Add edge iteration support in quadtree

Author: mbastian

src/main/java/org/gephi/graph/api/SpatialIndex.java

@@ -49,6 +49,17 @@ public interface SpatialIndex {
      */
     EdgeIterable getEdgesInArea(Rect2D rect);
 
+    /**
+     * Returns the edges in the given area using a faster, but approximate method.
+     * <p>
+     * All edges in the provided area are guaranteed to be returned, but some edges
+     * outside the area may also be returned.
+     *
+     * @param rect area to query
+     * @return edges in the area
+     */
+    EdgeIterable getApproximateEdgesInArea(Rect2D rect);
+
     /**
      * Returns the bounding rectangle that contains all nodes in the graph. The
      * boundaries are calculated based on each node's position and size.

src/main/java/org/gephi/graph/impl/EdgeStore.java

@@ -807,6 +807,10 @@ public boolean add(final Edge e) {
                 undirectedSize++;
             }
 
+            if (spatialIndex != null) {
+                spatialIndex.addEdge(edge);
+            }
+
             size++;
             typeSize[type]++;
             return true;
@@ -832,6 +836,10 @@ public boolean remove(final Object o) {
                 viewStore.removeEdge(edge);
             }
 
+            if (spatialIndex != null) {
+                spatialIndex.removeEdge(edge);
+            }
+
             edge.destroyAttributes();
 
             int storeIndex = id / GraphStoreConfiguration.EDGESTORE_BLOCK_SIZE;

src/main/java/org/gephi/graph/impl/GraphViewDecorator.java

@@ -299,7 +299,7 @@ public boolean contains(Node node) {
         checkValidNodeObject(node);
         graphStore.autoReadLock();
         try {
-            return view.containsNode((NodeImpl) node);
+            return view.containsNode(node);
         } finally {
             graphStore.autoReadUnlock();
         }
@@ -812,15 +812,15 @@ void checkValidNodeObject(final Node n) {
         if (!(n instanceof NodeImpl)) {
             throw new ClassCastException("Object must be a NodeImpl object");
         }
-        if (((NodeImpl) n).storeId == NodeStore.NULL_ID) {
+        if (n.getStoreId() == NodeStore.NULL_ID) {
             throw new IllegalArgumentException("Node should belong to a store");
         }
     }
 
     void checkValidInViewNodeObject(final Node n) {
         checkValidNodeObject(n);
 
-        if (!view.containsNode((NodeImpl) n)) {
+        if (!view.containsNode(n)) {
             throw new RuntimeException("Node doesn't belong to this view");
         }
     }
@@ -832,15 +832,15 @@ void checkValidEdgeObject(final Edge n) {
         if (!(n instanceof EdgeImpl)) {
             throw new ClassCastException("Object must be a EdgeImpl object");
         }
-        if (((EdgeImpl) n).storeId == EdgeStore.NULL_ID) {
+        if (n.getStoreId() == EdgeStore.NULL_ID) {
             throw new IllegalArgumentException("Edge should belong to a store");
         }
     }
 
     void checkValidInViewEdgeObject(final Edge e) {
         checkValidEdgeObject(e);
 
-        if (!view.containsEdge((EdgeImpl) e)) {
+        if (!view.containsEdge(e)) {
             throw new RuntimeException("Edge doesn't belong to this view");
         }
     }
@@ -871,69 +871,39 @@ public NodeIterable getNodesInArea(Rect2D rect) {
         if (graphStore.spatialIndex == null) {
             throw new UnsupportedOperationException("Spatial index is disabled (from Configuration)");
         }
-        return new NodeIterableWrapper(
-                () -> new NodeViewIterator(graphStore.spatialIndex.getNodesInArea(rect).iterator()),
-                graphStore.spatialIndex.nodesTree.lock);
+        return graphStore.spatialIndex.getNodesInArea(rect, view::containsNode);
     }
 
