathcs/JTransforms -->
+	<dependency>
+	    <groupId>edu.emory.mathcs</groupId>
+	    <artifactId>JTransforms</artifactId>
+	    <version>2.4</version>
+	</dependency>
+
+	<!-- https://mvnrepository.com/artifact/com.sun.mail/javax.mail -->
+	<dependency>
+	    <groupId>com.sun.mail</groupId>
+	    <artifactId>javax.mail</artifactId>
+	    <version>1.6.2</version>
+	</dependency>
+
+	<!-- https://mvnrepository.com/artifact/com.diffplug.matsim/matfilerw -->
+	<dependency>
+	    <groupId>com.diffplug.matsim</groupId>
+	    <artifactId>matfilerw</artifactId>
+	    <version>3.1.1</version>
+	</dependency>
+
+	<!-- https://mvnrepository.com/artifact/com.drewnoakes/metadata-extractor -->
+	<dependency>
+	    <groupId>com.drewnoakes</groupId>
+	    <artifactId>metadata-extractor</artifactId>
+	    <version>2.12.0</version>
+	</dependency>
+
+	<!-- https://mvnrepository.com/artifact/mysql/mysql-connector-java -->
+	<dependency>
+	    <groupId>mysql</groupId>
+	    <artifactId>mysql-connector-java</artifactId>
+	    <version>8.0.18</version>
+	</dependency>
+
+	<!-- https://mvnrepository.com/artifact/com.google.protobuf/protobuf-java -->
+	<!-- this is needed so that tensorflow models run properly (used in Deep Learning plugin) -->
+	<!-- NOTE it is important this is included before edu.ucar.netcdfAll so 
+		that this version is used instead of the internal version - exclusions do 
+		not seem to work otherwise -->
+	<dependency>
+		<groupId>com.google.protobuf</groupId>
+		<artifactId>protobuf-java</artifactId>
+		<version>3.17.0</version>
+	</dependency>
+
+	<!-- https://docs.unidata.ucar.edu/netcdf-java/5.2/userguide/using_netcdf_java_artifacts.html -->
+	<!--  exclusions have been added here to fix problem with Deep Learning plugin - see above -->
+	<dependency>
+	  <groupId>edu.ucar</groupId>
+	  <artifactId>netcdfAll</artifactId>
+	  <version>4.6.14</version>
+	  <exclusions>
+		<exclusion>
+			<groupId>com.google.protobuf</groupId>
+			<artifactId>protobuf-java</artifactId>
+		</exclusion>
+		<exclusion>
+			<groupId>com.google.protobuf</groupId>
+			<artifactId>protobuf-java-util</artifactId>
+		</exclusion>
+	</exclusions>
+	  <scope>compile</scope>
+	</dependency>
+
+	<!-- https://mvnrepository.com/artifact/com.opencsv/opencsv -->
+	<dependency>
+	    <groupId>com.opencsv</groupId>
+	    <artifactId>opencsv</artifactId>
+	    <version>5.0</version>
+	</dependency>
+
+	<!-- https://mvnrepository.com/artifact/org.springframework/org.springframework.core -->
+
+	<!-- https://mvnrepository.com/artifact/org.postgresql/postgresql -->
+	<!-- <dependency>
+	    <groupId>org.postgresql</groupId>
+	    <artifactId>postgresql</artifactId>
+	    <version>42.3.1</version>
+	</dependency>-->
+
+	<!-- https://mvnrepository.com/artifact/org.renjin/renjin-script-engine -->
+	<dependency>
+	    <groupId>org.renjin</groupId>
+	    <artifactId>renjin-script-engine</artifactId>
+	    <version>0.9.2725</version>
+	</dependency>
+	
+	<!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-api
+	this one is only needed to get rid of an annoying warning that shows up during startup -->
+	<dependency>
+	    <groupId>org.slf4j</groupId>
+	    <artifactId>slf4j-api</artifactId>
+	    <version>1.8.0-beta4</version>
+	</dependency>
+ 	 
+	
+	
+	<!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-nop
+	this one is only needed to get rid of an annoying warning that shows up during startup -->
+	<dependency>
+	    <groupId>org.slf4j</groupId>
+	    <artifactId>slf4j-nop</artifactId>
+	    <version>1.8.0-beta4</version>
+	</dependency>
+ 	 
+	
+
+	<!-- https://mvnrepository.com/artifact/org.docx4j/docx4j-JAXB-ReferenceImpl -->
+	<!--  note that we are excluding slf4j-api here, because if we don't then one of the
+	transitive dependencies of docx4j (jcl-over-slf4j) will try to load an older
+	version of slf4j-api, resulting in a weird warning/error that shows up every time that
