Author: pwang
Date: 2010-09-24 15:25:37 -0700 (Fri, 24 Sep 2010)
New Revision: 22052
Added:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayoutTask.java
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
Log:
Refactored
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
2010-09-24 21:45:17 UTC (rev 22051)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
2010-09-24 22:25:37 UTC (rev 22052)
@@ -1,8 +1,8 @@
/* vim: set ts=2: */
package csplugins.layout.algorithms.graphPartition;
-import static org.cytoscape.model.CyTableEntry.NODE;
+
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
@@ -13,20 +13,23 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTableManager;
import org.cytoscape.view.layout.AbstractGraphPartition;
+import org.cytoscape.view.layout.AbstractLayout;
import org.cytoscape.view.layout.LayoutNode;
import org.cytoscape.view.layout.LayoutPartition;
+import org.cytoscape.work.TaskIterator;
+import org.cytoscape.work.TunableValidator;
import org.cytoscape.work.undo.UndoSupport;
/**
*
*/
-public class DegreeSortedCircleLayout extends AbstractGraphPartition {
+public class DegreeSortedCircleLayout extends AbstractLayout implements
TunableValidator {
private static final String DEGREE_ATTR_NAME = "degree";
-
private CyTableManager tableMgr;
+
/**
* Creates a new DegreeSortedCircleLayout object.
*/
@@ -35,6 +38,16 @@
this.tableMgr = tableMgr;
}
+ // TODO
+ public boolean tunablesAreValid(final Appendable errMsg) {
+ return true;
+ }
+
+ public TaskIterator getTaskIterator() {
+ return new TaskIterator(new
DegreeSortedCircleLayoutTask(networkView, getName(), selectedOnly, staticNodes,
+ DEGREE_ATTR_NAME, tableMgr));
+ }
+
/**
* DOCUMENT ME!
*
@@ -52,69 +65,4 @@
public String getName() {
return "degree-circle";
}
-
- /**
- * DOCUMENT ME!
- *
- * @param partition DOCUMENT ME!
- */
- public void layoutPartion(LayoutPartition partition) {
- // Create attribute
- if(tableMgr.getTableMap(NODE,
network).get(CyNetwork.DEFAULT_ATTRS).getUniqueColumns().contains(DEGREE_ATTR_NAME)
== false) {
- tableMgr.getTableMap(NODE,
network).get(CyNetwork.DEFAULT_ATTRS).createColumn(DEGREE_ATTR_NAME,
- Double.class, false);
- }
-
- // just add the unlocked nodes
- List<LayoutNode> nodes = new ArrayList<LayoutNode>();
- for ( LayoutNode ln : partition.getNodeList() ) {
- if ( !ln.isLocked() ) {
- nodes.add(ln);
- }
- }
-
- if (canceled)
- return;
-
- // sort the Nodes based on the degree
- Collections.sort(nodes,
- new Comparator<LayoutNode>() {
- public int compare(LayoutNode o1, LayoutNode
o2) {
- final CyNode node1 = o1.getNode();
- final CyNode node2 = o2.getNode();
- // FIXME: should allow parametrization
of edge type? (expose as tunable)
- final int d1 =
network.getAdjacentEdgeList(node1, CyEdge.Type.ANY).size();
- final int d2 =
network.getAdjacentEdgeList(node2, CyEdge.Type.ANY).size();
-
- // Create Degree Attribute
- node1.attrs().set(DEGREE_ATTR_NAME,
(double)d1);
- node2.attrs().set(DEGREE_ATTR_NAME,
(double)d2);
-
- return (d2 - d1);
- }
-
- public boolean equals(Object o) {
- return false;
- }
- });
-
- if (canceled)
- return;
-
- // place each Node in a circle
- int r = 100 * (int) Math.sqrt(nodes.size());
- double phi = (2 * Math.PI) / nodes.size();
- partition.resetNodes(); // We want to figure out our mins &
maxes anew
-
- for (int i = 0; i < nodes.size(); i++) {
- LayoutNode node = nodes.get(i);
- node.setX(r + (r * Math.sin(i * phi)));
- node.setY(r + (r * Math.cos(i * phi)));
- partition.moveNodeToLocation(node);
- }
- }
-
- public void construct() {
- super.construct();
- }
}
Added:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayoutTask.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayoutTask.java
(rev 0)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayoutTask.java
2010-09-24 22:25:37 UTC (rev 22052)
@@ -0,0 +1,106 @@
+package csplugins.layout.algorithms.graphPartition;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+import java.util.Set;
+
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyTableManager;
+import org.cytoscape.view.layout.AbstractGraphPartition;
+import org.cytoscape.view.layout.LayoutNode;
+import org.cytoscape.view.layout.LayoutPartition;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.model.View;
+import org.cytoscape.model.CyTableEntry;
+
+public class DegreeSortedCircleLayoutTask extends AbstractGraphPartition {
+
+ private String DEGREE_ATTR_NAME = "degree";
+ private CyTableManager tableMgr;
+ CyNetwork network;
+
+ /**
+ * Creates a new GridNodeLayout object.
