Author: ghuck
Date: 2011-06-21 19:16:51 -0700 (Tue, 21 Jun 2011)
New Revision: 25874
Modified:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/CircleLayout.java
Log:
Fixed issue while laying out only selected nodes in Circle Layout
Modified:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/CircleLayout.java
===================================================================
---
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/CircleLayout.java
2011-06-22 00:13:18 UTC (rev 25873)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/CircleLayout.java
2011-06-22 02:16:51 UTC (rev 25874)
@@ -13,7 +13,7 @@
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
+along with this program. If not, see <http://www.gnu.org/licenses/>.
**************************************************************************************/
@@ -167,17 +167,17 @@
double[] y = new double[numNodes];
// Load graph into native library
- HashMap<Integer,Integer> mapping = loadGraphPartition(part);
+ HashMap<Integer,Integer> mapping = loadGraphPartition(part,
selectedOnly);
- // Simplify graph
- IgraphInterface.simplify();
-
// Check whether it has been canceled by the user
if (canceled)
return;
// Show message on the task monitor
taskMonitor.setStatus("Calling native code: Partition: " +
part.getPartitionNumber());
+
+ // Simplify graph
+ IgraphInterface.simplify();
// Make native method call
IgraphInterface.layoutCircle(x, y);
@@ -185,12 +185,11 @@
// Check whether it has been canceled by the user
if (canceled)
return;
+
// Show message on the task monitor
taskMonitor.setStatus("Updating display");
-
-
// Find which ratio is required to 'scale up' the node positions so
that nodes don't overlap
double upRatio = 0.0;
double actualRatio = 0.0;
@@ -199,6 +198,9 @@
LayoutNode n1 = edge.getSource();
LayoutNode n2 = edge.getTarget();
+ if (n1.isLocked() || n2.isLocked())
+ continue;
+
double n1Size = Math.max(n1.getHeight(), n1.getWidth());
double n2Size = Math.max(n2.getHeight(), n2.getWidth());
@@ -218,10 +220,6 @@
}
- //if (upRatio > 1000)
- // upRatio = Math.log(upRatio) + 1000;
- //upRatio = Math.min(upRatio, 100.0);
-
// Check whether the ratio is not zero
if (upRatio < 1.0){
upRatio = 1.0;
@@ -229,9 +227,9 @@
double oldUpRatio = upRatio;
- // logger.info("upRatio = " + upRatio);
- //message = "upRatio = " + upRatio;
- //JOptionPane.showMessageDialog(Cytoscape.getDesktop(), message);
+ // logger.info("upRatio = " + upRatio);
+ // message = "upRatio = " + upRatio;
+ // JOptionPane.showMessageDialog(Cytoscape.getDesktop(), message);
// Move nodes to their position
@@ -244,7 +242,7 @@
double minY = y[0];
// Get the 'offset' of the whole partition, so that we can
eliminate it
- for (int i = 1; i < numNodes; i++) {
+ for (int i = 1; i < mapping.size(); i++) {
if (x[i] < minX)
minX = x[i];
@@ -258,9 +256,6 @@
// Reset the nodes so we get the new average location
part.resetNodes();
-
- // Iterate over all nodes
- int currentNode = 0;
// Create an iterator for processing the nodes
Iterator<LayoutNode> iterator2 = part.getNodeList().iterator();
@@ -269,17 +264,17 @@
// Get next node
LayoutNode node = (LayoutNode) iterator2.next();
-
- // Set node's X and Y positions
- node.setX(upRatio * x[mapping.get(node.getIndex())] - minX);
- node.setY(upRatio * y[mapping.get(node.getIndex())] - minY);
- //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++;
