Required changes for the OpenGL grapher in the core

src/main/java/org/mastodon/mamut/feature/SpotPositionFeature.java

@@ -55,7 +55,7 @@ public class SpotPositionFeature implements Feature< Spot >
 
 	private final LinkedHashMap< FeatureProjectionKey, FeatureProjection< Spot > > projections;
 
-	private static final List< FeatureProjectionSpec > PROJECTION_SPECS = new ArrayList<>( 3 );
+	public static final List< FeatureProjectionSpec > PROJECTION_SPECS = new ArrayList<>( 3 );
 	static
 	{
 		for ( int d = 0; d < 3; d++ )

src/main/java/org/mastodon/mamut/views/AbstractMamutViewFactory.java

@@ -240,11 +240,6 @@ private static void restoreFramePosition( final Window frame, final Map< String,
 		final int[] pos = ( int[] ) guiState.get( FRAME_POSITION_KEY );
 		if ( null != pos )
 			frame.setBounds( pos[ 0 ], pos[ 1 ], pos[ 2 ], pos[ 3 ] );
-		else
-		{
-			frame.setSize( 650, 400 );
-			frame.setLocationRelativeTo( null );
-		}
 	}
 
 	private static void restoreGroupHandle( final GroupHandle groupHandle, final Map< String, Object > guiState )

src/main/java/org/mastodon/mamut/views/grapher/GrapherInitializer.java

@@ -123,9 +123,8 @@ public class GrapherInitializer< V extends Vertex< E > & HasTimepoint & HasLabel
 		coloringAdapter = new GraphColorGeneratorAdapter<>( viewGraph.getVertexMap(), viewGraph.getEdgeMap() );
 
 		// Options
-		final DataDisplayOptions options = DataDisplayOptions.options()
-				.shareKeyPressedEvents( appModel.getKeyPressedManager() )
-				.style( forwardDefaultStyle )
+		final DataDisplayOptions< DataVertex, DataEdge > options = DataDisplayOptions.options();
+		options.shareKeyPressedEvents( appModel.getKeyPressedManager() ).style( forwardDefaultStyle )
 				.graphColorGenerator( coloringAdapter );
 
 		// Navigation

src/main/java/org/mastodon/mamut/views/table/MamutViewTable.java

@@ -100,6 +100,10 @@ public class MamutViewTable extends MamutView< ViewGraph< Spot, Link, Spot, Link
 		implements HasContextChooser< Spot >, HasColoringModel
 {
 
+	private static final int DEFAULT_WIDTH = 500;
+
+	private static final int DEFAULT_HEIGHT = 300;
+
 	public static String csvExportPath = null;
 
 	private static final String[] CONTEXTS = new String[] { KeyConfigContexts.TABLE };
@@ -163,6 +167,10 @@ protected MamutViewTable( final ProjectModel projectModel, final boolean selecti
 					.navigationHandler( branchGraphNavigation( projectModel, navigationHandler ) )
 					.done()
 				.title( selectionTable ? "Selection table" : "Data table" )
+				.x( -1 )
+				.y( -1 )
+				.width( DEFAULT_WIDTH )
+				.height( DEFAULT_HEIGHT )
 				.get();
 		setFrame( frame );
 		frame.setIconImages( TABLE_VIEW_ICON );

src/main/java/org/mastodon/views/bdv/SharedBigDataViewerData.java

@@ -126,7 +126,9 @@ private SharedBigDataViewerData(
 		this.setups = setups;
 		this.cache = cache;
 
-		final ViewerOptions lvo = new ViewerOptions();
+		final ViewerOptions lvo = new ViewerOptions()
+				.width( 650 )
+				.height( 400 );
 		this.inputTriggerConfig = ( lvo.values.getInputTriggerConfig() != null )
 				? lvo.values.getInputTriggerConfig()
 				: new InputTriggerConfig();

src/main/java/org/mastodon/views/grapher/display/DataDisplayFrame.java

@@ -82,7 +82,7 @@ public DataDisplayFrame(
 			final UndoPointMarker undoPointMarker,
 			final GroupHandle groupHandle,
 			final ContextChooser< V > contextChooser,
-			final DataDisplayOptions optional )
+			final DataDisplayOptions< DataVertex, DataEdge > optional )
 	{
 		super( "Grapher" );
 
