work on species mapping

src/PamguardMVC/PamDataBlock.java

@@ -52,6 +52,7 @@ import Acquisition.AcquisitionProcess;
 import pamScrollSystem.ViewLoadObserver;
 import tethys.pamdata.AutoTethysProvider;
 import tethys.pamdata.TethysDataProvider;
+import tethys.species.DataBlockSpeciesManager;
 import dataGram.DatagramProvider;
 import dataMap.BespokeDataMapGraphic;
 import dataMap.OfflineDataMap;
@@ -3103,13 +3104,13 @@ public class PamDataBlock<Tunit extends PamDataUnit> extends PamObservable {
 		this.tethysDataProvider = tethysDataProvider;
 	}
 	
-
 	/**
 	 * Get information about species types that may occur within this data 
-	 * block.  
+	 * block.  Primarily for conversion into Tethys compatible data, but may 
+	 * prove to have other uses. 
 	 * @return Types of species information available within this datablock. 
 	 */
-	public tethys.species.SpeciesTypes getSpeciesTypes() {
+	public DataBlockSpeciesManager<Tunit> getDatablockSpeciesManager() {
 		return null;
 	}
 

src/clickDetector/ClickClassifiers/ClickBlockSpeciesManager.java

@@ -0,0 +1,35 @@
+package clickDetector.ClickClassifiers;
+
+import clickDetector.ClickControl;
+import clickDetector.ClickDataBlock;
+import clickDetector.ClickDetection;
+import tethys.species.DataBlockSpeciesManager;
+import tethys.species.DataBlockSpeciesTypes;
+
+public class ClickBlockSpeciesManager extends DataBlockSpeciesManager<ClickDetection> {
+
+	private ClickControl clickControl;
+	
+	public ClickBlockSpeciesManager(ClickControl clickControl, ClickDataBlock clickDataBlock) {
+		super(clickDataBlock);
+		this.clickControl = clickControl;
+	}
+
+	@Override
+	public DataBlockSpeciesTypes getSpeciesTypes() {
+		ClickTypeMasterManager masterManager = clickControl.getClickTypeMasterManager();
+		if (masterManager == null) {
+			return null;
+		}
+		String[] speciesList = masterManager.getSpeciesList();
+		
+		return new DataBlockSpeciesTypes(speciesList);
+	}
+
+	@Override
+	public String getSpeciesString(ClickDetection dataUnit) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+}

src/clickDetector/ClickDataBlock.java

@@ -3,6 +3,7 @@ package clickDetector;
 import java.util.ListIterator;
 
 import pamScrollSystem.ViewLoadObserver;
+import tethys.species.DataBlockSpeciesManager;
 //import staticLocaliser.StaticLocaliserControl;
 //import staticLocaliser.StaticLocaliserProvider;
 //import staticLocaliser.panels.AbstractLocaliserControl;
@@ -10,6 +11,7 @@ import pamScrollSystem.ViewLoadObserver;
 import alarm.AlarmCounterProvider;
 import alarm.AlarmDataSource;
 import binaryFileStorage.BinaryStore;
+import clickDetector.ClickClassifiers.ClickBlockSpeciesManager;
 import clickDetector.dataSelector.ClickDataSelectCreator;
 import clickDetector.offlineFuncs.OfflineClickLogging;
 import clickDetector.toad.ClickTOADCalculator;
@@ -41,6 +43,8 @@ public class ClickDataBlock extends AcousticDataBlock<ClickDetection>  implement
 	
 	private boolean isViewer;
 	
+	private ClickBlockSpeciesManager clickBlockSpeciesManager;
+	
 	
 	public ClickDataBlock(ClickControl clickControl, PamProcess parentProcess, int channelMap) {
 
@@ -304,5 +308,13 @@ public class ClickDataBlock extends AcousticDataBlock<ClickDetection>  implement
 		}
 	}
 
+	@Override
+	public DataBlockSpeciesManager<ClickDetection> getDatablockSpeciesManager() {
+		if (clickBlockSpeciesManager == null) {
+			clickBlockSpeciesManager = new ClickBlockSpeciesManager(clickControl, this);
+		}
+		return clickBlockSpeciesManager;
+	}
+
 
