Merge branch 'main' of https://github.com/douggillespie/PAMGuard into main

.classpath

@@ -8,7 +8,6 @@
 	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
 		<attributes>
-			<attribute name="module" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>

README.html

@@ -388,7 +388,10 @@ PamguardBeta_ViewerMode.exe):</p>
 
 <h1><a name="_LATEST_VERSION_2.02.03"></a><a name="_VERSION_2.02.07_January"></a><em><span
 style='font-size:12.0pt;font-family:"Cambria",serif;font-style:normal'><a
-href="#_Latest_Version_2.02.07">LATEST VERSION 2.02.07 January 2023</a></span></em></h1>
+href="#_Latest_Version_2.02.08">LATEST VERSION 2.02.08 May 2023</a></span></em></h1>
+
+<h1><em><span style='font-size:12.0pt;font-family:"Cambria",serif;font-style:
+normal'><a href="#_Latest_Version_2.02.07">Version 2.02.07 January 2023</a></span></em></h1>
 
 <h1><em><span style='font-size:12.0pt;font-family:"Cambria",serif;font-style:
 normal'><a href="#_Latest_Version_2.02.06">Version 2.02.06 November 2022</a></span></em></h1>
@@ -450,14 +453,35 @@ Version 2.00.10 June 2017</a></span></h1>
 <h1><span style='font-size:12.0pt'><a href="#_Older_Versions">Older Versions</a></span></h1>
 
 <h1><a name="_Latest_Version_2.02.03_1"></a><a name="_Latest_Version_2.02.05"></a><a
-name="_Latest_Version_2.02.06"></a><a name="_Latest_Version_2.02.07"></a><span
+name="_Latest_Version_2.02.06"></a><a name="_Latest_Version_2.02.07"></a><a
-lang=EN-US>Latest Version 2.02.07 January 2023</span></h1>
+name="_Latest_Version_2.02.08"></a><span lang=EN-US>Latest Version 2.02.08 May
+2023</span></h1>
 
 <h2><span lang=EN-US>Bug Fixes</span></h2>
 
-<p class=MsoNormal><span lang=EN-US>Use of localization sensor and orientation data
+<p class=MsoNormal><span lang=EN-US>ROCCA Memory Leak: A memory leak in ROCCA,
-for static hydrophones had a bug whereby it would continually ‘forget’ angle
+which mostly occurred when processing large datasets of many offline files, has
-offsets applied to static hydrophones in viewer mode. This is now fixed. </span></p>
+been fixed.</span></p>
+
+<h2><span lang=EN-US>New Features</span></h2>
+
+<p class=MsoNormal><span lang=EN-US>Restart Options: When you restart
+processing of offline files, if output data already exist (binary data of
+within database tables) you will be asked if you want to overwrite the data, cancel,
+or try to continue from where to left off. </span></p>
+
+<p class=MsoNormal><span lang=EN-US>Updated SoundTrap sud file interface so
+that PAMGuard now extracts and stores the Click Detector settings from the sud
+files and stores them within the PAMGuard configuration. This does not affect
+processing, but is important for record keeping. </span></p>
+
+<h1><span lang=EN-US>Version 2.02.07 January 2023</span></h1>
+
+<h2><span lang=EN-US>Bug Fixes</span></h2>
+
+<p class=MsoNormal><span lang=EN-US>Use of localization sensor and orientation
+data for static hydrophones had a bug whereby it would continually ‘forget’
+angle offsets applied to static hydrophones in viewer mode. This is now fixed. </span></p>
 
 <p class=MsoNormal><span lang=EN-US>Click tool bar: Correctly shows event
 selection options even if no species classification options are in place. </span></p>
@@ -467,8 +491,8 @@ selection options even if no species classification options are in place. </span
 mode. Now fixed. </span></p>
 
 <p class=MsoNormal><span lang=EN-US>ROCCA: Fixed (another) memory leak which
-caused PAMGuard to crash when processing large data sets with the ROCCA
+caused PAMGuard to crash when processing large data sets with the ROCCA classifier.
-classifier. </span></p>
+</span></p>
 
