Author: scooter
Date: 2011-08-04 19:02:26 -0700 (Thu, 04 Aug 2011)
New Revision: 26382
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodePlugin2.java
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNodeManager.java
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/ViewUtils.java
Log:
Make sure to update settings from session files
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodePlugin2.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodePlugin2.java
2011-08-05 02:01:17 UTC (rev 26381)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodePlugin2.java
2011-08-05 02:02:26 UTC (rev 26382)
@@ -147,6 +147,9 @@
Cytoscape.getPropertyChangeSupport()
.addPropertyChangeListener(
Cytoscape.CYTOSCAPE_INITIALIZED, this);
+ Cytoscape.getPropertyChangeSupport()
+ .addPropertyChangeListener(
Cytoscape.SESSION_LOADED, this);
+
// Add our context menu
Cytoscape.getCurrentNetworkView().addNodeContextMenuListener(this);
Cytoscape.getCurrentNetworkView().addGraphViewChangeListener(this);
@@ -188,7 +191,10 @@
// Handle interaction with other plugins
groupViewer.registerWithGroupPanel();
groupViewer.haveNodeCharts();
+ groupViewer.getSettingsDialog().reloadSettings();
groupViewer.getSettingsDialog().updateNodeChartTypes();
+ } else if (e.getPropertyName() == Cytoscape.SESSION_LOADED) {
+ groupViewer.getSettingsDialog().reloadSettings();
}
}
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
2011-08-05 02:01:17 UTC (rev 26381)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
2011-08-05 02:02:26 UTC (rev 26382)
@@ -85,6 +85,7 @@
private AttributeManager attributeManager = null;
private boolean hideMetanode = true;
+ private boolean dontExpandEmpty = true;
private double metanodeOpacity = 0.;
private boolean useNestedNetworks = false;
private String nodeChartAttribute = null;
@@ -220,6 +221,9 @@
if (!isCollapsed())
return;
+ if (dontExpandEmpty && metaGroup.getNodes().size() == 0)
+ return;
+
// Handle the case where we're hidden by a collapsed parent
if (isHidden()) {
expandParent(view);
@@ -368,6 +372,15 @@
}
/**
+ * Sets whether or not we should expand empty metanodes.
+ *
+ * @param dontExpandEmpty if 'true' we will use nested networks
+ */
+ public void setDontExpandEmpty(boolean dontExpandEmpty) {
+ this.dontExpandEmpty = dontExpandEmpty;
+ }
+
+ /**
* Sets the metanode opacity
*
* @param opacity the metanode opacity
@@ -517,10 +530,10 @@
while(iterator.hasNext()) {
CyEdge edge = iterator.next();
CyNode node = getPartner(edge);
- // logger.debug("Outer edge = "+edge.getIdentifier());
+ logger.debug("Outer edge = "+edge.getIdentifier());
if (ignoreMetaEdges && isMeta(edge)) {
- // logger.debug("...ignoring");
+ logger.debug("...ignoring");
addMetaEdge(edge);
continue;
}
@@ -531,7 +544,6 @@
if (edge.getSource() == groupNode || edge.getTarget()
== groupNode)
continue;
-
// Create the meta-edge to the external node, but
maintain the directionality of the
// original edge
CyEdge metaEdge = null;
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNodeManager.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNodeManager.java
2011-08-05 02:01:17 UTC (rev 26381)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNodeManager.java
2011-08-05 02:02:26 UTC (rev 26382)
@@ -60,6 +60,7 @@
protected static boolean hideMetanodeDefault = true;
protected static double metanodeOpacityDefault = 255.;
protected static boolean useNestedNetworksDefault = false;
+ protected static boolean dontExpandEmptyDefault = true;
protected static String chartTypeDefault = null;
protected static String nodeChartAttributeDefault = null;
protected static AttributeManager defaultAttributeManager = new
AttributeManager();
@@ -113,6 +114,7 @@
metaMap.put(metaGroup.getGroupNode(), mn);
mn.setUseNestedNetworks(useNestedNetworksDefault);
+ mn.setDontExpandEmpty(dontExpandEmptyDefault);
mn.setHideMetaNode(hideMetanodeDefault);
mn.setMetaNodeOpacity(metanodeOpacityDefault);
mn.setChartType(chartTypeDefault);
@@ -258,11 +260,9 @@
}
/**
- * Sets whether or not we size the metnode to the bounding box
- * of all of the children when we expand the network. NOTE:
- * this only makes sense if hideMetanode is false.
+ * Sets whether or not we use the nested network viewer
*
- * @param useNestedNetworks if 'true' we use nexted networks when we
collapse
+ * @param useNestedNetworks if 'true' we use nested networks when we
collapse
*/
static public void setUseNestedNetworksDefault(boolean
useNestedNetworks) {
MetaNodeManager.useNestedNetworksDefault = useNestedNetworks;
@@ -279,6 +279,24 @@
}
/**
+ * Sets whether or not we expand empty metanodes
+ *
+ * @param dontExpandEmpty if 'true' we won't expand empty metanodes
+ */
+ static public void setDontExpandEmptyDefault(boolean dontExpandEmpty) {
+ MetaNodeManager.dontExpandEmptyDefault = dontExpandEmpty;
+ }
+
+ /**
+ * Returns 'true' if we don't expand empty metanodes.
+ *
+ * @return 'true' if we don't expand empty metanodes.
