Author: kono
Date: 2010-01-19 12:22:55 -0800 (Tue, 19 Jan 2010)
New Revision: 18963
Modified:
csplugins/trunk/ucsd/ruschein/BipartiteVisualiser/src/org/cytoscape/BipartiteVisualiserPlugin/duallayout/LayoutEngine.java
csplugins/trunk/ucsd/ruschein/BipartiteVisualiser/src/org/cytoscape/BipartiteVisualiserPlugin/duallayout/VisualStyleBuilder.java
Log:
First working version of Visualizer.
Modified:
csplugins/trunk/ucsd/ruschein/BipartiteVisualiser/src/org/cytoscape/BipartiteVisualiserPlugin/duallayout/LayoutEngine.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/BipartiteVisualiser/src/org/cytoscape/BipartiteVisualiserPlugin/duallayout/LayoutEngine.java
2010-01-19 20:19:56 UTC (rev 18962)
+++
csplugins/trunk/ucsd/ruschein/BipartiteVisualiser/src/org/cytoscape/BipartiteVisualiserPlugin/duallayout/LayoutEngine.java
2010-01-19 20:22:55 UTC (rev 18963)
@@ -14,16 +14,19 @@
import cytoscape.CyNode;
import cytoscape.Cytoscape;
import cytoscape.data.CyAttributes;
+import cytoscape.layout.CyLayoutAlgorithm;
import cytoscape.layout.CyLayouts;
+import cytoscape.layout.Tunable;
import cytoscape.task.TaskMonitor;
import cytoscape.view.CyNetworkView;
-import cytoscape.view.CyNodeView;
import cytoscape.visual.VisualStyle;
public class LayoutEngine {
static String MM_EDGE_ATTR_PREFIX = "MM-";
+
+ private static final String LAYOUT_ALGORITHM = "force-directed";
private final EdgeView edgeView;
@@ -106,9 +109,12 @@
final Set<CyNode> rightSet = new HashSet<CyNode>();
categoriseNodes(result, leftSet, rightSet);
+ // First, apply global layout
final CyNetworkView networkView =
Cytoscape.createNetworkView(result);
- CyLayouts.getDefaultLayout().doLayout(networkView);
-
+ final CyLayoutAlgorithm layoutAlgorithm =
CyLayouts.getLayout(LAYOUT_ALGORITHM);
+
layoutAlgorithm.getSettings().get("defaultSpringLength").setValue((Double)200.0);
+ layoutAlgorithm.doLayout(networkView);
+
final double[] xMin = new double[3];
final double[] xMax = new double[3];
final double[] yMin = new double[3];
@@ -152,7 +158,10 @@
while (nodeViewsIterator.hasNext())
((NodeView)nodeViewsIterator.next()).setNodePosition(true);
- final VisualStyle style =
VisualStyleBuilder.getVisualStyle(visualStyleName, network1.getTitle(),
network2.getTitle());
+ VisualStyle style =
Cytoscape.getVisualMappingManager().getCalculatorCatalog().getVisualStyle(visualStyleName);
+ if(style == null || style.getName().equals("default")) {
+ style =
VisualStyleBuilder.getVisualStyle(visualStyleName, network1.getTitle(),
network2.getTitle());
+ }
networkView.setVisualStyle(style.getName());
Cytoscape.getVisualMappingManager().setVisualStyle(style);
networkView.redrawGraph(false, true);
Modified:
csplugins/trunk/ucsd/ruschein/BipartiteVisualiser/src/org/cytoscape/BipartiteVisualiserPlugin/duallayout/VisualStyleBuilder.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/BipartiteVisualiser/src/org/cytoscape/BipartiteVisualiserPlugin/duallayout/VisualStyleBuilder.java
2010-01-19 20:19:56 UTC (rev 18962)
+++
csplugins/trunk/ucsd/ruschein/BipartiteVisualiser/src/org/cytoscape/BipartiteVisualiserPlugin/duallayout/VisualStyleBuilder.java
2010-01-19 20:22:55 UTC (rev 18963)
@@ -89,10 +89,10 @@
nac.getDefaultAppearance().set(VisualPropertyType.NODE_LABEL_POSITION,
POSITION);
-
nac.getDefaultAppearance().set(VisualPropertyType.NODE_LINE_WIDTH, 5);
+
nac.getDefaultAppearance().set(VisualPropertyType.NODE_LINE_WIDTH, 3);
nac.getDefaultAppearance().set(VisualPropertyType.NODE_BORDER_COLOR,
NODE_BORDER_COLOR_1);
- nac.getDefaultAppearance().set(VisualPropertyType.NODE_SIZE,
45);
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_SIZE,
35);
nac.getDefaultAppearance().set(VisualPropertyType.NODE_LABEL_COLOR,
NODE_LABEL_COLOR);
@@ -118,7 +118,7 @@
eac.getDefaultAppearance().set(VisualPropertyType.EDGE_LABEL_COLOR,
EDGE_LABEL_COLOR);
eac.getDefaultAppearance().set(VisualPropertyType.EDGE_FONT_SIZE, 5);
- eac.getDefaultAppearance().set(VisualPropertyType.EDGE_OPACITY,
190);
+ eac.getDefaultAppearance().set(VisualPropertyType.EDGE_OPACITY,
100);
eac.getDefaultAppearance().set(
VisualPropertyType.EDGE_SRCARROW_OPACITY, 120);
eac.getDefaultAppearance().set(
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