 <p class=MsoNormal><span lang=EN-US>Ishmael Modules: Fixed bug which
 occasionally caused crashes when processing many files offline. </span></p>
@@ -1169,8 +1193,8 @@ Bug 441. Plot coordinate calculations incorrect in PamAxis.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>10. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-lang=EN-US> </span>Bug 442. BT Display does not change click symbol color when Colour
+lang=EN-US> </span>Bug 442. BT Display does not change click symbol color when
-By Superdetection is selected.</p>
+Colour By Superdetection is selected.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>11. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
@@ -1194,7 +1218,8 @@ Spectrogram display.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>15. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
-Bug 447. Viewer mode throws exception when trying to load beamformer localisations</p>
+Bug 447. Viewer mode throws exception when trying to load beamformer
+localisations</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>16. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
@@ -1207,8 +1232,8 @@ Bug 449. Rocca Encounter Stats output file calculating incorrect values.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>18. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-lang=EN-US> </span>Bug 450. Ishmael Detectors subscribing to FFTDataBlock twice,
+lang=EN-US> </span>Bug 450. Ishmael Detectors subscribing to FFTDataBlock
-meaning they process each data unit 2x doubling the output.</p>
+twice, meaning they process each data unit 2x doubling the output.</p>
 
 <p class=MsoNormal><b><span lang=EN-US>Upgrades</span></b></p>
 
@@ -1596,9 +1621,9 @@ lang=EN-US> </span>Added decimal degrees option to latitude/longitude dialog.</p
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>2. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-lang=EN-US> </span>Added option in the Click Delay parameters to restrict the number
+lang=EN-US> </span>Added option in the Click Delay parameters to restrict the
-of initial samples used in the calculation. This can be useful for cleaning up
+number of initial samples used in the calculation. This can be useful for
-delays in the presence of echoes and small time delays.</p>
+cleaning up delays in the presence of echoes and small time delays.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>3. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
@@ -1971,8 +1996,8 @@ User is now able to specify Soundtrap date/time format</p>
 <h1><a name="_Latest_Beta_Version_2.00.11"></a><span lang=EN-US>Beta Version
 2.00.11 October 2017</span></h1>
 
-<p class=MsoNormal><span lang=EN-US>PAMGuard Version 2 contains major updates. You
+<p class=MsoNormal><span lang=EN-US>PAMGuard Version 2 contains major updates.
-should read and understand the notes listed for <a
+You should read and understand the notes listed for <a
 href="#_Latest_Beta_Version_2.00.10">Beta Version 2.00.10</a> before proceeding
 with installation and use of this version.</span></p>
 
@@ -2126,8 +2151,8 @@ to colour them by the colour assigned to the group. </span></p>
 
 <h3><span lang=EN-US>Using Old PAMGuard Configurations</span></h3>
 
-<p class=MsoNormal><span lang=EN-US>Old PAMGuard configurations will work with the
+<p class=MsoNormal><span lang=EN-US>Old PAMGuard configurations will work with
-new version. However please note the following:</span></p>
+the new version. However please note the following:</span></p>
 
 <p class=MsoListParagraph style='margin-left:54.0pt;text-indent:-36.0pt'><span
 lang=EN-US>1.</span><span lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -3147,8 +3172,8 @@ correctly calculated in real world coordinates. </p>
 <p class=MsoNormal><i>Wild ArcGIS Interface</i> (Maps and Mapping group)</p>
 
 <p class=MsoNormal>This module, developed by Michael Oswald / SWFSC, allows
-PAMGuard to output data in a format suitable for display in the WILD ArcGIS
+PAMGuard to output data in a format suitable for display in the WILD ArcGIS marine
-marine mammal survey package. See online help for details. </p>
+mammal survey package. See online help for details. </p>
 
