Author: scooter
Date: 2011-06-08 18:28:57 -0700 (Wed, 08 Jun 2011)
New Revision: 25685
Modified:
cytoscape/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExecuteGetRecordByCPathId.java
cytoscape/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/NetworkUtil.java
Log:
Remove references to retired biopax class LayoutUtil.
Modified:
cytoscape/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExecuteGetRecordByCPathId.java
===================================================================
---
cytoscape/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExecuteGetRecordByCPathId.java
2011-06-09 01:17:34 UTC (rev 25684)
+++
cytoscape/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExecuteGetRecordByCPathId.java
2011-06-09 01:28:57 UTC (rev 25685)
@@ -26,7 +26,6 @@
import cytoscape.coreplugins.biopax.MapBioPaxToCytoscape;
import cytoscape.coreplugins.biopax.util.BioPaxUtil;
import cytoscape.coreplugins.biopax.util.CytoscapeWrapper;
-import cytoscape.coreplugins.biopax.util.LayoutUtil;
import cytoscape.coreplugins.biopax.action.NetworkListener;
import cytoscape.coreplugins.biopax.view.BioPaxContainer;
import cytoscape.coreplugins.biopax.util.BioPaxVisualStyleUtil;
@@ -266,7 +265,7 @@
VisualStyle visualStyle =
BinarySifVisualStyleUtil.getVisualStyle();
// Set up the right layout algorithm.
- LayoutUtil layoutAlgorithm = new LayoutUtil();
+ CyLayoutAlgorithm layoutAlgorithm =
CyLayouts.getLayout("force-directed");
// Now, create the view.
// Use local create view option, so that we don't mess up the
visual style.
@@ -325,7 +324,7 @@
VisualStyle visualStyle =
BioPaxVisualStyleUtil.getBioPaxVisualStyle();
// Set up the right layout algorithm.
- LayoutUtil layoutAlgorithm = new LayoutUtil();
+ CyLayoutAlgorithm layoutAlgorithm =
CyLayouts.getLayout("force-directed");
// Now, create the view.
// Use local create view option, so that we don't mess up the
visual style.
@@ -396,7 +395,7 @@
if (n==0) {
SwingUtilities.invokeLater(new Runnable() {
public void run() {
- LayoutUtil layoutAlgorithm = new LayoutUtil();
+ CyLayoutAlgorithm layoutAlgorithm =
CyLayouts.getLayout("force-directed");
networkView.applyLayout(layoutAlgorithm);
Cytoscape.getCurrentNetworkView().fitContent();
}
Modified:
cytoscape/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/NetworkUtil.java
===================================================================
---
cytoscape/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/NetworkUtil.java
2011-06-09 01:17:34 UTC (rev 25684)
+++
cytoscape/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/NetworkUtil.java
2011-06-09 01:28:57 UTC (rev 25685)
@@ -36,12 +36,13 @@
import cytoscape.CyNetwork;
import cytoscape.Cytoscape;
import cytoscape.data.CyAttributes;
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.layout.CyLayouts;
import cytoscape.task.ui.JTaskConfig;
import cytoscape.task.util.TaskManager;
import cytoscape.view.CyNetworkView;
import cytoscape.view.CytoscapeDesktop;
import ding.view.NodeContextMenuListener;
-import cytoscape.coreplugins.biopax.util.LayoutUtil;
import org.cytoscape.coreplugin.cpath2.task.MergeNetworkTask;
import org.cytoscape.coreplugin.cpath2.task.LoadNetworkFromUrlTask;
@@ -235,8 +236,8 @@
// if do layout, do it
if (doLayout) {
- LayoutUtil layoutUtil = new LayoutUtil();
- layoutUtil.doLayout(view);
+ CyLayoutAlgorithm layout = CyLayouts.getLayout("force-directed");
+ view.applyLayout(layout);
view.fitContent();
}
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
