Author: kono
Date: 2011-05-27 12:17:33 -0700 (Fri, 27 May 2011)
New Revision: 25568
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithmTask.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/Graph.java
Log:
Circular layout algorithm fixed. TODO: Tunables are not used in current
implementation.
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
2011-05-27 17:58:41 UTC (rev 25567)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
2011-05-27 19:17:33 UTC (rev 25568)
@@ -1,19 +1,17 @@
package csplugins.layout.algorithms.circularLayout;
-import java.util.HashMap;
-import java.util.LinkedList;
-
-import org.cytoscape.model.CyNode;
import org.cytoscape.view.layout.AbstractLayoutAlgorithm;
-import org.cytoscape.view.model.View;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.TunableValidator;
import org.cytoscape.work.undo.UndoSupport;
-public class CircularLayoutAlgorithm extends AbstractLayoutAlgorithm
implements TunableValidator{
+public class CircularLayoutAlgorithm extends AbstractLayoutAlgorithm
implements TunableValidator {
+
+ //TODO: these are not used in current implementations.
+
@Tunable(description="Horizontal spacing between nodes")
public int nodeHorizontalSpacing = 64;
@Tunable(description="Vertical spacing between nodes")
@@ -39,11 +37,11 @@
return true;
}
+
+ @Override
public TaskIterator getTaskIterator() {
return new TaskIterator(
- new CircularLayoutAlgorithmTask(networkView, getName(),
selectedOnly,
- staticNodes,
nodeHorizontalSpacing,
- nodeVerticalSpacing,
leftEdge, topEdge,
- rightMargin,
singlePartition));
+ new CircularLayoutAlgorithmTask(
+ networkView, getName(),
selectedOnly, singlePartition, staticNodes));
}
}
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithmTask.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithmTask.java
2011-05-27 17:58:41 UTC (rev 25567)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithmTask.java
2011-05-27 19:17:33 UTC (rev 25568)
@@ -4,6 +4,8 @@
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
import java.util.Set;
import org.cytoscape.model.CyNode;
@@ -15,51 +17,30 @@
import org.cytoscape.view.model.View;
import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
import org.cytoscape.work.TaskMonitor;
-import org.cytoscape.work.Tunable;
import csplugins.layout.algorithms.hierarchicalLayout.Edge;
import csplugins.layout.algorithms.hierarchicalLayout.Graph;
public class CircularLayoutAlgorithmTask extends AbstractPartitionLayoutTask {
- public int nodeHorizontalSpacing; // = 64;
- public int nodeVerticalSpacing;// = 32;
- public int leftEdge;// = 32;
- public int topEdge;// = 32;
- public int rightMargin;// = 1000;
-
+
private int[][] bc;
private boolean[] posSet;
private boolean[] depthPosSet;
- private HashMap<Integer, Integer> nodeHeights;
- private LinkedList<Integer>[] edgesFrom;
- //private NodeView[] nodeView;
- private HashMap<Integer, View<CyNode>> nodeViews;
- private HashMap<Integer, Integer> node2BiComp;
+ private Map<Integer, Integer> nodeHeights;
+ private List<Integer>[] edgesFrom;
+ private Map<Integer, View<CyNode>> nodeViews;
+ private Map<Integer, Integer> node2BiComp;
private boolean[] drawnBiComps;
- public CircularLayoutAlgorithmTask(
- final CyNetworkView networkView, final String name, final
boolean selectedOnly,
- final Set<View<CyNode>> staticNodes, final int
nodeHorizontalSpacing,
- final int nodeVerticalSpacing, final int leftEdge, final int
topEdge,
- final int rightMargin, final boolean singlePartition)
- {
+ public CircularLayoutAlgorithmTask(final CyNetworkView networkView,
final String name,
+ final boolean singlePartition, final boolean
selectedOnly, final Set<View<CyNode>> staticNodes) {
super(networkView, name, singlePartition, selectedOnly,
staticNodes);
-
- this.nodeHorizontalSpacing = nodeHorizontalSpacing;
- this.nodeVerticalSpacing = nodeVerticalSpacing;
- this.leftEdge = leftEdge;
- this.topEdge = topEdge;
- this.rightMargin = rightMargin;
}
- /**
- * DOCUMENT ME!
- *
- * @param partition DOCUMENT ME!