 <p class=MsoNormal><i>Alarms</i> (Utilities Group)</p>
 
@@ -3288,8 +3313,8 @@ whistle.</p>
      forms which did not display correctly in 'night' mode. </li>
  <li class=MsoNormal style='margin-bottom:0cm'>Bug fix in simulator. No longer
      stops or fails to start generating sounds. </li>
- <li class=MsoNormal style='margin-bottom:0cm'>Bug in calculated spectrum levels
+ <li class=MsoNormal style='margin-bottom:0cm'>Bug in calculated spectrum
-     if data were decimated (<a
+     levels if data were decimated (<a
      href="http://sourceforge.net/p/pamguard/bugs/187/">http://sourceforge.net/p/pamguard/bugs/187/</a>)
      . Did not affect band level calculations. </li>
  <li class=MsoNormal style='margin-bottom:0cm'>Bug in noise band monitor.
@@ -3373,9 +3398,9 @@ databases.</p>
 <p class=MsoNormal style='margin-left:36.0pt'>National Instruments cards: Added
 code in support of the new x-series devices. </p>
 
-<p class=MsoNormal style='margin-left:36.0pt'>ASIO sound cards: Added support for
+<p class=MsoNormal style='margin-left:36.0pt'>ASIO sound cards: Added support
-a new open source ASIO driver system (jasiohost). The old system has been left
+for a new open source ASIO driver system (jasiohost). The old system has been
-in place for now while we assess users response to the newer system. </p>
+left in place for now while we assess users response to the newer system. </p>
 
 <p class=MsoNormal style='margin-left:36.0pt'><i>AIS</i></p>
 
@@ -3450,14 +3475,14 @@ have implemented database storage for output of these modules. </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Radar Display: A bug which stopped the radar display from correctly
+</span>Radar Display: A bug which stopped the radar display from correctly displaying
-displaying bearings to whistles from arrays containing more than two hydrophone
+bearings to whistles from arrays containing more than two hydrophone elements
-elements has been fixed. </p>
+has been fixed. </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Database Speed: A substantial rewriting of some of the indexing methods in
+</span>Database Speed: A substantial rewriting of some of the indexing methods
-the database module has led to a significant increase in the speed at which
+in the database module has led to a significant increase in the speed at which
 data are written to the database (orders of magnitude for large databases).
 This is having a significant impact on the overall reliability of the software.
 Other changes have increased the speed (again by orders of magnitude) at which
@@ -3564,8 +3589,8 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Bearings can be calculated using the envelope of the waveform rather
+</span>Bearings can be calculated using the envelope of the waveform rather than
-than the full waveform. The waveform or envelope can also be filtered prior to
+the full waveform. The waveform or envelope can also be filtered prior to
 bearing calculation.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
@@ -3698,11 +3723,11 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
 
 <p class=MsoNormal>2. Improved offline viewer functionality. </p>
 
-<p class=MsoNormal>The offline viewer is much improved with better data scrolling
+<p class=MsoNormal>The offline viewer is much improved with better data
-and the ability to view data either stored in the database or the binary
+scrolling and the ability to view data either stored in the database or the
-storage system. Work has stated on functions which read and use data stored in
+binary storage system. Work has stated on functions which read and use data
-audio files. This is currently limited to re-calculating and displaying
+stored in audio files. This is currently limited to re-calculating and
-displaying spectrogram data during viewer mode operation.&nbsp; </p>
+displaying displaying spectrogram data during viewer mode operation.&nbsp; </p>
 
 <p class=MsoNormal>3. Heading sensor readout</p>
 
@@ -3721,8 +3746,8 @@ frequency division (i.e. previous versions would convert well from 96kHz to
 
 <p class=MsoNormal><b>Bug fixes</b></p>
 
-<p class=MsoNormal>1. Placement of axes on some displays (array manager and
+<p class=MsoNormal>1. Placement of axes on some displays (array manager and depth
-depth side panel). Problem in 1.9.01 Beta now fixed. </p>
+side panel). Problem in 1.9.01 Beta now fixed. </p>
 