 }

src/tethys/species/DataBlockSpeciesManager.java

@@ -0,0 +1,58 @@
+package tethys.species;
+
+import PamController.PamController;
+import PamguardMVC.PamDataBlock;
+import PamguardMVC.PamDataUnit;
+import tethys.species.swing.DataBlockSpeciesDialog;
+
+/**
+ * Manage species conversion for a single datablock.
+ * @author dg50
+ *
+ */
+abstract public class DataBlockSpeciesManager<T extends PamDataUnit> {
+	
+	private DataBlockSpeciesMap datablockSpeciesMap;
+	
+	private PamDataBlock<T> dataBlock;
+
+	public abstract DataBlockSpeciesTypes getSpeciesTypes();
+	
+	public abstract String getSpeciesString(T dataUnit);
+
+	public DataBlockSpeciesManager(PamDataBlock<T> dataBlock) {
+		super();
+		this.dataBlock = dataBlock;
+	}
+	
+	public SpeciesMapItem getSpeciesItem(T dataUnit) {
+		String speciesString = getSpeciesString(dataUnit);
+		if (speciesString == null) {
+			return null;
+		}
+		DataBlockSpeciesMap speciesMap = getDatablockSpeciesMap();
+		if (speciesMap == null) {
+			return null;
+		}
+		return speciesMap.getItem(speciesString);
+	}
+	
+	public DataBlockSpeciesMap getDatablockSpeciesMap() {
+		return datablockSpeciesMap;
+	}
+
+	public void setDatablockSpeciesMap(DataBlockSpeciesMap datablockSpeciesMap) {
+		this.datablockSpeciesMap = datablockSpeciesMap;
+	}
+
+	public void showSpeciesDialog() {
+		DataBlockSpeciesDialog.showDialog(PamController.getMainFrame(), dataBlock);
+	}
+
+	/**
+	 * @return the dataBlock
+	 */
+	public PamDataBlock<T> getDataBlock() {
+		return dataBlock;
+	}
+}

src/tethys/species/DataBlockSpeciesMap.java

@@ -0,0 +1,37 @@
+package tethys.species;
+
+import java.io.Serializable;
+import java.util.HashMap;
+
+/**
+ * Species map for a specified data block
+ * @author dg50
+ *
+ */
+public class DataBlockSpeciesMap implements Serializable {
+
+	public static final long serialVersionUID = 1L;
+	
+	private HashMap<String, SpeciesMapItem> speciesTable = new HashMap<>();
+
+	protected HashMap<String, SpeciesMapItem> getSpeciesTable() {
+		return speciesTable;
+	}
+	
+	protected void setSpeciesTable(HashMap<String, SpeciesMapItem> speciesTable) {
+		this.speciesTable = speciesTable;
+	}
+	
+	public void putItem(String key, SpeciesMapItem speciesMapItem) {
+		speciesTable.put(key, speciesMapItem);
+	}
+	
+	public SpeciesMapItem getItem(String key) {
+		return speciesTable.get(key);
+	}
+	
+	public void removeItem(String key) {
+		speciesTable.remove(key);
+	}
+
+}

src/tethys/species/DataBlockSpeciesTypes.java

@@ -0,0 +1,43 @@
+package tethys.species;
+
+import java.util.ArrayList;
+
+/**
+ * Class to return lists of species codes or names for a datablock. 
+ * This information will then get incorporated into a more complicated translation table to 
+ * provide PAMGuard data on it's way to Tethys with more rigid species code definitions.  
+ * @author dg50
+ *
+ */
+public class DataBlockSpeciesTypes {
+
+	/**
+	 * List of species names / codes associated with this data block. 
+	 */
+	private ArrayList<String> speciesNames;
+	
+	/**
+	 * constructor to use with a array of String names. 
+	 * @param speciesList
+	 */
+	public DataBlockSpeciesTypes(String[] speciesList) {
+		if (speciesList == null) {
+			speciesNames = new ArrayList<>();
+		}
+		else {
+			speciesNames = new ArrayList<String>(speciesList.length);
+			for (int i = 0; i < speciesList.length; i++) {
+				speciesNames.add(speciesList[i]);
+			}
+		}
+	}
+
+	/**
+	 * @return the speciesNames
+	 */
+	public ArrayList<String> getSpeciesNames() {
+		return speciesNames;
+	}
+
+	
+}

src/tethys/species/DatablockSpeciesMap.java

@@ -1,12 +0,0 @@
-package tethys.species;
-
-import java.io.Serializable;
-
-/**
- * Species map for a specified data block
- * @author dg50
- *
- */
-public class DatablockSpeciesMap implements Serializable {
-
-}

src/tethys/species/SpeciesMapItem.java

@@ -2,18 +2,101 @@ package tethys.species;
 
 import java.io.Serializable;
 
+/**
+ * Information linking a name within a PAMGuard datablock to a ITIS species code and call type. 
+ * Also contains common and latin names for display purposes, though these are not essential. 
+ * @author dg50
+ *
+ */
 public class SpeciesMapItem implements Serializable, Cloneable {
 
 	public static final long serialVersionUID = 1L;
 
