Add javadoc

src/main/java/org/mastodon/mamut/tomancak/resolve/CreateConflictTagSet.java

@@ -34,8 +34,26 @@
 import gnu.trove.set.TIntSet;
 import gnu.trove.set.hash.TIntHashSet;
 
+/**
+ * Class that holds the code for creating a conflict tag set. Uses
+ * {@link HellingerDistance} to figure out which spots overlap
+ * significantly.
+ */
 public class CreateConflictTagSet
 {
+	/**
+	 * Add a new tag set to the model, with all conflicts between spots tagged.
+	 * A conflict is defined as two spots whose Hellinger distance is less than the
+	 * threshold.
+	 *
+	 * @param model      the model that contains the spot graph and to which the tag set
+	 *                   will be added.
+	 * @param tagSetName the name of the tag set to be created.
+	 * @param threshold  the Hellinger distance threshold. Two spot are considered in
+	 *                   conflict if their Hellinger distance is less than or equal to
+	 *                   this value.
+	 * @return the tag set that was created.
+	 */
 	public static TagSetStructure.TagSet run( final Model model, final String tagSetName, final double threshold )
 	{
 		final ModelGraph graph = model.getGraph();

src/main/java/org/mastodon/mamut/tomancak/resolve/CreateConflictTagSetCommand.java

@@ -9,6 +9,9 @@
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 
+/**
+ * The GUI command to create a conflict tag set.
+ */
 @Plugin( type = Command.class, name = "Create Conflict Tag Set" )
 public class CreateConflictTagSetCommand extends DefaultCancelable implements Command
 {

src/main/java/org/mastodon/mamut/tomancak/resolve/FuseSpotSelectionException.java

@@ -1,5 +1,15 @@
 package org.mastodon.mamut.tomancak.resolve;
 
+import java.util.Collection;
+
+import org.mastodon.mamut.model.Model;
+import org.mastodon.mamut.model.Spot;
+
+/**
+ * Exception that is thrown by {@link FuseSpots#run(Model, Collection, Spot)} whenever
+ * the set of spots don't fulfill the very specific requirements of the algorithm. The
+ * exception is meant to be caught and communicated to the user.
+ */
 public class FuseSpotSelectionException extends RuntimeException
 {
 	public FuseSpotSelectionException()

src/main/java/org/mastodon/mamut/tomancak/resolve/FuseSpots.java

@@ -22,9 +22,23 @@
 import org.mastodon.model.tag.TagSetModel;
 import org.mastodon.model.tag.TagSetStructure;
 
+/**
+ * Code for fusing spots in a {@link ProjectModel}.
+ */
 public class FuseSpots
 {
 
+	/**
+	 * Run the "fuse spots" operation on the specified {@link ProjectModel}.
+	 * <br>
+	 * The currently selected spots are fused into a single track. For
+	 * each timepoint, the position and covariance of the selected spots
+	 * are averaged. And assigned to a fused spot.
+	 * <br>
+	 * This method is meant to be called from the GUI. It takes care of
+	 * setting locks, undo points, and notifying listeners. Message dialogs
+	 * are shown in case of errors.
+	 */
 	public static void run( final ProjectModel projectModel ) {
 		final Model model = projectModel.getModel();
 		final ModelGraph graph = projectModel.getModel().getGraph();
@@ -63,6 +77,19 @@ public static void run( final ProjectModel projectModel ) {
 		}
 	}
 
+	/**
+	 * Fuse the specified spots into a single track.
+	 * <p>
+	 * This method is independent of the GUI and can be used in other contexts.
+	 * @param model the model to operate on. The graph is modified, some spots and links
+	 *              are removed. New edges are added, and the tags of the new edges are
+	 *              set.
+	 * @param spots the set of spots to fuse.
+	 * @param focus this selected spots that are connected to this spot are kept. Their
+	 *              position and covariance are updated.
+	 *
+	 * @see #run(ProjectModel)
+	 */
 	public static void run( final Model model, final Collection< Spot > spots, final Spot focus )
 	{
 		final ModelGraph graph = model.getGraph();

src/main/java/org/mastodon/mamut/tomancak/resolve/HellingerDistance.java

@@ -4,8 +4,19 @@
 
 import org.mastodon.mamut.model.Spot;
 
+/**
+ * Compute the Hellinger distance.
+ */
 public class HellingerDistance
 {
+	/**
+	 * @return The Hellinger distance of the two gaussian distributions associated
+	 * with the two specified spots. The distance is in [0,1], where 0 means the
+	 * two spots are identical, and 1 means they are completely different.
+	 * <br>
+	 * The Hellinger distance can be used as an indicator of roughly how much two
+	 * spots overlap.
+	 */
 	public static double hellingerDistance( final Spot a, final Spot b )
 	{
 		return hellingerDistance( a.positionAsDoubleArray(), covariance( a ), b.positionAsDoubleArray(), covariance( b ) );

src/main/java/org/mastodon/mamut/tomancak/resolve/LocateTagsFrame.java

@@ -55,6 +55,14 @@
 import org.mastodon.model.tag.TagSetModel;
 import org.mastodon.model.tag.TagSetStructure;
 
+/**
+ * Shows a window with a list of locations where the tags of a given tag set are
+ * found in the tracking data. The user can select a location in the list and
+ * the linked views will navigate to the corresponding spot.
+ * <br>
+ * Additionally, the selection of locations in the list will be reflected in the
+ * selection of spots. And tags can be removed from the selected spots.
+ */
 public class LocateTagsFrame extends JFrame
 {
 

src/main/java/org/mastodon/mamut/tomancak/resolve/RemoveTagComponents.java

@@ -14,8 +14,16 @@
 import org.mastodon.model.tag.TagSetModel;
 import org.mastodon.model.tag.TagSetStructure;
 
+/**
+ * Class for removing a "connected component of tags" from a model.
+ */
 public class RemoveTagComponents
 {
+	/**
+	 * For the given tag set remove the tag from the given spots and all the
+	 * spots that are connected to them by edges and have the same tag. The
+	 * tag for connected edges is also removed.
+	 */
 	public static void run( final ProjectModel projectModel, final TagSetStructure.TagSet tagSet, final Collection< Spot > spots )
 	{
 		final Model model = projectModel.getModel();

src/main/java/org/mastodon/mamut/tomancak/util/Glasbey.java

@@ -40,11 +40,11 @@ public class Glasbey
 
 	/**
 	 * Returns a color supplier for light Glasbey colors.
-	 * <p>
+	 * <br>
 	 * Each call to {@link IntSupplier#getAsInt()} returns the next color from the table.
 	 * The table contains 256 different colors, which are repeated if the supplier is
 	 * called more than 256 times. The colors are meant to be distinguishable from each
-	 * other. All colors are light colors, they have gut contrast to black background
+	 * other. All colors are light colors, they have good contrast to black background
 	 * or text.
 	 */
 	public static IntSupplier getGlasbeyLightColorSupplier()