CYTOSCAPE-12787 Add support for edge z-order.

presentation-api/src/main/java/org/cytoscape/view/presentation/property/BasicVisualLexicon.java

@@ -446,13 +446,30 @@ public class BasicVisualLexicon extends AbstractVisualLexicon {
 			"EDGE_LABEL_WIDTH", "Edge Label Width", CyEdge.class);
 
 
+	/**
+	 * The strategy to use to render edges when there are more than one edge between a pair of nodes.
+	 * <p><strong>Additional Details: </strong> {@see org.cytoscape.view.presentation.property.EdgeStackingVisualProperty} </p>
+	 */
 	public static final VisualProperty<EdgeStacking> EDGE_STACKING = new EdgeStackingVisualProperty(
 			EdgeStackingVisualProperty.AUTO_BEND, "EDGE_STACKING", "Edge Stacking", CyEdge.class);
 
+	/**
+	 * Controls how tightly packed edges are when there are more than one edge between a pair of nodes.
+	 */
 	public static final VisualProperty<Double> EDGE_STACKING_DENSITY = new DoubleVisualProperty(0.5, // default must be 0.5 for backwards compatibility
 			new ContinuousRange<>(Double.class, 0.0, 1.0, true, true), 
 			"EDGE_STACKING_DENSITY", "Stacking Density", CyEdge.class);
 
+
+	/**
+	 * When rendering edges in 2D, edges with a higher Z-order will be rendered on top of edges with lower Z-order.
+	 * If two edges overlap and have the same Z-order then the order they are rendered in is unpredictable.
+	 * <p><strong>Property Type: </strong> {@see java.lang.Double} </p>
+	 * <p><strong>Property Range:</strong> {@see java.lang.Double#NEGATIVE_INFINITY} &LT;= value &LT;= {@see java.lang.Double#POSITIVE_INFINITY}</p> 
+	 */
+	public static final VisualProperty<Double> EDGE_Z_ORDER = new DoubleVisualProperty(0.0, ARBITRARY_DOUBLE_RANGE,
+			"EDGE_Z_ORDER", "Edge Z Order", true, CyEdge.class);
+
 	// ////// Network VP ////////
 	/**
 	 * The zoom level of the network view.
@@ -629,6 +646,7 @@ protected void addVisualProperties(final VisualProperty<NullDataType> root) {
 		addVisualProperty(EDGE_LABEL_WIDTH, EDGE);
 		addVisualProperty(EDGE_STACKING, EDGE);
 		addVisualProperty(EDGE_STACKING_DENSITY, EDGE);
+		addVisualProperty(EDGE_Z_ORDER, EDGE);
 
 		// Level 3 - 4: Node-related VP
 		addVisualProperty(NODE_FILL_COLOR, NODE_PAINT);

presentation-api/src/test/java/org/cytoscape/view/presentation/BasicVisualLexiconTest.java

@@ -67,7 +67,7 @@ public void testLexiconInstances() {
 
 	@Test
 	public void test2DLexicon() throws Exception {
-		assertEquals(64, richLex.getAllVisualProperties().size());
+		assertEquals(65, richLex.getAllVisualProperties().size());
 	}
 
 	@Test
@@ -93,7 +93,7 @@ public void testGetAllDecendents() throws Exception {
 		assertEquals(26, nodeChildren.size());
 
 		Collection<VisualProperty<?>> edgeChildren = richLex.getAllDescendants(BasicVisualLexicon.EDGE);
-		assertEquals(24, edgeChildren.size());
+		assertEquals(25, edgeChildren.size());
 
 		Collection<VisualProperty<?>> leaf = richLex.getAllDescendants(BasicVisualLexicon.EDGE_LABEL_COLOR);
 		assertEquals(0, leaf.size());

viewmodel-api/src/main/java/org/cytoscape/view/model/CyNetworkViewSnapshot.java

@@ -4,7 +4,7 @@
 
 import org.cytoscape.model.CyEdge;
 import org.cytoscape.model.CyNode;
-import org.cytoscape.view.model.spacial.SpacialIndex2D;
+import org.cytoscape.view.model.spacial.NetworkSpacialIndex2D;
 
 
 /**
@@ -55,11 +55,11 @@ public interface CyNetworkViewSnapshot extends CyNetworkView {
 	CyNetworkView getMutableNetworkView();
 
 	/**
-	 * Returns an immutable SpacialIndex2D object that can be used to query the bounds
+	 * Returns an immutable NetworkSpacialIndex2D object that can be used to query the bounds
 	 * of nodes in the network view, or null if the SpacialIndex has been turned off.
 	 * @see CyNetworkViewFactoryConfig#setEnableSpacialIndex2D(boolean)
 	 */
-	SpacialIndex2D<Long> getSpacialIndex2D();
+	NetworkSpacialIndex2D getSpacialIndex2D();
 
 	/**
 	 * Returns the immutable node View for the given view SUID.

viewmodel-api/src/main/java/org/cytoscape/view/model/spacial/EdgeSpacialIndex2DEnumerator.java

@@ -0,0 +1,17 @@
+package org.cytoscape.view.model.spacial;
+
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.view.model.View;
+
+public interface EdgeSpacialIndex2DEnumerator {
+
+	int size();
+
+	boolean hasNext();
+
+	View<CyEdge> nextEdge();
+
+	View<CyEdge> nextEdgeWithNodeExtents(float[] sourceExtents, float[] targetExtents, View<CyNode>[] nodes);
+
+}

viewmodel-api/src/main/java/org/cytoscape/view/model/spacial/NetworkSpacialIndex2D.java

@@ -0,0 +1,18 @@
+package org.cytoscape.view.model.spacial;
+
+/**
+ * A spacial index used to query for locations of Nodes and Edges in a 2D representation of a network.
+ */
+public interface NetworkSpacialIndex2D extends SpacialIndex2D<Long> {
+
+
+	public NodeSpacialIndex2DEnumerator queryAllNodes();
+
+	public NodeSpacialIndex2DEnumerator queryOverlapNodes(float xMin, float yMin, float xMax, float yMax);
+
+
+	public EdgeSpacialIndex2DEnumerator queryAllEdges();
+
+	public EdgeSpacialIndex2DEnumerator queryOverlapEdges(float xMin, float yMin, float xMax, float yMax);
+
+}

viewmodel-api/src/main/java/org/cytoscape/view/model/spacial/NodeSpacialIndex2DEnumerator.java

@@ -0,0 +1,12 @@
+package org.cytoscape.view.model.spacial;
+
+import org.cytoscape.model.CyNode;
+import org.cytoscape.view.model.View;
+
+public interface NodeSpacialIndex2DEnumerator extends SpacialIndex2DEnumerator<Long> {
+
+	public View<CyNode> nextNode();
+
+	public View<CyNode> nextNodeExtents(float[] extents);
+
+}