- */
+ @Override
public void layoutPartion(LayoutPartition partition) {
if (cancelled)
return;
@@ -73,60 +54,51 @@
nodeViews = new HashMap<Integer, View<CyNode>>(numNodes);
- int nextNode = 0;
- //HashMap<Integer, Integer> ginyIndex2Index = new
HashMap<Integer, Integer>(numNodes * 2);
+ Map<CyNode, Integer> nodeIdexMap = new HashMap<CyNode,
Integer>();
+ int nodeIndex = 0;
- Iterator iter = partition.getNodeList().iterator(); /* all
nodes */
-
- while (iter.hasNext() && !cancelled) {
- View<CyNode> nv = ((LayoutNode)
(iter.next())).getNodeView();
-
- nodeViews.put(nextNode, nv);
- nextNode++;
-
+ Iterator<LayoutNode> nodeIter =
partition.getNodeList().iterator();
+ while (nodeIter.hasNext() && !cancelled) {
+ final View<CyNode> nv = nodeIter.next().getNodeView();
+ nodeViews.put(nodeIndex, nv);
+ nodeIdexMap.put(nv.getModel(), nodeIndex);
+ nodeIndex++;
}
if (cancelled)
return;
/* create edge list from edges between selected nodes */
- LinkedList<Edge> edges = new LinkedList<Edge>();
- iter = partition.edgeIterator();
+ final List<Edge> edges = new LinkedList<Edge>();
+ final Iterator<LayoutEdge> edgeIter = partition.edgeIterator();
+ while (edgeIter.hasNext() && !cancelled) {
+ final LayoutEdge ev = edgeIter.next();
+ final Integer edgeFrom =
nodeIdexMap.get(ev.getEdge().getSource());
+ final Integer edgeTo =
nodeIdexMap.get(ev.getEdge().getTarget());
- while (iter.hasNext()) {
- LayoutEdge ev = (LayoutEdge) (iter.next());
- Integer edgeFrom = ev.getEdge().getSource().getIndex();
- Integer edgeTo = ev.getEdge().getTarget().getIndex();
-
- if ((edgeFrom == null) || (edgeTo == null)) {
- // Must be from an unselected node
+ if ((edgeFrom == null) || (edgeTo == null))
continue;
- }
-
- if (cancelled)
- return;
-
- /* add edge to graph */
- edges.add(new Edge(edgeFrom.intValue(),
edgeTo.intValue()));
- edges.add(new Edge(edgeTo.intValue(),
edgeFrom.intValue()));
+
+ edges.add(new Edge(edgeFrom, edgeTo));
+ edges.add(new Edge(edgeTo, edgeFrom));
}
+ nodeIdexMap.clear();
+ nodeIdexMap = null;
+ if (cancelled)
+ return;
/* find horizontal and vertical coordinates of each node */
- Edge[] edge = new Edge[edges.size()];
+ final Edge[] edge = new Edge[edges.size()];
edges.toArray(edge);
- Graph graph = new Graph(numNodes, edge);
+ final Graph graph = new Graph(numNodes, edge);
if (cancelled)
return;
posSet = new boolean[nodeViews.size()]; // all false
depthPosSet = new boolean[nodeViews.size()]; // all false
-
- //System.out.println("plain component:\n" +
graph.getNodecount());
-
- Thread.yield();
-
+
bc = graph.biconnectedComponents();
int maxSize = -1;
@@ -159,12 +131,8 @@
}
}
- double radius = (48 * maxSize) / (2 * Math.PI);
-
- /*int[] resultingNodes = new int[bc[maxIndex].length];
- for (int i = 0; i < resultingNodes.length; i++)
- resultingNodes[i] = index2GinyIndex.get(bc[maxIndex][i]);*/
- double deltaAngle = (2 * Math.PI) / maxSize;
+ final double radius = (48 * maxSize) / (2 * Math.PI);
+ final double deltaAngle = (2 * Math.PI) / maxSize;
double angle = 0;
int startX = (int) radius;
@@ -177,9 +145,9 @@
// setting nodes on inner circle
for (int i = 0; i < bc[maxIndex].length; i++) {
- //System.out.println(bc[maxIndex][i] + " " +
part2NonPart[bc[maxIndex][i]] + " ");
- setOffset(nodeViews.get(bc[maxIndex][i]), startX +
(Math.cos(angle) * radius),
- startY -
(Math.sin(angle) * radius));
+ setOffset(nodeViews.get(bc[maxIndex][i]),
+ startX + (Math.cos(angle) * radius),
+ startY - (Math.sin(angle) * radius));
posSet[bc[maxIndex][i]] = true;
angle += deltaAngle;
@@ -194,15 +162,13 @@
if (cancelled)
return;
- iter = partition.nodeIterator();
+ nodeIter = partition.nodeIterator();
- while (iter.hasNext() && !cancelled) {
- LayoutNode ln = (LayoutNode) (iter.next());
- View<CyNode> nv = ln.getNodeView();