+ // If it is locked, skip it
+ if (!node.isLocked()) {
+
+ // Set node's X and Y positions
+ node.setX(upRatio * x[mapping.get(node.getIndex())] -
minX);
+ node.setY(upRatio * y[mapping.get(node.getIndex())] -
minY);
+
+ // Move node to desired location
+ part.moveNodeToLocation(node);
+ }
}
@@ -315,44 +310,6 @@
}//while(!success)
-
-
-
-
-
-
- // Actually move the pieces around
- // Note that we reset our min/max values before we start this
- // so we can get an accurate min/max for paritioning
-// part.resetNodes();
-
-// for (LayoutNode v: part.getNodeList()) {
-// // Set node's X and Y positions
-// v.setX(x[mapping.get(v.getIndex())]);
-// v.setY(y[mapping.get(v.getIndex())]);
-
-// // Actually move the node
-// 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);
-// }
-// }
-// }
-
-
}// layoutPartion(LayoutPartition part)
@@ -360,21 +317,35 @@
* This function loads a partition into igraph
*
*/
- public static HashMap<Integer,Integer> loadGraphPartition(LayoutPartition
part){
+ public static HashMap<Integer,Integer> loadGraphPartition(LayoutPartition
part, boolean selectedOnly){
CyLogger logger = CyLogger.getLogger(CircleLayout.class);
// Create a reverse mapping
int nodeCount = part.nodeCount();
- HashMap<Integer, Integer> nodeIdMapping = new HashMap<Integer,
Integer>(nodeCount);
+ HashMap<Integer, Integer> nodeIdMapping;
+ if (selectedOnly)
+ nodeIdMapping = new HashMap<Integer, Integer>(nodeCount -
part.lockedNodeCount());
+ else
+ nodeIdMapping = new HashMap<Integer, Integer>(nodeCount);
int j = 0;
- Iterator<LayoutNode> nodeIt = part.getNodeList().iterator();
- while(nodeIt.hasNext()){
- LayoutNode node = (LayoutNode) nodeIt.next();
- nodeIdMapping.put(node.getIndex(), j);
- j++;
+ Iterator<LayoutNode> nodeIt = part.nodeIterator();
+ if (selectedOnly) {
+ while(nodeIt.hasNext()) {
+ LayoutNode node = (LayoutNode) nodeIt.next();
+ if (!node.isLocked()) {
+ nodeIdMapping.put(node.getIndex(), j);
+ j++;
+ }
+ }
+ } else {
+ while(nodeIt.hasNext()) {
+ LayoutNode node = (LayoutNode) nodeIt.next();
+ nodeIdMapping.put(node.getIndex(), j);
+ j++;
+ }
}
// Write edges (as pairs of consecutive nodes) in edgeArray
@@ -383,20 +354,34 @@
Iterator<LayoutEdge> it = part.getEdgeList().iterator();
- while (it.hasNext()) {
- LayoutEdge e = (LayoutEdge) it.next();
+ if (selectedOnly) {
+ while (it.hasNext()) {
+ LayoutEdge e = (LayoutEdge) it.next();
- LayoutNode source = e.getSource();
- LayoutNode target = e.getTarget();
+ LayoutNode source = e.getSource();
+ LayoutNode target = e.getTarget();
- edgeArray[i] = nodeIdMapping.get(source.getIndex());
- edgeArray[i + 1] = nodeIdMapping.get(target.getIndex());
- i += 2;
-
+ if (source.isLocked() || target.isLocked())
+ continue;
+
+ edgeArray[i] = nodeIdMapping.get(source.getIndex());
+ edgeArray[i + 1] = nodeIdMapping.get(target.getIndex());
+ i += 2;
+ }
+ } else {
+ while (it.hasNext()) {
+ LayoutEdge e = (LayoutEdge) it.next();
+
+ LayoutNode source = e.getSource();
+ LayoutNode target = e.getTarget();
+
+ edgeArray[i] = nodeIdMapping.get(source.getIndex());
+ edgeArray[i + 1] = nodeIdMapping.get(target.getIndex());
+ i += 2;
+ }
}
IgraphInterface.createGraph(edgeArray, i);
- // IgraphInterface.simplify();
return nodeIdMapping;
} // loadGraphPartition()
--
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