Add a copy method to the detector and tracker factory.

This will break the external detectors we added in v7, so they will
need an update too.
This is required to properly copy a Settings object without any
undesirable side effect. All in all, the issue we are trying to address
is a design fault done early in TrackMate, where we allowed a tracker
and a detector factory to have instance fields.... What a mistake...

src/main/java/fiji/plugin/trackmate/detection/DogDetectorFactory.java

@@ -25,10 +25,6 @@
 import static fiji.plugin.trackmate.detection.DetectorKeys.KEY_DO_SUBPIXEL_LOCALIZATION;
 import static fiji.plugin.trackmate.detection.DetectorKeys.KEY_RADIUS;
 import static fiji.plugin.trackmate.detection.DetectorKeys.KEY_THRESHOLD;
-import net.imglib2.Interval;
-import net.imglib2.RandomAccessible;
-import net.imglib2.type.NativeType;
-import net.imglib2.type.numeric.RealType;
 
 import org.scijava.plugin.Plugin;
 
@@ -37,6 +33,10 @@
 import fiji.plugin.trackmate.gui.components.ConfigurationPanel;
 import fiji.plugin.trackmate.gui.components.detector.DogDetectorConfigurationPanel;
 import fiji.plugin.trackmate.util.TMUtils;
+import net.imglib2.Interval;
+import net.imglib2.RandomAccessible;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
 
 @Plugin( type = SpotDetectorFactory.class )
 public class DogDetectorFactory< T extends RealType< T > & NativeType< T >> extends LogDetectorFactory< T >
@@ -98,4 +98,9 @@ public ConfigurationPanel getDetectorConfigurationPanel( final Settings lSetting
 		return new DogDetectorConfigurationPanel( lSettings, model, DogDetectorFactory.THIS_INFO_TEXT, DogDetectorFactory.THIS_NAME );
 	}
 
+	@Override
+	public DogDetectorFactory< T > copy()
+	{
+		return new DogDetectorFactory<>();
+	}
 }

src/main/java/fiji/plugin/trackmate/detection/LabeImageDetectorFactory.java

@@ -215,4 +215,10 @@ public ImageIcon getIcon()
 	{
 		return null;
 	}
+
+	@Override
+	public LabeImageDetectorFactory< T > copy()
+	{
+		return new LabeImageDetectorFactory<>();
+	}
 }

src/main/java/fiji/plugin/trackmate/detection/LogDetectorFactory.java

@@ -264,4 +264,9 @@ public ImageIcon getIcon()
 		return null;
 	}
 
+	@Override
+	public LogDetectorFactory< T > copy()
+	{
+		return new LogDetectorFactory< >();
+	}
 }

src/main/java/fiji/plugin/trackmate/detection/ManualDetectorFactory.java

@@ -205,4 +205,10 @@ public ImageIcon getIcon()
 	{
 		return null;
 	}
+
+	@Override
+	public ManualDetectorFactory< T > copy()
+	{
+		return new ManualDetectorFactory<>();
+	}
 }

src/main/java/fiji/plugin/trackmate/detection/MaskDetectorFactory.java

@@ -187,4 +187,10 @@ public ImageIcon getIcon()
 	{
 		return null;
 	}
+
+	@Override
+	public MaskDetectorFactory< T > copy()
+	{
+		return new MaskDetectorFactory<>();
+	}
 }

src/main/java/fiji/plugin/trackmate/detection/SpotDetectorFactoryBase.java

@@ -143,4 +143,11 @@ public default boolean has2Dsegmentation()
 	{
 		return false;
 	}
+
+	/**
+	 * Returns a copy the current instance.
+	 * 
+	 * @return a new instance of this detector factory.
+	 */
+	public SpotDetectorFactoryBase< T > copy();
 }

src/main/java/fiji/plugin/trackmate/detection/ThresholdDetectorFactory.java

@@ -226,4 +226,10 @@ public ImageIcon getIcon()
 	{
 		return null;
 	}
+
+	@Override
+	public ThresholdDetectorFactory< T > copy()
+	{
+		return new ThresholdDetectorFactory<>();
+	}
 }

src/main/java/fiji/plugin/trackmate/tracking/ManualTrackerFactory.java

@@ -21,10 +21,6 @@
  */
 package fiji.plugin.trackmate.tracking;
 