+	PAMGuard start up -->
+	<!--  DONT BOTHER WITH EXCLUSION, DOESN'T MAKE THE ERROR GO AWAY.  Leaving code here
+	just in case the older version does cause a conflict at some point -->
+	<dependency>
+	    <groupId>org.docx4j</groupId>
+	    <artifactId>docx4j-JAXB-ReferenceImpl</artifactId>
+	    <version>11.1.3</version>
+	    <!-- 
+	    <exclusions>
+	    	<exclusion>
+			    <groupId>org.slf4j</groupId>
+			    <artifactId>slf4j-api</artifactId>
+	    	</exclusion>
+	    </exclusions>
+	     -->
+	</dependency>
+
+	<!-- https://mvnrepository.com/artifact/org.xerial/sqlite-jdbc -->
+	<dependency>
+	    <groupId>org.xerial</groupId>
+	    <artifactId>sqlite-jdbc</artifactId>
+	    <version>3.28.0</version>
+	</dependency>
+
+	<!-- https://mvnrepository.com/artifact/net.sf.ucanaccess/ucanaccess -->
+	<dependency>
+	    <groupId>net.sf.ucanaccess</groupId>
+	    <artifactId>ucanaccess</artifactId>
+	    <version>4.0.4</version>
+	</dependency>
+
+	<!-- https://mvnrepository.com/artifact/nz.ac.waikato.cms.weka/weka-dev -->
+	<dependency>
+	    <groupId>nz.ac.waikato.cms.weka</groupId>
+	    <artifactId>weka-dev</artifactId>
+	    <version>3.7.7</version>
+	</dependency>
+
+	<!-- https://mvnrepository.com/artifact/javax.vecmath/vecmath -->
+	<dependency>
+	    <groupId>javax.vecmath</groupId>
+	    <artifactId>vecmath</artifactId>
+	    <version>1.5.2</version>
+	</dependency>
+
+	<!-- Jave2 (https://github.com/a-schild/jave2) - fork of original jave from sauronsoft.  A LOT bigger; the win64 files alone are > 60Mb compared
+	to 14Mb originally.  Since the old one worked fine, let's stick with it for now and save the space
+	<dependency>
+    	<groupId>ws.schild</groupId>
+	   	<artifactId>jave-core</artifactId>
+   		<version>2.7.1</version>
+	</dependency>
+	<dependency>
+		<groupId>ws.schild</groupId>
+		<artifactId>jave-nativebin-win64</artifactId>
+		<version>2.7.1</version>
+	</dependency>
+	-->
+	
+	<!-- https://mvnrepository.com/artifact/it.sauronsoftware/jave
+	DOESN'T WORK - NOT IN THE ICM REPOSITORY ANYMORE.  STICK WITH ORIG JAR FILE
+	<dependency>
+	    <groupId>it.sauronsoftware</groupId>
+	    <artifactId>jave</artifactId>
+	    <version>1.0.2</version>
+	</dependency>
+	 -->
+	 
+	<!-- not in Maven repository -->
+ 	<dependency>
+	    <groupId>pamguard.org</groupId>
+	    <artifactId>x3</artifactId>
+	    <version>2.0.0</version>
+	</dependency>
+	
+		<!-- https://mvnrepository.com/artifact/it.sauronsoftware/jave -->
+ 	<dependency>
+	    <groupId>it.sauronsoftware</groupId>
+	    <artifactId>jave</artifactId>
+	    <version>1.0.2</version>
+	</dependency>
+	
+	<!-- not in Maven repository -->
+ 	<dependency>
+	    <groupId>com.synthbot</groupId>
+	    <artifactId>jasiohost</artifactId>
+	    <version>1.0.0</version>
+	</dependency>
+
+	<!-- https://mvnrepository.com/artifact/com.fasterxml.jackson.dataformat/jackson-dataformat-xml -->
+	<!-- 
+ 	<dependency>
+ 		<groupId>com.fasterxml.jackson.dataformat</groupId>
+ 		<artifactId>jackson-dataformat-xml</artifactId>
+ 		<version>2.10.1</version>
+ 	</dependency>
+ 	 -->
+ 	 
+ 	<!-- https://mvnrepository.com/artifact/org.springframework/spring-core -->
+	<dependency>
+	    <groupId>org.springframework</groupId>
+	    <artifactId>spring-core</artifactId>
+	    <version>5.2.3.RELEASE</version>
+	</dependency>
+ 	
+ 	<!-- https://mvnrepository.com/artifact/com.1stleg/jnativehook -->
+ 	<!-- For global hotkeys, especially in Logger -->
+	<dependency>
+	    <groupId>com.1stleg</groupId>
+	    <artifactId>jnativehook</artifactId>
+	    <version>2.1.0</version>
+	</dependency>
+	
+	<!-- https://mvnrepository.com/artifact/org.swinglabs.swingx/swingx-all -->
+	<!-- For new Network Receive Module -->
+	<dependency>
+	    <groupId>org.swinglabs.swingx</groupId>
+	    <artifactId>swingx-all</artifactId>
+	    <version>1.6.5-1</version>
+	</dependency>
+	
+ 	
+  </dependencies>
+</project>
\ No newline at end of file