+	/**
+	 * ITIS code. May be a real ITIS code or one of the -ve species that we're defining ourselves. 
+	 */
 	private int itisCode;
 	
+	/**
+	 * Species code that was used within PAMGuard. Redundant information, but useful 
+	 * for bookkeeping. 
+	 */
 	private String pamguardName;
 	
+	/**
+	 * Latin name extracted from ITIS database. Can be null if unknown. 
+	 * Probably not written to Tethys. 
+	 */
 	private String latinName;
 	
+	/**
+	 * Common species name from ITIS database. Can be null if unknown. 
+	 * Probably not written to Tethys. 
+	 */
 	private String commonName;
 	
+	/**
+	 * Type of call. Descriptive name for type of sound, e.g. 'click', 'whistle', 'D-call',
+	 * etc. to complement the itis species code. Will be written to Tethys.  
+	 */
 	private String callType;
 
+	public SpeciesMapItem(int itisCode, String callType, String pamguardName, String latinName, String commonName) {
+		super();
+		this.itisCode = itisCode;
+		this.callType = callType;
+		this.pamguardName = pamguardName;
+		this.latinName = latinName;
+		this.commonName = commonName;
+	}
+
+	public SpeciesMapItem(int itisCode, String callType, String pamguardName) {
+		super();
+		this.itisCode = itisCode;
+		this.callType = callType;
+		this.pamguardName = pamguardName;
+		this.latinName = null;
+		this.commonName = null;
+	}
+
+	/**
+	 * ITIS code. May be a real ITIS code or one of the -ve species that we're defining ourselves. 
+	 * @return the itisCode
+	 */
+	public int getItisCode() {
+		return itisCode;
+	}
+
+	/**
+	 * Species code that was used within PAMGuard. Redundant information, but useful 
+	 * @return the pamguardName
+	 */
+	public String getPamguardName() {
+		return pamguardName;
+	}
+
+	/**
+	 * Latin name extracted from ITIS database. Can be null if unknown. 
+	 * @return the latinName
+	 */
+	public String getLatinName() {
+		return latinName;
+	}
+
+	/**
+	 * Common species name from ITIS database. Can be null if unknown. 
+	 * @return the commonName
+	 */
+	public String getCommonName() {
+		return commonName;
+	}
+
+	/**
+	 * Type of call. Descriptive name for type of sound, e.g. 'click', 'whistle', 'D-call',
+	 * @return the callType
+	 */
+	public String getCallType() {
+		return callType;
+	}
+	
 }

src/tethys/species/SpeciesTest.java

@@ -5,7 +5,7 @@ import dbxml.Queries;
 import tethys.dbxml.DBQueryResult;
 import tethys.dbxml.TethysQueryException;
 
-public class SpeciesTest extends SpeciesTypes {
+public class SpeciesTest {
 
 	String uri = "http://localhost:9779";
 	public static void main(String[] args) {

src/tethys/species/SpeciesTypes.java

@@ -1,20 +0,0 @@
-package tethys.species;
-
-import java.util.ArrayList;
-
-/**
- * Class to return lists of species codes or names for a datablock. 
- * This information will then get incorporated into a more complicated translation table to 
- * provide PAMGuard data on it's way to Tethys with more rigid species code definitions.  
- * @author dg50
- *
- */
-public class SpeciesTypes {
-
-
-	/**
-	 * List of species names / codes associated with this data block. 
-	 */
-	private ArrayList<String> speciesNames;
-	
-}

src/tethys/species/swing/DataBlockSpeciesDialog.java

@@ -0,0 +1,47 @@
+package tethys.species.swing;
+
+import java.awt.Window;
+
+import PamView.dialog.PamDialog;
+import PamguardMVC.PamDataBlock;
+
+public class DataBlockSpeciesDialog extends PamDialog {
+
+	private static final long serialVersionUID = 1L;
+
+	DataBlockSpeciesPanel speciesPanel;
+	
+	private DataBlockSpeciesDialog(Window parentFrame, PamDataBlock dataBlock) {
+		super(parentFrame, dataBlock.getDataName() +  " species", false);
+		speciesPanel = new DataBlockSpeciesPanel(dataBlock);
+		setDialogComponent(speciesPanel.getDialogComponent());
+	}
+	
+	public static void showDialog(Window parentFrame, PamDataBlock dataBlock) {
+		DataBlockSpeciesDialog speciesDialog = new DataBlockSpeciesDialog(parentFrame, dataBlock);
+		speciesDialog.setParams();
+		speciesDialog.setVisible(true);
+	}
+
+	private void setParams() {
+		speciesPanel.setParams();
+	}
+
+	@Override
+	public boolean getParams() {
+		return speciesPanel.getParams();
+	}
+
+	@Override
+	public void cancelButtonPressed() {
+		// TODO Auto-generated method stub
+
+	}
+
+	@Override
+	public void restoreDefaultSettings() {
+		// TODO Auto-generated method stub
+
+	}
+
+}

