Author: paperwing
Date: 2011-07-21 06:47:46 -0700 (Thu, 21 Jul 2011)
New Revision: 26231
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/Graphics.java
Log:
updated layout implementation
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/Graphics.java
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/Graphics.java
2011-07-21 13:40:21 UTC (rev 26230)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/Graphics.java
2011-07-21 13:47:46 UTC (rev 26231)
@@ -1653,156 +1653,222 @@
public void generalLayout() {
- // Find the central node
- // ---------------------
+ LinkedHashSet<CyNode> totalNodesToVisit = new
LinkedHashSet<CyNode>();
+ totalNodesToVisit.addAll(networkView.getModel().getNodeList());
- // Approach: Use node with most edges
+ Vector3 currentCentralLocation = new Vector3();
+ Vector3 nextCentralLocation = new Vector3();
- HashSet<CyNode> plantedNodes = new HashSet<CyNode>();
+ double greatestDistanceSquared = -1;
- CyNetwork network = networkView.getModel();
+ // System.out.println("Initial total: " +
totalNodesToVisit.size());
- CyNode centerNode = null;
- int highestNeighborCount = -1;
- int neighbourCount;
- for (CyNode node : network.getNodeList()) {
- neighbourCount = network.getNeighborList(node,
Type.ANY).size();
+ do {
- if (centerNode == null) {
- centerNode = node;
- highestNeighborCount = neighbourCount;
- } else {
- if (neighbourCount > highestNeighborCount) {
+ // Find the central node
+ // ---------------------
+
+ // Approach: Use node with most edges
+
+ LinkedHashSet<CyNode> plantedNodes = new
LinkedHashSet<CyNode>();
+
+ CyNetwork network = networkView.getModel();
+
+ CyNode centerNode = null;
+ int highestNeighborCount = -1;
+ int neighbourCount;
+
+ for (CyNode node : totalNodesToVisit) {
+ neighbourCount = network.getNeighborList(node,
Type.ANY).size();
+
+ if (centerNode == null) {
centerNode = node;
highestNeighborCount = neighbourCount;
+ } else {
+ if (neighbourCount >
highestNeighborCount) {
+ centerNode = node;
+ highestNeighborCount =
neighbourCount;
+ }
}
}
- }
-
- // Mark as planted
- plantedNodes.add(centerNode);
-
- // Plant the center node
- // ---------------------
-
-
networkView.getNodeView(centerNode).setVisualProperty(RichVisualLexicon.NODE_X_LOCATION,
0.0);
-
networkView.getNodeView(centerNode).setVisualProperty(RichVisualLexicon.NODE_Y_LOCATION,
0.0);
-
networkView.getNodeView(centerNode).setVisualProperty(RichVisualLexicon.NODE_Z_LOCATION,
0.0);
-
- // Plant the first neighbors
- // -------------------------
-
- // Idea: 2nd and further neighbors arranged in an x degree cone
- // facing outwards from the last edge
-
- HashMap<CyNode, Vector3> outwardDirections = new
HashMap<CyNode, Vector3>();
-
-
- double nodeDistance = 0.6 * DISTANCE_SCALE;
-
- LinkedHashSet<CyNode> firstNeighbors = new
LinkedHashSet<CyNode>();
-
- // Removes duplicates as well
- firstNeighbors.addAll(network.getNeighborList(centerNode,
Type.ANY));
-
- int firstNeighborCount = firstNeighbors.size();
-
- double rotation = 0;
-
- if (firstNeighborCount > 0) {
- rotation = Math.PI * 2 / firstNeighborCount;
- }
-
- Vector3 current = new Vector3(0, 0, 0);
- Vector3 offset = new Vector3(0, 1, 0);
- offset.multiplyLocal(nodeDistance);
-
- for (CyNode firstNeighbor : firstNeighbors) {
-
networkView.getNodeView(firstNeighbor).setVisualProperty(RichVisualLexicon.NODE_X_LOCATION,
- offset.x() + current.x());
-
networkView.getNodeView(firstNeighbor).setVisualProperty(RichVisualLexicon.NODE_Y_LOCATION,
- offset.y() + current.y());
-
networkView.getNodeView(firstNeighbor).setVisualProperty(RichVisualLexicon.NODE_Z_LOCATION,
- offset.z() + current.z());
- outwardDirections.put(firstNeighbor, offset);
+ // Mark as planted
+ plantedNodes.add(centerNode);
- offset = offset.rotate(new Vector3(0, 0, 1), rotation);
+ // Plant the center node
+ // ---------------------
- // Mark as planted
- plantedNodes.add(firstNeighbor);
- }
-
-
- // Plant the next neighbors
- // ------------------------
+
networkView.getNodeView(centerNode).setVisualProperty(RichVisualLexicon.NODE_X_LOCATION,
currentCentralLocation.x());
+