+ */
+ public DegreeSortedCircleLayoutTask(final CyNetworkView networkView,
final String name,
+ final boolean selectedOnly, final
Set<View<CyNode>> staticNodes,
+ final String DEGREE_ATTR_NAME, CyTableManager
tableMgr)
+ {
+ super(networkView, name, selectedOnly, staticNodes);
+
+ this.DEGREE_ATTR_NAME= DEGREE_ATTR_NAME;
+ this.tableMgr = tableMgr;
+ this.network = networkView.getModel();
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param partition DOCUMENT ME!
+ */
+ public void layoutPartion(LayoutPartition partition) {
+ // Create attribute
+ if(tableMgr.getTableMap(CyTableEntry.NODE,
network).get(CyNetwork.DEFAULT_ATTRS).getUniqueColumns().contains(DEGREE_ATTR_NAME)
== false) {
+ tableMgr.getTableMap(CyTableEntry.NODE,
network).get(CyNetwork.DEFAULT_ATTRS).createColumn(DEGREE_ATTR_NAME,
+ Double.class, false);
+ }
+
+ // just add the unlocked nodes
+ List<LayoutNode> nodes = new ArrayList<LayoutNode>();
+ for ( LayoutNode ln : partition.getNodeList() ) {
+ if ( !ln.isLocked() ) {
+ nodes.add(ln);
+ }
+ }
+
+ if (cancelled)
+ return;
+
+ // sort the Nodes based on the degree
+ Collections.sort(nodes,
+ new Comparator<LayoutNode>() {
+ public int compare(LayoutNode o1, LayoutNode
o2) {
+ final CyNode node1 = o1.getNode();
+ final CyNode node2 = o2.getNode();
+ // FIXME: should allow parametrization
of edge type? (expose as tunable)
+ final int d1 =
network.getAdjacentEdgeList(node1, CyEdge.Type.ANY).size();
+ final int d2 =
network.getAdjacentEdgeList(node2, CyEdge.Type.ANY).size();
+
+ // Create Degree Attribute
+ node1.attrs().set(DEGREE_ATTR_NAME,
(double)d1);
+ node2.attrs().set(DEGREE_ATTR_NAME,
(double)d2);
+
+ return (d2 - d1);
+ }
+
+ public boolean equals(Object o) {
+ return false;
+ }
+ });
+
+ if (cancelled)
+ return;
+
+ // place each Node in a circle
+ int r = 100 * (int) Math.sqrt(nodes.size());
+ double phi = (2 * Math.PI) / nodes.size();
+ partition.resetNodes(); // We want to figure out our mins &
maxes anew
+
+ for (int i = 0; i < nodes.size(); i++) {
+ LayoutNode node = nodes.get(i);
+ node.setX(r + (r * Math.sin(i * phi)));
+ node.setY(r + (r * Math.cos(i * phi)));
+ partition.moveNodeToLocation(node);
+ }
+ }
+
+ //public void construct() {
+ // super.construct();
+ //}
+
+}
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