 <p class=MsoNormal>2. Fixed problems of NMEA read out not restarting after a
 serial drop out. NMEA now restarts correctly. </p>
@@ -3799,12 +3824,12 @@ re-label those channels 0,1,2,3. </p>
 numbering scheme. For instance, if you had a configuration which worked in real
 time using channels 7 and 8 of a sound card, you could not use that same
 configuration to analyse wav files, which would always read their data as
-channels 0 and 1. Similarly if you switched sound cards, you may have to reconfigure
+channels 0 and 1. Similarly if you switched sound cards, you may have to
-every detector and several of the displays to handle the changes in channel
+reconfigure every detector and several of the displays to handle the changes in
-numbering. </p>
+channel numbering. </p>
 
-<p class=MsoNormal>I have spent a considerable amount of time trying to work out
+<p class=MsoNormal>I have spent a considerable amount of time trying to work
-a better system for handling channel numbering in PAMGUARD and have decided
+out a better system for handling channel numbering in PAMGUARD and have decided
 that the only practical thing to do is to force all software channel numbering
 back to a zero indexed system. i.e. even if you read out hardware channels
 3,4,5 and 6, within PAMGUARD, everywhere apart from the Sound acquisition
@@ -3997,10 +4022,10 @@ synchronisation.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Wigner time-frequency plot for the click detector. Clicks are NOT
+</span>Wigner time-frequency plot for the click detector. Clicks are NOT automatically
-automatically displayed in the Winger window as they are for the waveform and
+displayed in the Winger window as they are for the waveform and spectrum
-spectrum windows since the Wigner transformation is very time consuming. Clicks
+windows since the Wigner transformation is very time consuming. Clicks will be
-will be displayed if you select them with the mouse.</p>
+displayed if you select them with the mouse.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -4392,9 +4417,9 @@ a serial port </p>
 
 <p class=MsoNormal>New Likelihood detector. </p>
 
-<p class=MsoNormal>The likelihood detector module is an implementation of a likelihood
+<p class=MsoNormal>The likelihood detector module is an implementation of a
-ratio test with flexible algorithms and configuration to estimate likelihood.
+likelihood ratio test with flexible algorithms and configuration to estimate
-It is </p>
+likelihood. It is </p>
 
 <p class=MsoNormal>suitable for detecting both short duration Odontocete clicks
 (Sperm, Beaked, etc.) as well as moderate duration Mysticete calls (Humpback,
@@ -4676,8 +4701,7 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
 
 <h2>0.5b&nbsp;&nbsp;&nbsp; 31 August 2007 </h2>
 
-<p class=MsoNormal>Requires Java 6 Update 2
+<p class=MsoNormal>Requires Java 6 Update 2 (http://java.com/en/download/manual.jsp)</p>
-(http://java.com/en/download/manual.jsp)</p>
 
 <p class=MsoNormal>Major new features include:</p>
 
@@ -4720,8 +4744,8 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
 <p class=MsoNormal>&nbsp;</p>
 
 <p class=MsoNormal><a name="_Toc312065304"></a><a name="_Toc312063949"></a><span
-class=Heading2Char><span style='font-size:13.0pt'>1.0Beta 22 Jan 2008 -
+class=Heading2Char><span style='font-size:13.0pt'>1.0Beta 22 Jan 2008 - Pamguard
-Pamguard starts two releases, core and beta release</span></span>, </p>
+starts two releases, core and beta release</span></span>, </p>
 