- double xPos =
nv.getVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION);
- double yPos =
nv.getVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION);
- ln.setX(xPos);
- ln.setY(yPos);
+ while (nodeIter.hasNext() && !cancelled) {
+ final LayoutNode ln = nodeIter.next();
+ final View<CyNode> nv = ln.getNodeView();
+
ln.setX(nv.getVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION));
+
ln.setY(nv.getVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION));
partition.moveNodeToLocation(ln);
}
}
@@ -221,14 +187,14 @@
double startY, int firstTouched) {
int outerNodesCount = 0;
int rnc = 0;
- Iterator iter;
- HashMap<Integer, Integer> outerCircle = new HashMap<Integer,
Integer>();
+ Iterator<Integer> iter;
+ Map<Integer, Integer> outerCircle = new HashMap<Integer,
Integer>();
for (int i = 0; i < bc[compIndex].length; i++) {
iter = edgesFrom[bc[compIndex][i]].iterator();
while (iter.hasNext()) {
- int currNeighbour = ((Integer)
iter.next()).intValue();
+ int currNeighbour = iter.next();
if (!posSet[currNeighbour]) {
outerNodesCount +=
(NoOfChildren(currNeighbour, outerCircle) + 1);
@@ -238,9 +204,7 @@
}
}
- double outerRadius;
- //Math.round((nodeHorizontalSpacing * outerNodesCount) / (2 *
Math.PI));
- outerRadius = 1.5 * innerCircleRadius;
+ double outerRadius = 1.5 * innerCircleRadius;
// + 5 * nodeHorizontalSpacing;
int tryCount = (int) ((2 * Math.PI * outerRadius) / 32);
@@ -453,7 +417,7 @@
* @param outerCircle
* @return
*/
- private int NoOfChildren(int nodeID, HashMap<Integer, Integer>
outerCircle) {
+ private int NoOfChildren(int nodeID, Map<Integer, Integer> outerCircle)
{
int toReturn = 0;
Iterator iter = edgesFrom[nodeID].iterator();
@@ -535,92 +499,8 @@
return toReturn;
}
- /**
- * Sort the nodes from biconnected component to get the best ordering
in terms
- * of minimizing inner circle crossings
- * @param icNodes - nodes from biconnected component
- * @return
- */
- private int[] ReduceInnerCircleCrossings1(int[] icNodes) {
- int[] toReturn = new int[icNodes.length];
- HashMap<Integer, Boolean> alreadySet = new HashMap<Integer,
Boolean>();
-
- for (int i = 0; i < icNodes.length; i++)
- alreadySet.put(Integer.valueOf(icNodes[i]), new
Boolean(false));
-
- int x = 0;
- int p = 0;
- toReturn[0] = icNodes[0];
- alreadySet.put(Integer.valueOf(toReturn[0]), new Boolean(true));
-
- while (p < (icNodes.length - 1)) {
-// if ((p == x) && (p != 0))
- //System.out.println("p = " + p + " x = " + x +
" count = " + icNodes.length);
-
- Iterator iter = edgesFrom[toReturn[p]].iterator();
-
- while (iter.hasNext()) {
- int neigh = ((Integer) iter.next()).intValue();
-
- if
(alreadySet.containsKey(Integer.valueOf(neigh))
- &&
!alreadySet.get(Integer.valueOf(neigh)).booleanValue()) {
- toReturn[x++] = neigh;
- alreadySet.put(Integer.valueOf(neigh),
new Boolean(true));
- }
- }
-
- p++;
- }
-
- return toReturn;
- }
-
/**
- * Sort the nodes from biconnected component to get the best ordering
in terms
- * of minimizing inner circle crossings
- * @param icNodes - nodes from biconnected component
- * @return
- */
- private int[] ReduceInnerCircleCrossings(int[] icNodes) {
- int[] toReturn = new int[icNodes.length];
-
- HashMap<Integer, Boolean> alreadySet = new HashMap<Integer,
Boolean>();
- HashMap<Integer, Integer> nodeDegree = new HashMap<Integer,
Integer>();
-
- for (int i = 0; i < icNodes.length; i++) {
- alreadySet.put(Integer.valueOf(icNodes[i]), new
Boolean(false));
- toReturn[i] = icNodes[i];
- }
-
- for (int i = 0; i < icNodes.length; i++) {
- int degree = 0;
- Iterator iter = edgesFrom[icNodes[i]].iterator();
-
- while (iter.hasNext()) {
- int neigh = ((Integer) iter.next()).intValue();
-
- if
(alreadySet.containsKey(Integer.valueOf(neigh)))
- degree++;
- }
-
