Author: scooter
Date: 2011-01-18 11:06:16 -0800 (Tue, 18 Jan 2011)
New Revision: 23492
Modified:
cytoscape/trunk/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutEdge.java
cytoscape/trunk/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutNode.java
cytoscape/trunk/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/force/ForceDirectedLayout.java
Log:
Provide a "discrete layout" setting for ForceDirected, and in support of that,
make LayoutEdge and LayoutNode implement Comparable.
Modified:
cytoscape/trunk/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutEdge.java
===================================================================
---
cytoscape/trunk/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutEdge.java
2011-01-18 18:18:13 UTC (rev 23491)
+++
cytoscape/trunk/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutEdge.java
2011-01-18 19:06:16 UTC (rev 23492)
@@ -54,7 +54,7 @@
* to information about the weights associated with edges, and pointers to the
* LayoutNodes that are joined by this edge.
*/
-public class LayoutEdge {
+public class LayoutEdge implements Comparable <LayoutEdge> {
// instance variables
private LayoutNode v1;
private LayoutNode v2;
@@ -181,6 +181,15 @@
return this.edge;
}
+ /**
+ * Return the edge's identifier.
+ *
+ * @return String containing the edge's identifier
+ */
+ public String getIdentifier() {
+ return this.edge.getIdentifier();
+ }
+
/**
* Return a string representation for this LayoutEdge.
*
@@ -219,4 +228,16 @@
return "normal";
}
}
+
+ /**
+ * Returns the natural order of two LayoutEdges determined by comparing
the edge
+ * identifiers.
+ *
+ * @param o2 the LayoutEdge we're comparing ourselves to
+ * @return -1 if this is less than o2, 0 if they are equal, and 1 if
this is greater than o2
+ */
+ public int compareTo(LayoutEdge o2) {
+ return getIdentifier().compareTo(o2.getIdentifier());
+ }
+
}
Modified:
cytoscape/trunk/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutNode.java
===================================================================
---
cytoscape/trunk/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutNode.java
2011-01-18 18:18:13 UTC (rev 23491)
+++
cytoscape/trunk/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutNode.java
2011-01-18 19:06:16 UTC (rev 23492)
@@ -77,7 +77,7 @@
/**
*/
-public abstract class LayoutNode {
+public abstract class LayoutNode implements Comparable<LayoutNode> {
// static (class) variables
static final double EPSILON = 0.0000001D;
@@ -400,5 +400,16 @@
return this.index;
}
+ /**
+ * Returns the natural order of two LayoutNodes determined by
comparing the node
+ * identifiers.
+ *
+ * @param o2 the LayoutNode we're comparing ourselves to
+ * @return -1 if this is less than o2, 0 if they are equal, and
1 if this is greater than o2
+ */
+ public int compareTo(LayoutNode o2) {
+ return getIdentifier().compareTo(o2.getIdentifier());
+ }
-}
\ No newline at end of file
+
+}
Modified:
cytoscape/trunk/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/force/ForceDirectedLayout.java
===================================================================
---
cytoscape/trunk/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/force/ForceDirectedLayout.java
2011-01-18 18:18:13 UTC (rev 23491)
+++
cytoscape/trunk/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/force/ForceDirectedLayout.java
2011-01-18 19:06:16 UTC (rev 23492)
@@ -73,6 +73,7 @@
double defaultSpringCoefficient = 1e-4f;
double defaultSpringLength = 50;
double defaultNodeMass = 3.0;
+ boolean discrete = false;
/**
* Value to set for doing unweighted layouts
@@ -135,8 +136,16 @@
forceItems.clear();
+ List<LayoutNode> nodeList = part.getNodeList();
+ List<LayoutEdge> edgeList = part.getEdgeList();
+
+ if (discrete) {
+ Collections.sort(nodeList);
+ Collections.sort(edgeList);
+ }
+
// initialize nodes
- for (LayoutNode ln: part.getNodeList()) {
+ for (LayoutNode ln: nodeList) {
if ( !forceItems.containsKey(ln) )
forceItems.put(ln, new ForceItem());
ForceItem fitem = forceItems.get(ln);
@@ -147,7 +156,7 @@
}
// initialize edges
- for (LayoutEdge e: part.getEdgeList()) {
+ for (LayoutEdge e: edgeList) {
LayoutNode n1 = e.getSource();
ForceItem f1 = forceItems.get(n1);
LayoutNode n2 = e.getTarget();
@@ -276,7 +285,7 @@
edgeWeighter.getWeightTunables(layoutProperties,
getInitialAttributeList());
layoutProperties.add(new Tunable("force_alg_settings",
"Algorithm settings",
- Tunable.GROUP, new
Integer(5)));
+ Tunable.GROUP, new
Integer(6)));
layoutProperties.add(new Tunable("defaultSpringCoefficient",
"Default Spring Coefficient",
Tunable.DOUBLE, new
Double(defaultSpringCoefficient)));
@@ -290,6 +299,9 @@
layoutProperties.add(new Tunable("numIterations", "Number of
Iterations",
Tunable.INTEGER, new
Integer(numIterations)));
+ layoutProperties.add(new Tunable("discrete", "Force discrete
layouts (slower)",
+ Tunable.BOOLEAN, new
Boolean(false)));
+
// layoutProperties.add(new Tunable("integrator", "Integration
algorithm to use",
// Tunable.LIST, new Integer(0),
// (Object) integratorArray,
(Object) null, 0));
@@ -353,7 +365,14 @@
}
+ t = layoutProperties.get("discrete");
+ if ((t != null) && (t.valueChanged() || force)) {
+ discrete = ((Boolean) t.getValue()).booleanValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(),
t.getValue().toString());
+ }
+
integrator = new RungeKuttaIntegrator();
/*
t = layoutProperties.get("integrator");
--
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