@@ -112,7 +112,7 @@ public DataDisplayFrame(
 		 */
 
 		sidePanel = new GrapherSidePanel( nSources, contextChooser );
-		sidePanel.btnPlot.addActionListener( e -> dataDisplayPanel.plot( sidePanel.getGraphConfig(), featureModel ) );
+		sidePanel.getBtnPlot().addActionListener( e -> dataDisplayPanel.plot( sidePanel.getGraphConfig(), featureModel ) );
 
 		final FeatureModelListener featureModelListener = () -> sidePanel.setFeatures(
 				FeatureUtils.collectFeatureMap( featureModel, vertexClass ),
@@ -163,8 +163,14 @@ public void windowClosing( final WindowEvent e )
 		mouseAndKeyHandler.setBehaviourMap( triggerbindings.getConcatenatedBehaviourMap() );
 		mouseAndKeyHandler.setKeypressManager( optional.values.getKeyPressedManager(), dataDisplayPanel.getDisplay() );
 		dataDisplayPanel.getDisplay().addHandler( mouseAndKeyHandler );
-		setLocation( optional.values.getX(), optional.values.getY() );
 		setIconImages( FEATURES_ICON );
+
+		final int x = optional.values.getX();
+		final int y = optional.values.getY();
+		if ( x <= 0 && y <= 0 )
+			setLocationRelativeTo( null );
+		else
+			setLocation( x, y );
 	}
 
 	public DataDisplayPanel< V, E > getDataDisplayPanel()

src/main/java/org/mastodon/views/grapher/display/DataDisplayOptions.java

@@ -30,24 +30,24 @@
 
 import java.awt.event.KeyListener;
 
+import org.mastodon.graph.Edge;
+import org.mastodon.graph.Vertex;
 import org.mastodon.ui.NavigationEtiquette;
 import org.mastodon.ui.coloring.DefaultGraphColorGenerator;
 import org.mastodon.ui.coloring.GraphColorGenerator;
-import org.mastodon.views.grapher.datagraph.DataEdge;
-import org.mastodon.views.grapher.datagraph.DataVertex;
 import org.mastodon.views.grapher.display.DataDisplayOverlay.DataDisplayOverlayFactory;
 import org.mastodon.views.grapher.display.style.DataDisplayStyle;
 import org.mastodon.views.trackscheme.display.TrackSchemeFrame;
 import org.mastodon.views.trackscheme.display.TrackSchemePanel;
 import org.scijava.ui.behaviour.KeyPressedManager;
 
-public class DataDisplayOptions
+public class DataDisplayOptions< V extends Vertex< E >, E extends Edge< V > >
 {
-	public final Values values = new Values();
+	public final Values< V, E > values = new Values<>();
 
-	public static DataDisplayOptions options()
+	public static < V extends Vertex< E >, E extends Edge< V > > DataDisplayOptions< V, E > options()
 	{
-		return new DataDisplayOptions();
+		return new DataDisplayOptions<>();
 	}
 