From f03f66782a25079ebc539ca00071aa8b591f16f9 Mon Sep 17 00:00:00 2001
From: douggillespie <dg50@st-andrews.ac.uk>
Date: Mon, 10 Jan 2022 10:24:21 +0000
Subject: [PATCH 4/4] Revert "Added fullstop"

This reverts commit 255c663af12b2339eda05fe3b04522e1c6577fd6.
---
 .classpath                              | 2 +-
 .gitignore                              | 1 -
 pom.xml                                 | 6 +++---
 src/Acquisition/AcquisitionControl.java | 2 +-
 4 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/.classpath b/.classpath
index fe69133f..43cd7cd5 100644
--- a/.classpath
+++ b/.classpath
@@ -6,7 +6,7 @@
 			<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/AdoptOpenJDK 16">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/jdk-16.0.1">
 		<attributes>
 			<attribute name="module" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
diff --git a/.gitignore b/.gitignore
index c836fce5..a1c2a238 100644
--- a/.gitignore
+++ b/.gitignore
@@ -21,4 +21,3 @@
 
 # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
 hs_err_pid*
-/target/
diff --git a/pom.xml b/pom.xml
index 98f428a9..78063ef3 100644
--- a/pom.xml
+++ b/pom.xml
@@ -660,11 +660,11 @@
 	<!-- https://mvnrepository.com/artifact/org.springframework/org.springframework.core -->
 
 	<!-- https://mvnrepository.com/artifact/org.postgresql/postgresql -->
-	<!-- <dependency>
+	<dependency>
 	    <groupId>org.postgresql</groupId>
 	    <artifactId>postgresql</artifactId>
-	    <version>42.3.1</version>
-	</dependency>-->
+	    <version>42.2.24</version>
+	</dependency>
 
 	<!-- https://mvnrepository.com/artifact/org.renjin/renjin-script-engine -->
 	<dependency>
diff --git a/src/Acquisition/AcquisitionControl.java b/src/Acquisition/AcquisitionControl.java
index 8cbce2fe..afe5defe 100644
--- a/src/Acquisition/AcquisitionControl.java
+++ b/src/Acquisition/AcquisitionControl.java
@@ -88,7 +88,7 @@ import PamguardMVC.dataOffline.OfflineDataLoadInfo;
  * NI cards (via UDP), files, directories of files, etc.
  * <p>
  * Uses a plug in architecture to allow new types to be added. This
- * is done through RegisterDaqType().
+ * is done through RegisterDaqType()
  * 
  * @author Doug Gillespie
  *