     @Override
     public NodeIterable getApproximateNodesInArea(Rect2D rect) {
         if (graphStore.spatialIndex == null) {
             throw new UnsupportedOperationException("Spatial index is disabled (from Configuration)");
         }
-        return new NodeIterableWrapper(
-                () -> new NodeViewIterator(graphStore.spatialIndex.getApproximateNodesInArea(rect).iterator()),
-                graphStore.spatialIndex.nodesTree.lock);
+        return graphStore.spatialIndex.getApproximateNodesInArea(rect, view::containsNode);
     }
 
     @Override
     public EdgeIterable getEdgesInArea(Rect2D rect) {
         if (graphStore.spatialIndex == null) {
             throw new UnsupportedOperationException("Spatial index is disabled (from Configuration)");
         }
-        return new EdgeIterableWrapper(
-                () -> new EdgeViewIterator(graphStore.spatialIndex.getEdgesInArea(rect).iterator()),
-                graphStore.spatialIndex.nodesTree.lock);
+        return graphStore.spatialIndex.getEdgesInArea(rect, view::containsEdge);
     }
 
     @Override
-    public Rect2D getBoundaries() {
-        graphStore.autoReadLock();
-        try {
-            float minX = Float.POSITIVE_INFINITY;
-            float minY = Float.POSITIVE_INFINITY;
-            float maxX = Float.NEGATIVE_INFINITY;
-            float maxY = Float.NEGATIVE_INFINITY;
-
-            boolean hasNodes = false;
-
-            // Iterate only through nodes visible in this view
-            for (Node node : getNodes()) {
-                hasNodes = true;
-                final float x = node.x();
-                final float y = node.y();
-                final float size = node.size();
-
-                final float nodeMinX = x - size;
-                final float nodeMinY = y - size;
-                final float nodeMaxX = x + size;
-                final float nodeMaxY = y + size;
-
-                if (nodeMinX < minX)
-                    minX = nodeMinX;
-                if (nodeMinY < minY)
-                    minY = nodeMinY;
-                if (nodeMaxX > maxX)
-                    maxX = nodeMaxX;
-                if (nodeMaxY > maxY)
-                    maxY = nodeMaxY;
-            }
+    public EdgeIterable getApproximateEdgesInArea(Rect2D rect) {
+        if (graphStore.spatialIndex == null) {
+            throw new UnsupportedOperationException("Spatial index is disabled (from Configuration)");
+        }
+        return graphStore.spatialIndex.getApproximateEdgesInArea(rect, view::containsEdge);
+    }
 
-            return hasNodes ? new Rect2D(minX, minY, maxX, maxY) : new Rect2D(Float.NEGATIVE_INFINITY,
-                    Float.NEGATIVE_INFINITY, Float.POSITIVE_INFINITY, Float.POSITIVE_INFINITY);
-        } finally {
-            graphStore.autoReadUnlock();
+    @Override
+    public Rect2D getBoundaries() {
+        if (graphStore.spatialIndex == null) {
+            throw new UnsupportedOperationException("Spatial index is disabled (from Configuration)");
         }
+        return graphStore.spatialIndex.getBoundaries(view::containsNode);
     }
 
     private final class NodeViewSpliterator implements Spliterator<Node> {

src/main/java/org/gephi/graph/impl/GraphViewImpl.java

@@ -462,15 +462,15 @@ public void fill() {
         }
     }
 
-    public boolean containsNode(final NodeImpl node) {
+    public boolean containsNode(final Node node) {
         if (!nodeView) {
             return true;
         }
-        return nodeBitVector.get(node.storeId);
+        return nodeBitVector.get(node.getStoreId());
     }
 
-    public boolean containsEdge(final EdgeImpl edge) {
-        return edgeBitVector.get(edge.storeId);
+    public boolean containsEdge(final Edge edge) {
+        return edgeBitVector.get(edge.getStoreId());
     }
 
     public void intersection(final GraphViewImpl otherView) {
@@ -915,7 +915,7 @@ private void checkValidNodeObject(final Node n) {
         if (!(n instanceof NodeImpl)) {
             throw new ClassCastException("Object must be a NodeImpl object");
         }
-        if (((NodeImpl) n).storeId == NodeStore.NULL_ID) {
+        if (n.getStoreId() == NodeStore.NULL_ID) {
             throw new IllegalArgumentException("Node should belong to a store");
         }
     }