src/tethys/species/swing/DataBlockSpeciesPanel.java

@@ -0,0 +1,65 @@
+package tethys.species.swing;
+
+import java.awt.BorderLayout;
+import java.util.ArrayList;
+
+import javax.swing.BoxLayout;
+import javax.swing.JComponent;
+import javax.swing.JPanel;
+import javax.swing.border.TitledBorder;
+
+import PamView.dialog.PamDialogPanel;
+import PamguardMVC.PamDataBlock;
+import tethys.species.DataBlockSpeciesManager;
+import tethys.species.DataBlockSpeciesMap;
+import tethys.species.DataBlockSpeciesTypes;
+import tethys.species.SpeciesMapItem;
+
+public class DataBlockSpeciesPanel implements PamDialogPanel {
+	
+	private JPanel mainPanel;
+	
+	private PamDataBlock dataBlock;
+	
+	private JPanel speciesPanel;
+
+	public DataBlockSpeciesPanel(PamDataBlock dataBlock) {
+		super();
+		this.dataBlock = dataBlock;
+		mainPanel = new JPanel(new BorderLayout());
+		speciesPanel = new JPanel();
+		mainPanel.add(speciesPanel, BorderLayout.CENTER);
+		mainPanel.setBorder(new TitledBorder(dataBlock.getDataName()));
+	}
+
+	@Override
+	public JComponent getDialogComponent() {
+		return mainPanel;
+	}
+
+	@Override
+	public void setParams() {
+		speciesPanel.removeAll();
+		speciesPanel.setLayout(new BoxLayout(speciesPanel, BoxLayout.Y_AXIS));
+		
+		DataBlockSpeciesManager speciesManager = dataBlock.getDatablockSpeciesManager();
+		DataBlockSpeciesTypes speciesTypes = speciesManager.getSpeciesTypes();
+		ArrayList<String> speciesNames = speciesTypes.getSpeciesNames();
+		DataBlockSpeciesMap speciesMap = speciesManager.getDatablockSpeciesMap();
+		for (String aSpecies : speciesNames) {
+			SpeciesSubPanel subPanel = new SpeciesSubPanel(aSpecies);
+			speciesPanel.add(subPanel.getDialogComponent());
+			if (speciesMap != null) {
+				SpeciesMapItem speciesInfo = speciesMap.getItem(aSpecies);
+				subPanel.setParams(speciesInfo);
+			}
+		}
+	}
+
+	@Override
+	public boolean getParams() {
+		// TODO Auto-generated method stub
+		return false;
+	}
+
+}

src/tethys/species/swing/SpeciesSubPanel.java

@@ -0,0 +1,95 @@
+package tethys.species.swing;
+
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.border.BevelBorder;
+
+import PamView.dialog.PamGridBagContraints;
+import tethys.species.SpeciesMapItem;
+
+public class SpeciesSubPanel {
+	
+	private JPanel mainPanel;
+	
+	private JLabel pamguardName;
+	private JTextField itisCode, callType, latinName, commonName;
+	private JButton searchButton;
+
+	public SpeciesSubPanel(String aSpecies) {
+		mainPanel = new JPanel(new GridBagLayout());
+		mainPanel.setBorder(new BevelBorder(BevelBorder.RAISED));
+		GridBagConstraints c = new PamGridBagContraints();
+		mainPanel.add(new JLabel("Name ", JLabel.RIGHT), c);
+		c.gridx++;
+		mainPanel.add(pamguardName = new JLabel(aSpecies), c);
+		c.gridx++;
+		mainPanel.add(new JLabel(" ITIS code ", JLabel.RIGHT), c);
+		c.gridx++;
+		mainPanel.add(itisCode = new JTextField(3), c);
+		c.gridx ++;
+		mainPanel.add(searchButton = new JButton("Find"));
+		
+		int w1 = 2;
+		int w2 = 3;
+		c.gridx = 0;
+		c.gridy++;
+		c.gridwidth = w1;
+		mainPanel.add(new JLabel("Call / sound type ", JLabel.RIGHT), c);
+		c.gridx+= c.gridwidth;
+		c.gridwidth = w2;
+		mainPanel.add(callType = new JTextField(15), c);
+		c.gridx = 0;
+		c.gridy++;
+		c.gridwidth = w1;
+		mainPanel.add(new JLabel("Scientific name ", JLabel.RIGHT), c);
+		c.gridx+= c.gridwidth;
+		c.gridwidth = w2;
+		mainPanel.add(latinName = new JTextField(15), c);
+		c.gridx = 0;
+		c.gridy++;
+		c.gridwidth = w1;
+		mainPanel.add(new JLabel("Common name ", JLabel.RIGHT), c);
+		c.gridx+= c.gridwidth;
+		c.gridwidth = w2;
+		mainPanel.add(commonName = new JTextField(15), c);
+		
+		pamguardName.setToolTipText("Internal name within PAMGuard module");
+		itisCode.setToolTipText("ITIS species code");
+		searchButton.setToolTipText("Search for species code");
+		callType.setToolTipText("Descriptive name for call type or measurement");
+		latinName.setToolTipText("Scientific name");
+		commonName.setToolTipText("Common name");
+		
+	}
+
+	public JComponent getDialogComponent() {
+		return mainPanel;
+	}
+
+	public void setParams(SpeciesMapItem speciesMapItem) {
+		if (speciesMapItem == null) {
+			itisCode.setText(null);
+			callType.setText(null);
+			latinName.setText(null);
+			commonName.setText(null);
+			return;
+		}
+		pamguardName.setText(speciesMapItem.getPamguardName());
+		itisCode.setText(String.format("%d", speciesMapItem.getItisCode()));
+		callType.setText(speciesMapItem.getCallType());
+		latinName.setText(speciesMapItem.getLatinName());
+		commonName.setText(speciesMapItem.getCommonName());
+	}
+
+	public SpeciesMapItem getParams() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+}