 <p class=MsoNormal>this is the beta release</p>
 
@@ -4739,8 +4763,8 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Multi animal click tracking with least squares fit calculation of
+</span>Multi animal click tracking with least squares fit calculation of position
-position on map</p>
+on map</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

dependency-reduced-pom.xml

@@ -4,7 +4,7 @@
   <groupId>org.pamguard</groupId>
   <artifactId>Pamguard</artifactId>
   <name>Pamguard Java12+</name>
-  <version>2.02.07f</version>
+  <version>2.02.07ab</version>
   <description>Pamguard for Java 12+, using Maven to control dependcies</description>
   <url>www.pamguard.org</url>
   <organization>

pom.xml

@@ -4,7 +4,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.pamguard</groupId>
   <artifactId>Pamguard</artifactId>
-  <version>2.02.07f</version>
+  <version>2.02.07ab</version>
   <name>Pamguard Java12+</name>
   <description>Pamguard for Java 12+, using Maven to control dependcies</description>
 	<url>www.pamguard.org</url>
@@ -801,7 +801,10 @@
 	</dependency>
 	 -->
 
-	<!-- not in Maven repository  -->
+	<!-- not in Maven repository  
+you may need to copy files from your downloaded PAMGuard source code, e.g. C:\Users\*yourreposfolder*\source\repos\PAMGuardPAMGuard\repo\pamguard\org\x3\2.2.2 to 
+C:\Users\*yourusername*\.m2\repository\pamguard\org\x3\2.2.2
+-->
  	<dependency>
 	    <groupId>pamguard.org</groupId>
 	    <artifactId>x3</artifactId>

repo/pamguard/org/x3/2.2.2/_remote.repositories

@@ -0,0 +1,4 @@
+#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
+#Mon May 08 15:05:07 BST 2023
+x3-2.2.2.jar>=
+x3-2.2.2.pom>=

repo/pamguard/org/x3/2.2.2/m2e-lastUpdated.properties

@@ -0,0 +1,15 @@
+#Sat May 06 19:10:45 BST 2023
+bedatadriven|https\://nexus.bedatadriven.com/content/groups/public/|javadoc=1683396645122
+repo|file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardPAMGuard/repo|javadoc=1683137958887
+repo|file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardDG/repo|javadoc=1683137015763
+talan|https\://nexus.talanlabs.com/content/repositories/releases/|sources=1683368185314
+bedatadriven|https\://nexus.bedatadriven.com/content/groups/public/|sources=1683368185314
+unidata-all|https\://artifacts.unidata.ucar.edu/repository/unidata-all/|sources=1683368185314
+repo|file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardTethys/repo|sources=1683368185314
+repo|file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardDG/repo|sources=1683136978098
+repo|file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardPAMGuard/repo|sources=1683137602295
+talan|https\://nexus.talanlabs.com/content/repositories/releases/|javadoc=1683396645122
+central|https\://repo1.maven.org/maven2|sources=1683368185314
+unidata-all|https\://artifacts.unidata.ucar.edu/repository/unidata-all/|javadoc=1683396645122
+repo|file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardTethys/repo|javadoc=1683396645122
+central|https\://repo1.maven.org/maven2|javadoc=1683396645122

repo/pamguard/org/x3/2.2.2/x3-2.2.2-javadoc.jar.lastUpdated

@@ -0,0 +1,16 @@
+#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
+#Sat May 06 19:10:45 BST 2023
+@default-talan-https\://nexus.talanlabs.com/content/repositories/releases/.lastUpdated=1683137015553
+file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardDG/repo/.error=
+https\://repo1.maven.org/maven2/.error=
+file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardPAMGuard/repo/.lastUpdated=1683137958884
+file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardTethys/repo/.lastUpdated=1683396645119
+https\://artifacts.unidata.ucar.edu/repository/unidata-all/.error=
+https\://nexus.bedatadriven.com/content/groups/public/.error=
+file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardTethys/repo/.error=
+https\://artifacts.unidata.ucar.edu/repository/unidata-all/.lastUpdated=1683137015146
+https\://repo1.maven.org/maven2/.lastUpdated=1683137015762
+https\://nexus.talanlabs.com/content/repositories/releases/.error=Could not transfer artifact pamguard.org\:x3\:jar\:javadoc\:2.2.2 from/to talan (https\://nexus.talanlabs.com/content/repositories/releases/)\: Access denied to https\://nexus.talanlabs.com/content/repositories/releases/pamguard/org/x3/2.2.2/x3-2.2.2-javadoc.jar. Error code 401, Unauthorized
+file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardDG/repo/.lastUpdated=1683137014154
+file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardPAMGuard/repo/.error=
+https\://nexus.bedatadriven.com/content/groups/public/.lastUpdated=1683137015343