- nodeDegree.put(Integer.valueOf(icNodes[i]),
Integer.valueOf(degree));
- }
-
- for (int i = 0; i < (toReturn.length - 1); i++) {
- for (int j = i + 1; j < toReturn.length; j++) {
- if
(nodeDegree.get(Integer.valueOf(toReturn[i])) >
nodeDegree.get(Integer.valueOf(toReturn[j]))) {
- int tmp = toReturn[i];
- toReturn[i] = toReturn[j];
- toReturn[j] = tmp;
- }
- }
- }
-
- return toReturn;
- }
-
- /**
* Function traverses graph starting from the node from outer circle
until
* it traverse all the nodes. When it comes along another biconnected
component
* it sets it out on circle and calls SetOuterCircle() again. The main
purpose of
@@ -1010,69 +890,10 @@
}*/
return startPos;
}
+
- private int BestFreePosition(int idealPosition, boolean[]
outerPositionsTaken) {
- //for (int i = 0; i < outerPositionsTaken.length; i++)
- //System.out.print(outerPositionsTaken[i] + " ");
- //System.out.println();
- //System.out.println(idealPosition);
- int startPosition = idealPosition;
-
- if (idealPosition < 0)
- startPosition = idealPosition %
outerPositionsTaken.length;
-
- int move = 0;
-
- while (move < ((outerPositionsTaken.length / 2) + 1)) {
- if (!outerPositionsTaken[(startPosition + move) %
outerPositionsTaken.length]) {
- outerPositionsTaken[(startPosition + move) %
outerPositionsTaken.length] = true;
-
- //System.out.println((startPosition + move) %
outerPositionsTaken.length);
- return (startPosition + move) %
outerPositionsTaken.length;
- }
-
- if (!outerPositionsTaken[(startPosition - move) %
outerPositionsTaken.length]) {
- outerPositionsTaken[(startPosition - move) %
outerPositionsTaken.length] = true;
-
- // System.out.println((startPosition -
move) % outerPositionsTaken.length);
- return (startPosition - move) %
outerPositionsTaken.length;
- }
-
- move++;
- }
-
- return -1;
- }
-
- /**
- * DOCUMENT ME!
- */
- public void halt() {
- cancelled = true;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param tm DOCUMENT ME!
- */
- public void setTaskMonitor(TaskMonitor tm) {
- taskMonitor = tm;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getTitle() {
- return new String("Circular Layout");
- }
-
private void setOffset(View<CyNode> nv, double x, double y){
nv.setVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION, x);
nv.setVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION, y);
}
-
-
}
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/Graph.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/Graph.java
2011-05-27 17:58:41 UTC (rev 25567)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/Graph.java
2011-05-27 19:17:33 UTC (rev 25568)
@@ -220,6 +220,7 @@
/** number of passes to do adjacency exchange */
static int MAX_ADJACENT_EXCHANGE_PASSES = 5;
+
private byte[] status;
private int[] d;
private int[] low;
@@ -236,7 +237,7 @@
* @param a_edge An array of all edges in the graph (each edge holds
the source and destination node's indicies)
* @throws IllegalArgumentException If any edge refers to an out of
range node
*/
- public Graph(int a_nodecount, Edge[] a_edge) {
+ public Graph(int a_nodecount, final Edge[] a_edge) {
nodecount = a_nodecount;
edge = new Edge[a_edge.length];
edgesFrom = new LinkedList[nodecount];
@@ -255,9 +256,8 @@
int edgeTo = a_edge[x].getTo();
if ((edgeFrom < 0) || (edgeFrom >= nodecount) ||
(edgeTo < 0) || (edgeTo >= nodecount)) {
- throw new IllegalArgumentException("Edge
refered to node outside of valid range: "
- + "From=" +
edgeFrom + " To=" + edgeTo
- + " with
nodecount=" + nodecount + "\n");
+ throw new IllegalArgumentException("Edge
refered to node outside of valid range: " + "From=" + edgeFrom
+ + " To=" + edgeTo + " with
nodecount=" + nodecount + "\n");
}
edge[x] = new Edge(edgeFrom, edgeTo);
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