 	/**
@@ -58,7 +58,7 @@ public static DataDisplayOptions options()
 	 *            the X position.
 	 * @return this instance.
 	 */
-	public DataDisplayOptions x( final int x )
+	public DataDisplayOptions< V, E > x( final int x )
 	{
 		values.x = x;
 		return this;
@@ -72,7 +72,7 @@ public DataDisplayOptions x( final int x )
 	 *            the Y position.
 	 * @return this instance.
 	 */
-	public DataDisplayOptions y( final int y )
+	public DataDisplayOptions< V, E > y( final int y )
 	{
 		values.y = y;
 		return this;
@@ -85,7 +85,7 @@ public DataDisplayOptions y( final int y )
 	 *            the width.
 	 * @return this instance.
 	 */
-	public DataDisplayOptions width( final int w )
+	public DataDisplayOptions< V, E > width( final int w )
 	{
 		values.width = w;
 		return this;
@@ -98,7 +98,7 @@ public DataDisplayOptions width( final int w )
 	 *            the height.
 	 * @return this instance.
 	 */
-	public DataDisplayOptions height( final int h )
+	public DataDisplayOptions< V, E > height( final int h )
 	{
 		values.height = h;
 		return this;
@@ -111,7 +111,7 @@ public DataDisplayOptions height( final int h )
 	 *            the animation time in milliseconds.
 	 * @return this instance.
 	 */
-	public DataDisplayOptions animationDurationMillis( final long ms )
+	public DataDisplayOptions< V, E > animationDurationMillis( final long ms )
 	{
 		values.animationDurationMillis = ms;
 		return this;
@@ -131,7 +131,7 @@ public DataDisplayOptions animationDurationMillis( final long ms )
 	 *            the key-pressed manager.
 	 * @return this instance.
 	 */
-	public DataDisplayOptions shareKeyPressedEvents( final KeyPressedManager manager )
+	public DataDisplayOptions< V, E > shareKeyPressedEvents( final KeyPressedManager manager )
 	{
 		values.keyPressedManager = manager;
 		return this;
@@ -144,7 +144,7 @@ public DataDisplayOptions shareKeyPressedEvents( final KeyPressedManager manager
 	 *            the navigation etiquette.
 	 * @return this instance.
 	 */
-	public DataDisplayOptions navigationEtiquette( final NavigationEtiquette navigationEtiquette )
+	public DataDisplayOptions< V, E > navigationEtiquette( final NavigationEtiquette navigationEtiquette )
 	{
 		values.navigationEtiquette = navigationEtiquette;
 		return this;
@@ -157,7 +157,7 @@ public DataDisplayOptions navigationEtiquette( final NavigationEtiquette navigat
 	 *            the style.
 	 * @return this instance.
 	 */
-	public DataDisplayOptions style( final DataDisplayStyle style )
+	public DataDisplayOptions< V, E > style( final DataDisplayStyle style )
 	{
 		values.style = style;
 		return this;
@@ -170,7 +170,7 @@ public DataDisplayOptions style( final DataDisplayStyle style )
 	 *            the factory.
 	 * @return this instance.
 	 */
-	public DataDisplayOptions dataDisplayOverlayFactory( final DataDisplayOverlayFactory factory )
+	public DataDisplayOptions< V, E > dataDisplayOverlayFactory( final DataDisplayOverlayFactory factory )
 	{
 		values.dataDisplayOverlayFactory = factory;
 		return this;
@@ -184,7 +184,7 @@ public DataDisplayOptions dataDisplayOverlayFactory( final DataDisplayOverlayFac
 	 *            the color generator.
 	 * @return this instance.
 	 */
-	public DataDisplayOptions graphColorGenerator( final GraphColorGenerator< DataVertex, DataEdge > generator )
+	public DataDisplayOptions< V, E > graphColorGenerator( final GraphColorGenerator< V, E > generator )
 	{
 		values.graphColorGenerator = generator;
 		return this;
@@ -193,15 +193,15 @@ public DataDisplayOptions graphColorGenerator( final GraphColorGenerator< DataVe
 	/**
 	 * Read-only {@link DataDisplayOptions} values.
 	 */
-	public static class Values
+	public static class Values< V extends Vertex< E >, E extends Edge< V > >
 	{
 		private int x = 0;
 
 		private int y = 0;
 
-		private int width = 700;
+		private int width = 400;
 
-		private int height = 450;
+		private int height = 400;
 
 		private long animationDurationMillis = 500;
 
@@ -213,13 +213,19 @@ public static class Values
 
 		private DataDisplayOverlayFactory dataDisplayOverlayFactory = new DataDisplayOverlayFactory();
 
-		private GraphColorGenerator< DataVertex, DataEdge > graphColorGenerator = new DefaultGraphColorGenerator<>();
+		private GraphColorGenerator< V, E > graphColorGenerator = new DefaultGraphColorGenerator<>();
 
-		public DataDisplayOptions optionsFromValues()
+		public DataDisplayOptions< V, E > optionsFromValues()
 		{
-			return new DataDisplayOptions().x( x ).y( y ).width( width ).height( height )
-					.animationDurationMillis( animationDurationMillis ).navigationEtiquette( navigationEtiquette )
-					.style( style ).dataDisplayOverlayFactory( dataDisplayOverlayFactory )
+			return new DataDisplayOptions< V, E >()
+					.x( x )
+					.y( y )
+					.width( width )
+					.height( height )
+					.animationDurationMillis( animationDurationMillis )
+					.navigationEtiquette( navigationEtiquette )
+					.style( style )
+					.dataDisplayOverlayFactory( dataDisplayOverlayFactory )
 					.graphColorGenerator( graphColorGenerator );
 		}
 
@@ -268,7 +274,7 @@ public DataDisplayOverlayFactory getDataDisplayOverlayFactory()
 			return dataDisplayOverlayFactory;
 		}
 
-		public GraphColorGenerator< DataVertex, DataEdge > getGraphColorGenerator()
+		public GraphColorGenerator< V, E > getGraphColorGenerator()
 		{
 			return graphColorGenerator;
 		}

src/main/java/org/mastodon/views/grapher/display/DataDisplayOverlay.java

@@ -118,7 +118,7 @@ public DataDisplayOverlay(
 			final FocusModel< DataVertex > focus,
 			final PaintDecorations paintDecorations,
 			final PaintGraph paintGraph,
-			final DataDisplayOptions options )
+			final DataDisplayOptions< DataVertex, DataEdge > options )
 	{
 		this.graph = graph;
 		this.highlight = highlight;
@@ -380,7 +380,7 @@ public DataDisplayOverlay create(
 				final DataGraph< ?, ? > graph,
 				final HighlightModel< DataVertex, DataEdge > highlight,
 				final FocusModel< DataVertex > focus,
-				final DataDisplayOptions options )
+				final DataDisplayOptions< DataVertex, DataEdge > options )
 		{
 			return new DataDisplayOverlay(
 					graph,