networkView.getNodeView(centerNode).setVisualProperty(RichVisualLexicon.NODE_Y_LOCATION,
currentCentralLocation.y());
+
networkView.getNodeView(centerNode).setVisualProperty(RichVisualLexicon.NODE_Z_LOCATION,
currentCentralLocation.z());
+
+ // Plant the first neighbors
+ // -------------------------
+
+ // Idea: 2nd and further neighbors arranged in an x
degree cone
+ // facing outwards from the last edge
- double conicalAngle = 0.51;
- double outwardProjectionDistance = nodeDistance;
-
- LinkedHashSet<CyNode> currentNeighbors = firstNeighbors;
- LinkedHashSet<CyNode> nextToVisit = new LinkedHashSet<CyNode>();
-
- do {
+ HashMap<CyNode, Vector3> outwardDirections = new
HashMap<CyNode, Vector3>();
- nodeDistance *= 1.1;
- for (CyNode currentNeighbor : currentNeighbors) {
+ double nodeDistance = 1.03 * DISTANCE_SCALE;
+
+ LinkedHashSet<CyNode> firstNeighbors = new
LinkedHashSet<CyNode>();
+
+ // Removes duplicates as well
+
firstNeighbors.addAll(network.getNeighborList(centerNode, Type.ANY));
+
+ int firstNeighborCount = firstNeighbors.size();
+
+ double rotation = 0;
+
+ if (firstNeighborCount > 0) {
+ rotation = Math.PI * 2 / firstNeighborCount;
+ }
+
+ Vector3 current = currentCentralLocation; // TODO:
Simplify this part of the code
+ Vector3 offset = new Vector3(0, 1, 0);
+ offset.multiplyLocal(nodeDistance);
+
+ // Pre-rotation
+ // offset = offset.rotate(new Vector3(0, 0, 1),
Math.random() * 2 * Math.PI);
+
+ for (CyNode firstNeighbor : firstNeighbors) {
+
networkView.getNodeView(firstNeighbor).setVisualProperty(RichVisualLexicon.NODE_X_LOCATION,
+ offset.x() + current.x());
+
networkView.getNodeView(firstNeighbor).setVisualProperty(RichVisualLexicon.NODE_Y_LOCATION,
+ offset.y() + current.y());
+
networkView.getNodeView(firstNeighbor).setVisualProperty(RichVisualLexicon.NODE_Z_LOCATION,
+ offset.z() + current.z());
- LinkedHashSet<CyNode> nextNeighbors = new
LinkedHashSet<CyNode>();
+ outwardDirections.put(firstNeighbor, offset);
- // This will also remove redundant nodes from
the getNeighborList result
-
nextNeighbors.addAll(network.getNeighborList(currentNeighbor, Type.ANY));
+ offset = offset.rotate(new Vector3(0, 0, 1),
rotation);
- Vector3 outwardOffset =
outwardDirections.get(currentNeighbor);
- outwardOffset.normalizeLocal();
-
outwardOffset.multiplyLocal(outwardProjectionDistance);
+ // Mark as planted
+ plantedNodes.add(firstNeighbor);
- Vector3 perpendicularOffset =
outwardOffset.cross(new Vector3(0, 0, 1));
- perpendicularOffset.multiplyLocal(nodeDistance
* Math.tan(conicalAngle));
+ // Check for greatest distance
+ // ===========================
- double conicalRotation = 0;
+ Vector3 usedLocation = offset.add(current);
- if (nextNeighbors.size() > 0) {
- conicalRotation = 2 * Math.PI /
nextNeighbors.size();
+ if
(usedLocation.distanceSquared(currentCentralLocation) >
greatestDistanceSquared) {
+ greatestDistanceSquared =
usedLocation.distanceSquared(currentCentralLocation);
+
+ nextCentralLocation =
usedLocation.subtract(currentCentralLocation).normalize().multiply(3.4).add(usedLocation);
}
+ }
+
+
+ // Plant the next neighbors
+ // ------------------------
+
+ double conicalAngle = 0.51;
+ double outwardProjectionDistance = nodeDistance;
+
+ LinkedHashSet<CyNode> currentNeighbors = firstNeighbors;
+ LinkedHashSet<CyNode> nextToVisit = new
LinkedHashSet<CyNode>();
+
+ do {
- for (CyNode nextNeighbor : nextNeighbors) {
+ for (CyNode currentNeighbor : currentNeighbors)
{
- if
(!plantedNodes.contains(nextNeighbor)) {
-
networkView.getNodeView(nextNeighbor).setVisualProperty(RichVisualLexicon.NODE_X_LOCATION,
-
perpendicularOffset.x() + outwardOffset.x() +
-
networkView.getNodeView(currentNeighbor).
-
getVisualProperty(RichVisualLexicon.NODE_X_LOCATION));
-
networkView.getNodeView(nextNeighbor).setVisualProperty(RichVisualLexicon.NODE_Y_LOCATION,
-
perpendicularOffset.y() + outwardOffset.y() +
-
networkView.getNodeView(currentNeighbor).
-
getVisualProperty(RichVisualLexicon.NODE_Y_LOCATION));
-
networkView.getNodeView(nextNeighbor).setVisualProperty(RichVisualLexicon.NODE_Z_LOCATION,
-
perpendicularOffset.z() + outwardOffset.z() +
-
networkView.getNodeView(currentNeighbor).