repo/pamguard/org/x3/2.2.2/x3-2.2.2-sources.jar.lastUpdated

@@ -0,0 +1,16 @@
+#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
+#Sat May 06 11:16:25 BST 2023
+@default-talan-https\://nexus.talanlabs.com/content/repositories/releases/.lastUpdated=1683136977699
+file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardDG/repo/.error=
+https\://repo1.maven.org/maven2/.error=
+file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardPAMGuard/repo/.lastUpdated=1683137602291
+file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardTethys/repo/.lastUpdated=1683368185312
+https\://artifacts.unidata.ucar.edu/repository/unidata-all/.error=
+https\://nexus.bedatadriven.com/content/groups/public/.error=
+file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardTethys/repo/.error=
+https\://artifacts.unidata.ucar.edu/repository/unidata-all/.lastUpdated=1683136976818
+https\://repo1.maven.org/maven2/.lastUpdated=1683136978096
+https\://nexus.talanlabs.com/content/repositories/releases/.error=Could not transfer artifact pamguard.org\:x3\:jar\:sources\:2.2.2 from/to talan (https\://nexus.talanlabs.com/content/repositories/releases/)\: Access denied to https\://nexus.talanlabs.com/content/repositories/releases/pamguard/org/x3/2.2.2/x3-2.2.2-sources.jar. Error code 401, Unauthorized
+file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardDG/repo/.lastUpdated=1683136975590
+file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardPAMGuard/repo/.error=
+https\://nexus.bedatadriven.com/content/groups/public/.lastUpdated=1683136977227

repo/pamguard/org/x3/2.2.2/x3-2.2.2.pom

@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>pamguard.org</groupId>
+  <artifactId>x3</artifactId>
+  <version>2.2.2</version>
+  <description>POM was created from install:install-file</description>
+</project>

repo/pamguard/org/x3/2.2.2/x3-2.2.2.pom.lastUpdated

@@ -0,0 +1,12 @@
+#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
+#Thu May 04 11:43:09 BST 2023
+@default-talan-https\://nexus.talanlabs.com/content/repositories/releases/.lastUpdated=1683196988926
+file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardDG/repo/.error=
+https\://repo1.maven.org/maven2/.error=
+file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardDG/repo/.lastUpdated=1683196987083
+https\://artifacts.unidata.ucar.edu/repository/unidata-all/.error=
+https\://nexus.bedatadriven.com/content/groups/public/.error=
+https\://nexus.bedatadriven.com/content/groups/public/.lastUpdated=1683196988663
+https\://artifacts.unidata.ucar.edu/repository/unidata-all/.lastUpdated=1683196988452
+https\://repo1.maven.org/maven2/.lastUpdated=1683196989198
+https\://nexus.talanlabs.com/content/repositories/releases/.error=Could not transfer artifact pamguard.org\:x3\:pom\:2.2.2 from/to talan (https\://nexus.talanlabs.com/content/repositories/releases/)\: Access denied to https\://nexus.talanlabs.com/content/repositories/releases/pamguard/org/x3/2.2.2/x3-2.2.2.pom. Error code 401, Unauthorized

src/binaryFileStorage/BinaryStoreStatus.java

@@ -110,6 +110,9 @@ public class BinaryStoreStatus extends StoreStatus {
 	 * @param blockStatus
 	 */
 	public void considerBlockStatus(BinaryStoreStatus blockStatus) {
+		if (blockStatus == null) {
+			return;
+		}
 		considerFirstHeader(blockStatus.firstHeader);
 		considerLastFooter(blockStatus.lastFooter);
 		considerLastData(blockStatus.lastData);

