Better shortcuts to navigate and edit tracking data.

docs/Shortcuts for editing and navigating the main view of TrackMate.md

@@ -0,0 +1,46 @@
+# Shortcuts for editing and navigating the main view of TrackMate.
+
+## The TrackMate tool config panel.
+
+When a TrackMate session is running, the Fiji toolbar displays a new tool specific to TrackMate.
+
+![TrackMate_ConfigTool_01](TrackMate_ConfigTool_01.png)
+
+**This tool must be active for the shortcuts displayed below to work.**
+
+Double-clicking on the tool icon will bring the TrackMate tool config panel:
+
+![TrackMate_ConfigTool_02](TrackMate_ConfigTool_02.png)
+
+## Selection
+
+| Key / Mouse                  | Action                                                       |
+| ---------------------------- | ------------------------------------------------------------ |
+| `click` inside a spot        | Select the spot.                                             |
+| `shift` + `click`            | Add / Remove from selection.                                 |
+| `click` and `drag`           | Draws a freehand ROI. All spots in the current frame inside the ROI are selected. |
+| `shift` + `click` and `drag` | The spots across all frames inside the ROI are selected.     |
+
+## Navigation
+
+| Key / Mouse | Action                                                       |
+| ----------- | ------------------------------------------------------------ |
+| `↓` / `↑`   | When a spot is selected, navigate within a track, forward and backward in time. |
+| `←` / `→`   | Within a track, move across siblings. That is: move to a spot that belongs to the same track within the same frame. For instance: across two daughter cells after a cell division. |
+| `⇟` / `⇞`   | Navigate across tracks.                                      |
+| `f` / `g`   | Change the time-point currently displayed. Move backward / forward in time, by an amount specified in the TrackMate tool config panel. |
+
+## Editing.
+
+All editing commands require the mouse to be placed _inside_ a spot. No need to click.
+
+| Key / Mouse         | Action                                                       |
+| ------------------- | ------------------------------------------------------------ |
+| `a`                 | Add a new spot at the mouse location. <br />If the auto-linking mode is on, the new spot is automatically linked to the spot currently selected, and the new spot becomes selected. |
+| `d`                 | Delete the spot at the mouse location.                       |
+| `q` / `e`           | Change the radius of the spot at the mouse location. Make it smaller / bigger. |
+| `shift` + `q` / `e` | Like above, but with greater amount of changes.              |
+| `l`                 | Toggle a link between two spots in the selection. There must be exactly two spots selected, and they need to be not in the same frame. If a link already exists between the two selected spots, it is removed. |
+| `shift` + `a`       | Start semi-automatic tracking for the spot in the selection. The parameters for semi-automatic tracking can be edited in the TrackMate tool config panel. |
+| `shift` + `l`       | Toggle auto-linking mode on / off.                           |
+

src/main/java/fiji/plugin/trackmate/TrackModel.java

@@ -782,7 +782,9 @@ public SortedDepthFirstIterator< Spot, DefaultWeightedEdge > getSortedDepthFirst
 
 	public TimeDirectedNeighborIndex getDirectedNeighborIndex()
 	{
-		return new TimeDirectedNeighborIndex( graph );
+		final TimeDirectedNeighborIndex index = new TimeDirectedNeighborIndex( graph );
+		graph.addGraphListener( index );
+		return index;
 	}
 
 	/**

src/main/java/fiji/plugin/trackmate/visualization/hyperstack/HyperStackDisplayer.java

@@ -202,7 +202,7 @@ private void registerEditTool()
 		if ( !SpotEditTool.isLaunched() )
 			editTool.run( "" );
 
-		editTool.register( imp, this );
+		editTool.register( this );
 	}
 
 	@Override