src/tethys/swing/DatablockSynchPanel.java

@@ -1,6 +1,8 @@
 package tethys.swing;
 
 import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 import java.awt.event.ComponentEvent;
 import java.awt.event.ComponentListener;
 import java.awt.event.KeyAdapter;
@@ -10,7 +12,9 @@ import java.awt.event.MouseEvent;
 import java.util.ArrayList;
 
 import javax.swing.JComponent;
+import javax.swing.JMenuItem;
 import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
 import javax.swing.JScrollPane;
 import javax.swing.JTable;
 import javax.swing.border.TitledBorder;
@@ -25,6 +29,7 @@ import dataMap.OfflineDataMap;
 import tethys.TethysControl;
 import tethys.TethysState;
 import tethys.output.DatablockSynchInfo;
+import tethys.species.DataBlockSpeciesManager;
 
 public class DatablockSynchPanel extends TethysGUIPanel  {
 	
@@ -68,19 +73,61 @@ public class DatablockSynchPanel extends TethysGUIPanel  {
 	private class MouseActions extends MouseAdapter {
 		@Override
 		public void mouseClicked(MouseEvent e) {
-			selectRow();
+			int row = selectRow();
+			if (e.isPopupTrigger() && row >= 0) {
+				showPopup(e, row);
+			}
+		}
+
+		@Override
+		public void mousePressed(MouseEvent e) {
+			int row = selectRow();
+			if (e.isPopupTrigger() && row >= 0) {
+				showPopup(e, row);
+			}
+		}
+
+		@Override
+		public void mouseReleased(MouseEvent e) {
+			int row = selectRow();
+			if (e.isPopupTrigger() && row >= 0) {
+				showPopup(e, row);
+			}
 		}
 		
 	}
 	
-	private void selectRow() {
+	private int selectRow() {
 		int row = synchTable.getSelectedRow();
 		if (row < 0) {
-			return;
+			return row;
 		}
 		DatablockSynchInfo synchInfo = dataBlockSynchInfo.get(row);
 //		datablockDetectionsPanel.setDataBlock(synchInfo.getDataBlock());
 		notifyObservers(synchInfo.getDataBlock());
+		return row;
+	}
+	
+	public void showPopup(MouseEvent e, int row) {
+		DatablockSynchInfo synchInfo = dataBlockSynchInfo.get(row);
+		if (synchInfo == null) {
+			return;
+		}
+		PamDataBlock dataBlock = synchInfo.getDataBlock();
+		DataBlockSpeciesManager speciesManager = dataBlock.getDatablockSpeciesManager();
+		if (speciesManager == null) {
+			return;
+		}
+		JPopupMenu popMenu = new JPopupMenu();
+		JMenuItem menuItem = new JMenuItem("Species info ...");
+		menuItem.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				speciesManager.showSpeciesDialog();
+			}
+		});
+		popMenu.add(menuItem);
+		popMenu.show(e.getComponent(), e.getX(), e.getY());
 	}
 
 	@Override