-
getVisualProperty(RichVisualLexicon.NODE_Z_LOCATION));
+ LinkedHashSet<CyNode> nextNeighbors =
new LinkedHashSet<CyNode>();
+
+ // This will also remove redundant
nodes from the getNeighborList result
+
nextNeighbors.addAll(network.getNeighborList(currentNeighbor, Type.ANY));
+
+ Vector3 outwardOffset =
outwardDirections.get(currentNeighbor);
+ outwardOffset.normalizeLocal();
+
outwardOffset.multiplyLocal(outwardProjectionDistance);
+
+ Vector3 perpendicularOffset =
outwardOffset.cross(new Vector3(0, 0, 1));
+ perpendicularOffset.normalizeLocal();
+
perpendicularOffset.multiplyLocal(nodeDistance * Math.tan(conicalAngle));
+
+ double conicalRotation = 0;
+
+ if (nextNeighbors.size() > 0) {
+ conicalRotation = 2 * Math.PI /
nextNeighbors.size();
+ }
+
+ for (CyNode nextNeighbor :
nextNeighbors) {
-
outwardDirections.put(nextNeighbor, perpendicularOffset.add(outwardOffset));
-
- perpendicularOffset =
perpendicularOffset.rotate(outwardOffset, conicalRotation);
-
- // Mark as planted
- plantedNodes.add(nextNeighbor);
-
- nextToVisit.add(nextNeighbor);
+ if
(!plantedNodes.contains(nextNeighbor)) {
+
networkView.getNodeView(nextNeighbor).setVisualProperty(RichVisualLexicon.NODE_X_LOCATION,
+
perpendicularOffset.x() + outwardOffset.x() +
+
networkView.getNodeView(currentNeighbor).
+
getVisualProperty(RichVisualLexicon.NODE_X_LOCATION));
+
networkView.getNodeView(nextNeighbor).setVisualProperty(RichVisualLexicon.NODE_Y_LOCATION,
+
perpendicularOffset.y() + outwardOffset.y() +
+
networkView.getNodeView(currentNeighbor).
+
getVisualProperty(RichVisualLexicon.NODE_Y_LOCATION));
+
networkView.getNodeView(nextNeighbor).setVisualProperty(RichVisualLexicon.NODE_Z_LOCATION,
+
perpendicularOffset.z() + outwardOffset.z() +
+
networkView.getNodeView(currentNeighbor).
+
getVisualProperty(RichVisualLexicon.NODE_Z_LOCATION));
+
+
outwardDirections.put(nextNeighbor, perpendicularOffset.add(outwardOffset));
+
+ perpendicularOffset =
perpendicularOffset.rotate(outwardOffset, conicalRotation);
+
+ // Mark as planted
+
plantedNodes.add(nextNeighbor);
+
+
nextToVisit.add(nextNeighbor);
+
+ // Check for greatest
distance
+ //
===========================
+
+ Vector3
currentNeighborLocation = new Vector3(
+
networkView.getNodeView(currentNeighbor).
+
getVisualProperty(RichVisualLexicon.NODE_X_LOCATION),
+
networkView.getNodeView(currentNeighbor).
+
getVisualProperty(RichVisualLexicon.NODE_Y_LOCATION),
+
networkView.getNodeView(currentNeighbor).
+
getVisualProperty(RichVisualLexicon.NODE_Z_LOCATION));
+
+ Vector3 usedLocation =
perpendicularOffset.add(outwardOffset).add(currentNeighborLocation);
+
+ if
(usedLocation.distanceSquared(currentCentralLocation) >
greatestDistanceSquared) {
+
greatestDistanceSquared = usedLocation.distanceSquared(currentCentralLocation);
+
+
nextCentralLocation =
usedLocation.subtract(currentCentralLocation).normalize().multiply(3.4).add(usedLocation);
+ }
+ }
}
}
- }
+
+ currentNeighbors.clear();
+ currentNeighbors.addAll(nextToVisit);
+
+ nextToVisit.clear();
+
+ } while (!currentNeighbors.isEmpty());
- currentNeighbors.clear();
- currentNeighbors.addAll(nextToVisit);
+ // System.out.println("planted so far: " +
plantedNodes.size());
+ totalNodesToVisit.removeAll(plantedNodes);
+ // System.out.println("total after remove: " +
totalNodesToVisit.size());
- nextToVisit.clear();
- } while (!currentNeighbors.isEmpty());
-
+ double greatestDistance =
Math.sqrt(greatestDistanceSquared) * 0.75;
+
+ // currentCentralLocation.set(nextCentralLocation);
+ currentCentralLocation.addLocal(0,
+ (Math.random() * 2 * greatestDistance +
greatestDistance) * 1.25,
+ 0);
+
+ if (greatestDistanceSquared < 0.2) {
+ currentCentralLocation.addLocal(new
Vector3(0.6, -0.6, 0));
+ }
+
+ greatestDistanceSquared = -1;
+ } while (!totalNodesToVisit.isEmpty());
+
+
camera.moveTo(findAveragePosition(networkView.getModel().getNodeList())
+
.subtract(camera.getDirection().multiply(camera.getDistance())));
}
/*
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