added post process function for vertex overlap in tree layouts that are used with graphs that are not trees.

Ghidra/Features/GraphServices/src/main/java/ghidra/graph/visualization/LayoutTransitionManager.java

@@ -106,6 +106,8 @@ class LayoutTransitionManager {
 		}
 		if (layoutAlgorithm instanceof TreeLayout) {
 			((TreeLayout<AttributedVertex>) layoutAlgorithm).setRootPredicate(rootPredicate);
+			layoutAlgorithm.setAfter(new PostProcessRunnable<>(
+					visualizationServer.getVisualizationModel().getLayoutModel()));
 		}
 		// remove any previously added layout paintables
 		removePaintable(radialLayoutRings);
@@ -127,7 +129,9 @@ class LayoutTransitionManager {
 		if (layoutAlgorithm instanceof EdgeSorting) {
 			((EdgeSorting<AttributedEdge>) layoutAlgorithm).setEdgeComparator(edgeComparator);
 		}
-		LayoutAlgorithmTransition.apply(visualizationServer, layoutAlgorithm);
+		LayoutAlgorithmTransition.apply(visualizationServer,
+				layoutAlgorithm,
+				new PostProcessRunnable<>(visualizationServer.getVisualizationModel().getLayoutModel()));
 	}
 
 	private void removePaintable(VisualizationServer.Paintable paintable) {
@@ -146,6 +150,9 @@ class LayoutTransitionManager {
 					.setRootPredicate(rootPredicate);
 			((TreeLayout<AttributedVertex>) initialLayoutAlgorithm)
 					.setVertexBoundsFunction(vertexBoundsFunction);
+			initialLayoutAlgorithm.setAfter(new PostProcessRunnable<>(
+					visualizationServer.getVisualizationModel().getLayoutModel()));
+
 		}
 		if (initialLayoutAlgorithm instanceof EdgeSorting) {
 			((EdgeSorting<AttributedEdge>) initialLayoutAlgorithm)

Ghidra/Features/GraphServices/src/main/java/ghidra/graph/visualization/PostProcessRunnable.java

@@ -0,0 +1,80 @@
+/* ###
+ * IP: GHIDRA
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package ghidra.graph.visualization;
+
+import java.util.*;
+
+import org.jgrapht.Graph;
+import org.jungrapht.visualization.layout.model.LayoutModel;
+
+/**
+ * to post-process tree layouts to move vertices that overlap a vertical edge that
+ * is not incident on the vertex.
+ * This can be removed after jungrapht-layout-1.1
+ * @param <V> vertex type
+ * @param <E> edge type
+ */
+public class PostProcessRunnable<V, E> implements Runnable {
+
+	LayoutModel<V> layoutModel;
+
+	public PostProcessRunnable(LayoutModel<V> layoutModel) {
+		this.layoutModel = layoutModel;
+	}
+
+	@Override
+	public void run() {
+		moveVerticesThatOverlapVerticalEdges(layoutModel);
+	}
+
+	protected int moveVerticesThatOverlapVerticalEdges(LayoutModel<V> layoutModel) {
+		int offset = 100;
+		int moved = 0;
+		Graph<V, E> graph = layoutModel.getGraph();
+		Map<Double, Set<E>> verticalEdgeMap = new LinkedHashMap<>();
+		graph.edgeSet()
+				.stream()
+				.filter(e -> layoutModel.apply(graph.getEdgeSource(e)).x == layoutModel
+						.apply(graph.getEdgeTarget(e)).x)
+				.forEach(e -> verticalEdgeMap
+						.computeIfAbsent(layoutModel.apply(graph.getEdgeSource(e)).x,
+							k -> new HashSet<>())
+						.add(e));
+
+		for (V v : graph.vertexSet()) {
+			double x = layoutModel.apply(v).x;
+			for (E edge : verticalEdgeMap.getOrDefault(x, Collections.emptySet())) {
+				V source = graph.getEdgeSource(edge);
+				V target = graph.getEdgeTarget(edge);
+				if (!v.equals(source) && !v.equals(target)) {
+					double lowy = layoutModel.apply(source).y;
+					double hiy = layoutModel.apply(target).y;
+					if (lowy > hiy) {
+						double temp = lowy;
+						lowy = hiy;
+						hiy = temp;
+					}
+					double vy = layoutModel.apply(v).y;
+					if (lowy <= vy && vy <= hiy) {
+						layoutModel.set(v, layoutModel.apply(v).add(offset, 0));
+						moved++;
+					}
+				}
+			}
+		}
+		return moved;
+	}
+}

Ghidra/Features/GraphServices/src/main/resources/jungrapht.properties

@@ -61,7 +61,7 @@ jungrapht.circle.reduceEdgeCrossingMaxEdges=200
 jungrapht.initialDimensionVertexDensity=0.3f
 
 jungrapht.minScale=0.001
-jungrapht.maxScale=1.0
+jungrapht.maxScale=4.0
 
 # not using spatial data structures for vertices at this time. May remove after jungrapht 1.1
 jungrapht.vertexSpatialSupport=NONE