Author: pwang
Date: 2010-09-24 14:45:17 -0700 (Fri, 24 Sep 2010)
New Revision: 22051
Added:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayoutTask.java
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
Log:
Refactored
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
2010-09-24 21:24:43 UTC (rev 22050)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
2010-09-24 21:45:17 UTC (rev 22051)
@@ -40,17 +40,20 @@
import java.util.Map;
import java.util.Set;
-import org.cytoscape.view.layout.AbstractGraphPartition;
+//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.view.layout.LayoutPartition;
+import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.Tunable;
+import org.cytoscape.work.TunableValidator;
import org.cytoscape.work.undo.UndoSupport;
/**
*
*/
-public class AttributeCircleLayout extends AbstractGraphPartition {
+public class AttributeCircleLayout extends AbstractLayout implements
TunableValidator {
@Tunable(description="The attribute to use for the layout")
public String attribute = null;
@Tunable(description="The attribute namespace to use for the layout")
@@ -77,6 +80,21 @@
initialize(true);
}
+
+
+ //TODO
+ public boolean tunablesAreValid(final Appendable errMsg) {
+ return true;
+ }
+
+ public TaskIterator getTaskIterator() {
+
+ return new TaskIterator(new
AttributeCircleLayoutTask(networkView, getName(), selectedOnly, staticNodes,
+
attribute,namespace,spacing,supportNodeAttributes));
+ }
+
+
+
/**
* DOCUMENT ME!
*
@@ -158,88 +176,4 @@
return "attribute-circle";
}
- /**
- * DOCUMENT ME!
- *
- * @param partition DOCUMENT ME!
- */
- public void layoutPartion(LayoutPartition partition) {
- // just add the unlocked nodes
- List<LayoutNode> nodes = new ArrayList<LayoutNode>();
- for ( LayoutNode ln : partition.getNodeList() ) {
- if ( !ln.isLocked() ) {
- nodes.add(ln);
- }
- }
-
- int count = nodes.size();
- int r = (int) Math.sqrt(count);
- r *= spacing;
-
- if (this.attribute != null && count > 0) {
- Class<?> klass =
nodes.get(0).getNode().getCyRow(namespace).contains(attribute);
- if (klass != null &&
Comparable.class.isAssignableFrom(klass)){
- // FIXME: I assume this would be better, but
get type errors if I try:
- //Class<Comparable<?>> kasted =
(Class<Comparable<?>>) klass;
- //Collections.sort(nodes, new
AttributeComparator<Comparable<?>>(kasted));
- Collections.sort(nodes, new
AttributeComparator(klass));
- } else {
- /* FIXME Error! */
- }
- }
-
- // Compute angle step
- double phi = (2 * Math.PI) / count;
-
- partition.resetNodes(); // We want to figure out our mins &
maxes anew
- // Arrange vertices in a circle
-
- for (int i = 0; i < count; i++) {
- LayoutNode node = (LayoutNode) nodes.get(i);
- double x = r + (r * Math.sin(i * phi));
- double y = r + (r * Math.cos(i * phi));
- node.setX(x);
- node.setY(y);
- partition.moveNodeToLocation(node);
- }
- }
- private class AttributeComparator<T extends Comparable<T>> implements
Comparator<LayoutNode> {
- Class<T> klass;
- private AttributeComparator(Class<T> klass) {
- this.klass = klass;
- }
-
- public int compare(LayoutNode o1, LayoutNode o2) {
- T v1 = o1.getNode().getCyRow(namespace).get(attribute,
klass);
- T v2 = o2.getNode().getCyRow(namespace).get(attribute,
klass);
- if (String.class.isAssignableFrom(klass)){ // i.e. if
klass _is_ String.class
- String s1 = String.class.cast(v1);
- String s2 = String.class.cast(v2);
- if ((s1 != null) && (s2 != null))
- return s1.compareToIgnoreCase(s2);
- else if ((s1 == null) && (s2 != null))
- return -1;
- else if ((s1 == null) && (s2 == null))
- return 0;
- else if ((s1 != null) && (s2 == null))
- return 1;
-
- } else {
- return compareEvenIfNull(v1, v2);
- }
-
- return 0; // can't happen anyway
- }
-
- public int compareEvenIfNull(T v1, T v2){
- if ((v1 != null) && (v2 != null))
- return v1.compareTo(v2);
- else if ((v1 == null) && (v2 != null))
- return -1;
- else if ((v1 == null) && (v2 == null))
- return 0;
- else // if ((v1 != null) && (v2 == null)) // this is
the only possibility
- return 1;
- }
- }
}
Added:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayoutTask.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayoutTask.java
(rev 0)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayoutTask.java
2010-09-24 21:45:17 UTC (rev 22051)
@@ -0,0 +1,128 @@
+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.CyNode;
+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.work.Tunable;
+
+public class AttributeCircleLayoutTask extends AbstractGraphPartition {
+
+ public String attribute = null;
+ public String namespace = null;
+ public double spacing = 100.0;
+ boolean supportNodeAttributes = true;
+
+
+ /**
+ * Creates a new ForceDirectedLayout object.