+ */
+ static public boolean getDontExpandEmptyDefault() {
+ return MetaNodeManager.dontExpandEmptyDefault;
+ }
+
+ /**
* Sets the attribute to use for node charting.
*
* @param nodeChartAttribute the attribute to use for node charts
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
2011-08-05 02:01:17 UTC (rev 26381)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
2011-08-05 02:02:26 UTC (rev 26382)
@@ -56,6 +56,7 @@
import cytoscape.groups.CyGroupViewer;
import cytoscape.layout.Tunable;
import cytoscape.layout.TunableListener;
+import cytoscape.logger.CyLogger;
import cytoscape.visual.VisualPropertyDependency;
import cytoscape.visual.VisualStyle;
@@ -100,6 +101,7 @@
private List<Tunable>tunableEnablers = null;
private List<Tunable>nodeChartEnablers = null;
private boolean hideMetaNode = true;
+ private boolean dontExpandEmpty = true;
private boolean enableHandling = false;
private boolean useNestedNetworks = false;
private double metanodeOpacity = 255.0f;
@@ -208,7 +210,7 @@
metanodeProperties.add(new Tunable("appearanceGroup", "Metanode
Appearance",
- Tunable.GROUP, new
Integer(2),
+ Tunable.GROUP, new
Integer(4),
new Boolean(true), null,
Tunable.COLLAPSABLE));
{
{
@@ -219,6 +221,22 @@
metanodeProperties.add(t);
}
+ {
+ Tunable t = new Tunable("hideMetaNodes",
+ "Hide metanodes when
expanded",
+ Tunable.BOOLEAN, new
Boolean(true), 0);
+ t.addTunableValueListener(this);
+ metanodeProperties.add(t);
+ }
+
+ {
+ Tunable t = new Tunable("dontExpandEmpty",
+ "Don't expand empty
metanodes",
+ Tunable.BOOLEAN, new
Boolean(true), 0);
+ t.addTunableValueListener(this);
+ metanodeProperties.add(t);
+ }
+
// Sliders always look better when grouped
metanodeProperties.add(new Tunable("opacityGroup",
"Metanode Opacity",
Tunable.GROUP, new
Integer(1),
@@ -306,9 +324,6 @@
tunableEnablers.add(t);
}
- // We only really care about the property settings for our
defaults
- metanodeProperties.initializeProperties();
-
metanodeProperties.add(new Tunable("attributesGroup",
"Overrides for Specific
Attributes",
Tunable.GROUP, new
Integer(3),
@@ -336,6 +351,8 @@
// Update
tunableChanged(attrList);
}
+
+ reloadSettings();
updateSettings(true);
}
@@ -358,6 +375,13 @@
metanodeProperties.setProperty(t.getName(),
t.getValue().toString());
}
+ t = metanodeProperties.get("dontExpandEmpty");
+ if ((t != null) && (t.valueChanged() || force)) {
+ dontExpandEmpty = ((Boolean) t.getValue()).booleanValue();
+ MetaNodeManager.setHideMetaNodeDefault(dontExpandEmpty);
+ metanodeProperties.setProperty(t.getName(),
t.getValue().toString());
+ }
+
t = metanodeProperties.get("useNestedNetworks");
if ((t != null) && (t.valueChanged() || force)) {
useNestedNetworks = ((Boolean) t.getValue()).booleanValue();
@@ -433,6 +457,17 @@
}
/**
+ * Reload our properties (used when a new session is loaded)
+ */
+ public void reloadSettings() {
+ try {
+ metanodeProperties.initializeProperties();
+ } catch (Exception e) {
+ CyLogger.getLogger("metaNodePlugin").warning("Exception
when initializing properties: '"+e.getMessage()+"' -- continuing");
+ }
+ }
+
+ /**
* Update all of our attribute manager override values
*
* @param network the network we're updating our override values for
@@ -598,6 +633,7 @@
public void updateMetaNodeSettings(MetaNode mn) {
mn.setUseNestedNetworks(useNestedNetworks);
+ mn.setDontExpandEmpty(dontExpandEmpty);
// mn.setSizeToBoundingBox(sizeToBoundingBox);
mn.setHideMetaNode(hideMetaNode);
// System.out.println("setting opacity for "+mn+" to
"+metanodeOpacity);
@@ -611,6 +647,9 @@
if (t.getName().equals("hideMetanodes")) {
hideMetaNode = ((Boolean) t.getValue()).booleanValue();
MetaNodeManager.setHideMetaNodeDefault(hideMetaNode);
+ } else if (t.getName().equals("dontExpandEmpty")) {
+ dontExpandEmpty = ((Boolean) t.getValue()).booleanValue();
+
MetaNodeManager.setDontExpandEmptyDefault(dontExpandEmpty);
} else if (t.getName().equals("useNestedNetworks")) {
useNestedNetworks = ((Boolean) t.getValue()).booleanValue();
MetaNodeManager.setUseNestedNetworksDefault(useNestedNetworks);
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/ViewUtils.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/ViewUtils.java
2011-08-05 02:01:17 UTC (rev 26381)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/ViewUtils.java
2011-08-05 02:02:26 UTC (rev 26382)
@@ -258,11 +258,13 @@
* @param view the CyNetworkView
*/
public static void hideEdges(CyGroup metaGroup,
Collection<CyEdge>edgeList, CyNetworkView view) {
+ /*
CyNetwork network = metaGroup.getNetwork();
for (CyEdge edge: edgeList) {
if (network.containsEdge(edge))
network.hideEdge(edge);
}
+ */
}
/**
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