Author: ghuck
Date: 2009-08-14 08:57:43 -0700 (Fri, 14 Aug 2009)
New Revision: 17825
Modified:
csplugins/trunk/soc/ghuck/plugin_linux/src/ForceDirected.java
Log:
Fixed bug related to huge vaules of upRatio, which caused node visible size to
be zero.
Still has problems with some graphs, the layout is sometimes not very pretty..
Modified: csplugins/trunk/soc/ghuck/plugin_linux/src/ForceDirected.java
===================================================================
--- csplugins/trunk/soc/ghuck/plugin_linux/src/ForceDirected.java
2009-08-14 14:58:05 UTC (rev 17824)
+++ csplugins/trunk/soc/ghuck/plugin_linux/src/ForceDirected.java
2009-08-14 15:57:43 UTC (rev 17825)
@@ -67,8 +67,8 @@
{
private String message;
- private double H_SIZE = 10000.0;
- private double V_SIZE = 10000.0;
+ private double H_SIZE = 1000.0;
+ private double V_SIZE = 1000.0;
private String GPU_LIBRARY = "GpuLayout";
// Default values for algorithm parameters
@@ -407,7 +407,7 @@
+ Math.pow(node_positions[n1Index][1]
- node_positions[n2Index][1], 2)
);
// Check if edgeSize is not zero
- if (edgeSize > 0){
+ if (edgeSize > 0.0){
// actualRatio = minimun_desired_length / actual_length
actualRatio = (n1Size + n2Size) / edgeSize;
@@ -419,61 +419,112 @@
}
- upRatio = 5 * upRatio / 9;
+ //upRatio = 5 * upRatio / 9;
+ //upRatio = Math.min(upRatio, 100.0);
// Check whether the ratio is not zero
if (upRatio <= 0.0){
- message = "Error while performing node positions scale-up\nCannot
perform layout\nupRatio = " + upRatio;
+ message = "Error while performing node positions scale-up\nIgnoring
scaling upt\nupRatio = " + upRatio;
JOptionPane.showMessageDialog(Cytoscape.getDesktop(), message);
- return;
+ upRatio = 1.0;
}
- message = "upRatio. = " + upRatio;
- JOptionPane.showMessageDialog(Cytoscape.getDesktop(), message);
+ double oldUpRatio = upRatio;
+ logger.debug("upRatio = " + upRatio);
- // Update Node position
- part.resetNodes(); // reset the nodes so we get the new average location
+ //message = "upRatio = " + upRatio;
+ //JOptionPane.showMessageDialog(Cytoscape.getDesktop(), message);
- // Iterate over all nodes
- int currentNode = 0;
+ boolean success = false;
- // Create an iterator for processing the nodes
- Iterator<LayoutNode> iterator2 = nodeList.iterator();
+ // Move nodes to their position
+ while (!success){
+
+ try{
+ // We will keep track of the offset of the whole part so that
we can eliminate it
+ double minX = node_positions[0][0];
+ double minY = node_positions[0][1];
+
+ // Get the 'offset' of the whole partition, so that we can
eliminate it
+ for (int i = 0; i < numNodes; i++) {
+
+ if ( node_positions[i][0] < minX)
+ minX = node_positions[i][0];
+ if ( node_positions[i][1] < minY)
+ minY = node_positions[i][1];
+ }
- while (iterator2.hasNext()){
-
- // Get next node
- LayoutNode node = (LayoutNode) iterator2.next();
+ minX = upRatio * minX;
+ minY = upRatio * minY;
+
+ // Reset the nodes so we get the new average location
+ part.resetNodes();
+
+ // Iterate over all nodes
+ int currentNode = 0;
- // Set node's X and Y positions
- node.setX(upRatio * node_positions[currentNode][0]);
- node.setY(upRatio * node_positions[currentNode][1]);
+ // Create an iterator for processing the nodes
+ Iterator<LayoutNode> iterator2 = nodeList.iterator();
+
+
+ while (iterator2.hasNext()){
+
+ // Get next node
+ LayoutNode node = (LayoutNode) iterator2.next();
+
+ // Set node's X and Y positions
+ node.setX(upRatio * node_positions[currentNode][0] - minX);
+ node.setY(upRatio * node_positions[currentNode][1] - minY);
- // Move node to desired location
- part.moveNodeToLocation(node);
-
- currentNode++;
- }
+ //logger.debug("moving node " + currentNode + "to:\nX = " +
(upRatio * node_positions[currentNode][0]) + "\nY = " + (upRatio *
node_positions[currentNode][1]));
+
+ // Move node to desired location
+ part.moveNodeToLocation(node);
+
+ currentNode++;
+ }
- // Not quite done, yet. If we're only laying out selected nodes, we
need
- // to migrate the selected nodes back to their starting position
- if (selectedOnly) {
- double xDelta = 0.0;
- double yDelta = 0.0;
- Dimension finalLocation = part.getAverageLocation();
- xDelta = finalLocation.getWidth() - initialLocation.getWidth();
- yDelta = finalLocation.getHeight() - initialLocation.getHeight();
- for (LayoutNode v: part.getNodeList()) {
- if (!v.isLocked()) {
- v.decrement(xDelta, yDelta);
- part.moveNodeToLocation(v);
+ // Not quite done, yet. If we're only laying out selected
nodes, we need
+ // to migrate the selected nodes back to their starting position
+ if (selectedOnly) {
+ double xDelta = 0.0;
+ double yDelta = 0.0;
+ Dimension finalLocation = part.getAverageLocation();
+ xDelta = finalLocation.getWidth() -
initialLocation.getWidth();
+ yDelta = finalLocation.getHeight() -
initialLocation.getHeight();
+ for (LayoutNode v: part.getNodeList()) {
+ if (!v.isLocked()) {
+ v.decrement(xDelta, yDelta);
+ part.moveNodeToLocation(v);
+ }
+ }
}
+
+ success = true;
+
}
- }
+ catch(Exception excep){
+ upRatio = upRatio / 10.0;
+ if (upRatio <= 0.0){
+ message = "Sorry, cannot produce layout";
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
message);
+ return;
+ }
+ success = false;
+ }
+
+ }//while(!success)
+
+ /*if (oldUpRatio != upRatio){
+ message = "Initial upRatio = " + oldUpRatio + "\nFinal upRatio = "
+ upRatio;
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), message);
+ }*/
+
+
}// layoutPartion(LayoutPartition part)
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