src/binaryFileStorage/BinaryStoreStatusFuncs.java

@@ -49,6 +49,9 @@ public class BinaryStoreStatusFuncs {
 				continue;
 			}
 			BinaryStoreStatus blockStatus = getStreamStartEnd(dataSource);
+			if (blockStatus == null) {
+				continue;
+			}
 			binStoreStatus.considerBlockStatus(blockStatus);
 		}
 

src/soundtrap/STClickControl.java

@@ -40,11 +40,14 @@ import Acquisition.AcquisitionControl;
 import PamController.PamSensor;
 import PamController.PamControlledUnitSettings;
 import PamController.PamController;
+import PamController.PamSettingManager;
+import PamController.PamSettings;
 import PamguardMVC.PamRawDataBlock;
 import clickDetector.ClickBTDisplay;
 import clickDetector.ClickControl;
 import clickDetector.ClickDisplay;
 import clickDetector.ClickDisplayManager;
+import clickDetector.ClickParameters;
 import soundtrap.sud.SUDParamsDialog;
 import soundtrap.sud.SudFileDWVHandler;
 
@@ -77,6 +80,8 @@ public class STClickControl extends ClickControl implements PamSensor {
 		
 		sudFileDWVHandler = new SudFileDWVHandler(this);
 		sudFileDWVHandler.subscribeSUD();
+		
+		PamSettingManager.getInstance().registerSettings(new SUDSettings());
 	}
 
 	@Override
@@ -182,23 +187,30 @@ public class STClickControl extends ClickControl implements PamSensor {
 		}
 	}
 
-	@Override
+	// this was a bad idea since we need to keep hold of settings for the 
-	public long getSettingsVersion() {
+	// classifier, which are in with the main set ...
-		return SUDClickDetectorInfo.serialVersionUID;
+//	@Override
-	}
+//	public long getSettingsVersion() {
-
+//		return SUDClickDetectorInfo.serialVersionUID;
-	@Override
+//	}
-	public Serializable getSettingsReference() {
+//
-		return getSudClickDetectorInfo();
+//	@Override
-	}
+//	public Serializable getSettingsReference() {
+//		return getSudClickDetectorInfo();
+//	}
 
 	@Override
 	public boolean restoreSettings(PamControlledUnitSettings pamControlledUnitSettings) {
+		// have to leave this in since I've now run data with it using the ST settings, 
+		// so some configs may return these !
 		Object o = pamControlledUnitSettings.getSettings();
 		if (o instanceof SUDClickDetectorInfo) {
 			sudClickDetectorInfo = (SUDClickDetectorInfo) o;
 			return true;
 		}
+		if (o instanceof ClickParameters) {
+			return super.restoreSettings(pamControlledUnitSettings);
+		}
 		return false;
 	}
 
@@ -230,5 +242,44 @@ public class STClickControl extends ClickControl implements PamSensor {
 		return null;
 	}
 	
+	/**
+	 * Class to handle SoundTrap click detector settings without messing up
+	 * the standard click detector ones which are needed for the classifier. 
+	 * @author dg50
+	 *
+	 */
+	private class SUDSettings implements PamSettings {
+
+		@Override
+		public String getUnitName() {
+			return STClickControl.this.getUnitName();
+		}
+
+		@Override
+		public String getUnitType() {
+			return STUNITTYPE;
+		}
+
+		@Override
+		public Serializable getSettingsReference() {
+			return sudClickDetectorInfo;
+		}
+
+		@Override
+		public long getSettingsVersion() {
+			return SUDClickDetectorInfo.serialVersionUID;
+		}
+
+		@Override
+		public boolean restoreSettings(PamControlledUnitSettings pamControlledUnitSettings) {
+			Object o = pamControlledUnitSettings.getSettings();
+			if (o instanceof SUDClickDetectorInfo) {
+				sudClickDetectorInfo = (SUDClickDetectorInfo) o;
+				return true;
+			}
+			return false;
+		}
+		
+	}
 
 }