src/main/java/org/mastodon/views/grapher/display/DataDisplayPanel.java

@@ -205,14 +205,14 @@ public DataDisplayPanel(
 			final FocusModel< DataVertex > focus,
 			final SelectionModel< DataVertex, DataEdge > selection,
 			final NavigationHandler< DataVertex, DataEdge > navigation,
-			final DataDisplayOptions optional )
+			final DataDisplayOptions< DataVertex, DataEdge > optional )
 	{
 		super( new BorderLayout(), false );
 		this.graph = graph;
 		this.layout = layout;
 		this.selection = selection;
 
-		final Values options = optional.values;
+		final Values< DataVertex, DataEdge > options = optional.values;
 		animationMilleseconds = options.getAnimationDurationMillis();
 
 		/*
@@ -225,6 +225,8 @@ public DataDisplayPanel(
 		screenTransform.listeners().add( this );
 		transformEventHandler = new InertialScreenTransformEventHandler( screenTransform );
 
+		setPreferredSize( new Dimension( w, h ) );
+
 		/*
 		 * Make this instance listen to data graph and UI objects.
 		 */

src/main/java/org/mastodon/views/grapher/display/DataDisplayZoom.java

@@ -32,13 +32,14 @@
 import java.awt.Graphics;
 
 import javax.swing.ImageIcon;
+import javax.swing.JPanel;
 
 import org.mastodon.graph.Edge;
 import org.mastodon.graph.Vertex;
-import org.mastodon.ui.keymap.KeyConfigScopes;
 import org.mastodon.model.HasLabel;
 import org.mastodon.spatial.HasTimepoint;
 import org.mastodon.ui.keymap.KeyConfigContexts;
+import org.mastodon.ui.keymap.KeyConfigScopes;
 import org.mastodon.views.grapher.datagraph.ScreenTransform;
 import org.mastodon.views.grapher.display.OffsetAxes.OffsetAxesListener;
 import org.mastodon.views.trackscheme.display.TrackSchemeZoom;
@@ -65,9 +66,10 @@ public class DataDisplayZoom< V extends Vertex< E > & HasTimepoint & HasLabel, E
 		extends AbstractNamedBehaviour
 		implements DragBehaviour, OffsetAxesListener, TransformListener< ScreenTransform >
 {
-	private static final String TOGGLE_ZOOM = "box zoom";
 
-	private static final String[] TOGGLE_ZOOM_KEYS = new String[] { "Z" };
+	public static final String TOGGLE_ZOOM = "box zoom";
+
+	public static final String[] TOGGLE_ZOOM_KEYS = new String[] { "Z" };
 
 	/*
 	 * Command descriptions for all provided commands
@@ -90,7 +92,7 @@ public void getCommandDescriptions( final CommandDescriptions descriptions )
 	public static < V extends Vertex< E > & HasTimepoint & HasLabel, E extends Edge< V > > void
 			install( final Behaviours behaviours, final DataDisplayPanel< V, E > panel )
 	{
-		final DataDisplayZoom< V, E > zoom = new DataDisplayZoom<>( panel );
+		final DataDisplayZoom< V, E > zoom = new DataDisplayZoom<>( panel, panel.getTransformEventHandler() );
 
 		// Create and register overlay.
 		zoom.transformChanged( panel.getScreenTransform().get() );
@@ -107,7 +109,7 @@ public void getCommandDescriptions( final CommandDescriptions descriptions )
 
 	public static final Color ZOOM_GRAPH_OVERLAY_COLOR = Color.BLUE.darker();
 
-	private final DataDisplayPanel< V, E > panel;
+	private final JPanel panel;
 
 	private final InertialScreenTransformEventHandler transformEventHandler;
 
@@ -119,11 +121,11 @@ public void getCommandDescriptions( final CommandDescriptions descriptions )
 
 	private final ZoomOverlay overlay;
 
-	private DataDisplayZoom( final DataDisplayPanel< V, E > panel )
+	private DataDisplayZoom( final JPanel panel, final InertialScreenTransformEventHandler transformEventHandler )
 	{
 		super( TOGGLE_ZOOM );
 		this.panel = panel;
-		this.transformEventHandler = panel.getTransformEventHandler();
+		this.transformEventHandler = transformEventHandler;
 
 		dragging = false;
 		screenTransform = new ScreenTransform();