-import fiji.plugin.trackmate.Model;
-import fiji.plugin.trackmate.SpotCollection;
-import fiji.plugin.trackmate.gui.components.ConfigurationPanel;
-
 import java.util.Map;
 
 import javax.swing.ImageIcon;
@@ -33,6 +29,10 @@
 import org.scijava.Priority;
 import org.scijava.plugin.Plugin;
 
+import fiji.plugin.trackmate.Model;
+import fiji.plugin.trackmate.SpotCollection;
+import fiji.plugin.trackmate.gui.components.ConfigurationPanel;
+
 @Plugin( type = SpotTrackerFactory.class, priority = Priority.HIGH )
 public class ManualTrackerFactory implements SpotTrackerFactory
 {
@@ -117,4 +117,9 @@ public String getErrorMessage()
 		return errorMessage;
 	}
 
+	@Override
+	public ManualTrackerFactory copy()
+	{
+		return new ManualTrackerFactory();
+	}
 }

src/main/java/fiji/plugin/trackmate/tracking/SpotTrackerFactory.java

@@ -124,4 +124,11 @@ public interface SpotTrackerFactory extends TrackMateModule
 	 * @see #checkSettingsValidity(Map)
 	 */
 	public String getErrorMessage();
+
+	/**
+	 * Returns a copy the current instance.
+	 * 
+	 * @return a new instance of this tracker factory.
+	 */
+	public SpotTrackerFactory copy();
 }

src/main/java/fiji/plugin/trackmate/tracking/kalman/KalmanTrackerFactory.java

@@ -207,4 +207,10 @@ public String getErrorMessage()
 	{
 		return errorMessage;
 	}
+
+	@Override
+	public KalmanTrackerFactory copy()
+	{
+		return new KalmanTrackerFactory();
+	}
 }

src/main/java/fiji/plugin/trackmate/tracking/kdtree/NearestNeighborTrackerFactory.java

@@ -157,4 +157,10 @@ public String getErrorMessage()
 	{
 		return errorMessage;
 	}
+
+	@Override
+	public NearestNeighborTrackerFactory copy()
+	{
+		return new NearestNeighborTrackerFactory();
+	}
 }

src/main/java/fiji/plugin/trackmate/tracking/overlap/OverlapTrackerFactory.java

@@ -251,4 +251,10 @@ public String getErrorMessage()
 	{
 		return errorMessage;
 	}
+
+	@Override
+	public OverlapTrackerFactory copy()
+	{
+		return new OverlapTrackerFactory();
+	}
 }

src/main/java/fiji/plugin/trackmate/tracking/sparselap/SimpleSparseLAPTrackerFactory.java

@@ -67,4 +67,9 @@ public ConfigurationPanel getTrackerConfigurationPanel( final Model model )
 		return new SimpleLAPTrackerSettingsPanel( getName(), THIS2_INFO_TEXT, spaceUnits );
 	}
 
+	@Override
+	public SimpleSparseLAPTrackerFactory copy()
+	{
+		return new SimpleSparseLAPTrackerFactory();
+	}
 }

src/main/java/fiji/plugin/trackmate/tracking/sparselap/SparseLAPTrackerFactory.java

@@ -88,4 +88,9 @@ public SpotTracker create( final SpotCollection spots, final Map< String, Object
 		return new SparseLAPTracker( spots, settings );
 	}
 
+	@Override
+	public SparseLAPTrackerFactory copy()
+	{
+		return new SparseLAPTrackerFactory();
+	}
 }