+ */
+ public AttributeCircleLayoutTask(final CyNetworkView networkView, final
String name,
+ final boolean selectedOnly, final
Set<View<CyNode>> staticNodes,
+ final String attribute,final String
namespace,final double spacing,final boolean supportNodeAttributes)
+ {
+
+ super(networkView, name, selectedOnly, staticNodes);
+
+ this.attribute = attribute;
+ this.namespace = namespace;
+ this.spacing = spacing;
+ this.supportNodeAttributes = supportNodeAttributes;
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param partition DOCUMENT ME!
+ */
+ public void layoutPartion(LayoutPartition partition) {
+ // just add the unlocked nodes
+ List<LayoutNode> nodes = new ArrayList<LayoutNode>();
+ for ( LayoutNode ln : partition.getNodeList() ) {
+ if ( !ln.isLocked() ) {
+ nodes.add(ln);
+ }
+ }
+
+ int count = nodes.size();
+ int r = (int) Math.sqrt(count);
+ r *= spacing;
+
+ if (this.attribute != null && count > 0) {
+ Class<?> klass =
nodes.get(0).getNode().getCyRow(namespace).contains(attribute);
+ if (klass != null &&
Comparable.class.isAssignableFrom(klass)){
+ // FIXME: I assume this would be better, but
get type errors if I try:
+ //Class<Comparable<?>> kasted =
(Class<Comparable<?>>) klass;
+ //Collections.sort(nodes, new
AttributeComparator<Comparable<?>>(kasted));
+ Collections.sort(nodes, new
AttributeComparator(klass));
+ } else {
+ /* FIXME Error! */
+ }
+ }
+
+ // Compute angle step
+ double phi = (2 * Math.PI) / count;
+
+ partition.resetNodes(); // We want to figure out our mins &
maxes anew
+ // Arrange vertices in a circle
+
+ for (int i = 0; i < count; i++) {
+ LayoutNode node = (LayoutNode) nodes.get(i);
+ double x = r + (r * Math.sin(i * phi));
+ double y = r + (r * Math.cos(i * phi));
+ node.setX(x);
+ node.setY(y);
+ partition.moveNodeToLocation(node);
+ }
+ }
+
+ private class AttributeComparator<T extends Comparable<T>> implements
Comparator<LayoutNode> {
+ Class<T> klass;
+ private AttributeComparator(Class<T> klass) {
+ this.klass = klass;
+ }
+
+ public int compare(LayoutNode o1, LayoutNode o2) {
+ T v1 = o1.getNode().getCyRow(namespace).get(attribute,
klass);
+ T v2 = o2.getNode().getCyRow(namespace).get(attribute,
klass);
+ if (String.class.isAssignableFrom(klass)){ // i.e. if
klass _is_ String.class
+ String s1 = String.class.cast(v1);
+ String s2 = String.class.cast(v2);
+ if ((s1 != null) && (s2 != null))
+ return s1.compareToIgnoreCase(s2);
+ else if ((s1 == null) && (s2 != null))
+ return -1;
+ else if ((s1 == null) && (s2 == null))
+ return 0;
+ else if ((s1 != null) && (s2 == null))
+ return 1;
+
+ } else {
+ return compareEvenIfNull(v1, v2);
+ }
+
+ return 0; // can't happen anyway
+ }
+
+ public int compareEvenIfNull(T v1, T v2){
+ if ((v1 != null) && (v2 != null))
+ return v1.compareTo(v2);
+ else if ((v1 == null) && (v2 != null))
+ return -1;
+ else if ((v1 == null) && (v2 == null))
+ return 0;
+ else // if ((v1 != null) && (v2 == null)) // this is
the only possibility
+ return 1;
+ }
+ }
+
+}
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