Author: scooter
Date: 2008-10-31 13:05:18 -0700 (Fri, 31 Oct 2008)
New Revision: 15155
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/resources/plugin.props
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodePlugin2.java
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
Log:
Significantly enhanced to behave better across multiple views
Modified: csplugins/trunk/ucsf/scooter/metaNodePlugin2/resources/plugin.props
===================================================================
--- csplugins/trunk/ucsf/scooter/metaNodePlugin2/resources/plugin.props
2008-10-31 18:48:48 UTC (rev 15154)
+++ csplugins/trunk/ucsf/scooter/metaNodePlugin2/resources/plugin.props
2008-10-31 20:05:18 UTC (rev 15155)
@@ -13,7 +13,7 @@
pluginDescription=This plugin provides a viewer for groups that implements a
collapse/expand abstraction
# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
-pluginVersion=1.2
+pluginVersion=1.3
# Compatible Cytoscape version
cytoscapeVersion=2.6.1
@@ -31,4 +31,4 @@
pluginAuthorsIntsitutions=John "Scooter" Morris:UCSF
# Date this plugin/plugin version was released
-releaseDate=July 18, 2008
+releaseDate=October 31, 2008
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodePlugin2.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodePlugin2.java
2008-10-31 18:48:48 UTC (rev 15154)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodePlugin2.java
2008-10-31 20:05:18 UTC (rev 15155)
@@ -173,14 +173,14 @@
* @param group the CyGroup that was just created
*/
public void groupCreated(CyGroup group) {
- // logger.info("groupCreated("+group+")");
+ // logger.debug("groupCreated("+group+")");
if (MetaNode.getMetaNode(group) == null) {
MetaNode newNode = new MetaNode(group);
}
// Update the attributes of the group node
- // logger.info("registering");
+ // logger.debug("registering");
registerWithGroupPanel();
- // logger.info("done");
+ // logger.debug("done");
}
/**
@@ -193,7 +193,7 @@
* @param view the CyNetworkView that is being created
*/
public void groupCreated(CyGroup group, CyNetworkView myview) {
- // logger.info("groupCreated("+group+", view)");
+ // logger.debug("groupCreated("+group+", view)");
if (MetaNode.getMetaNode(group) == null) {
MetaNode newNode = new MetaNode(group);
@@ -208,9 +208,9 @@
network.hideNode(group.getGroupNode());
}
}
- // logger.info("registering");
+ // logger.debug("registering");
registerWithGroupPanel();
- // logger.info("done");
+ // logger.debug("done");
}
/**
@@ -223,10 +223,9 @@
*/
public void groupWillBeRemoved(CyGroup group) {
MetaNode mn = MetaNode.getMetaNode(group);
- // Expand the group
- if (group.getState() == COLLAPSED) {
- mn.expand(true, null, true);
- }
+ // Expand the group in any views that it's collapsed
+ mn.expand(true, null, true);
+
// Get rid of the MetaNode
MetaNode.removeMetaNode(mn);
}
@@ -265,6 +264,7 @@
public void propertyChange (PropertyChangeEvent e) {
if (e.getPropertyName() ==
CytoscapeDesktop.NETWORK_VIEW_CREATED) {
((CyNetworkView)e.getNewValue()).addNodeContextMenuListener(this);
+ MetaNode.newView((CyNetworkView)e.getNewValue());
}
}
@@ -406,6 +406,7 @@
private void addMenuItem(JMenu menu, Command command,
List<CyGroup>groupList,
CyNode contextNode, String label) {
+ CyNetworkView view = Cytoscape.getCurrentNetworkView();
if (groupList == null || groupList.size() == 0) {
if (contextNode == null) {
JMenuItem item = new JMenuItem(label);
@@ -435,13 +436,16 @@
} else if (contextNode.isaGroup() && command ==
Command.EXPAND) {
// Get the groups this group is a member of
CyGroup group =
CyGroupManager.findGroup(contextNode.getIdentifier());
- if (group.getState() == COLLAPSED) {
+ // Get the MetaNode
+ MetaNode metaNode =
MetaNode.getMetaNode(group.getGroupNode());
+ if (metaNode.isCollapsed(view)) {
addSubMenu(menu, label+"
"+group.getGroupName(),
command, group, contextNode);
}
} else if (CyGroupManager.isaGroup(contextNode) &&
command == Command.EXPANDNEW) {
CyGroup group =
CyGroupManager.findGroup(contextNode.getIdentifier());
- if (group.getState() == COLLAPSED) {
+ MetaNode metaNode =
MetaNode.getMetaNode(group.getGroupNode());
+ if (metaNode.isCollapsed(view)) {
addSubMenu(menu, label+"
"+group.getGroupName()+" into new network",
command, group, contextNode);
}
@@ -502,6 +506,7 @@
List<CyGroup>nodeGroups = null;
boolean foundItem = false;
if (groupList == null) return false;
+ CyNetworkView view = Cytoscape.getCurrentNetworkView();
if (command == Command.ADD && node != null) {
nodeGroups = node.getGroups();
@@ -512,15 +517,17 @@
List<CyGroup> parents = groupNode.getGroups();
if (group.getViewer() != null &&
group.getViewer().equals(groupViewer.getViewerName())) {
// Only present reasonable choices to
the user
- if ((command == Command.COLLAPSE &&
group.getState() == COLLAPSED) ||
- (command == Command.EXPAND &&
group.getState() == EXPANDED))
+ MetaNode metaNode =
MetaNode.getMetaNode(group.getGroupNode());
+ if ((command == Command.COLLAPSE &&
metaNode.isCollapsed(view)) ||
+ (command == Command.EXPAND &&
metaNode.isCollapsed(view)))
continue;
// If command is expand and we're a
child of a group that isn't
// yet expanded, don't give this as an
option
if ((command == Command.EXPAND) &&
(parents != null) && (parents.size() > 0)) {
boolean parentCollapsed = false;
for (CyGroup parent: parents) {
- if
(groupList.contains(parent) && (parent.getState() == COLLAPSED)) {
+ MetaNode metaParent =
MetaNode.getMetaNode(parent.getGroupNode());
+ if
(groupList.contains(parent) && (metaParent.isCollapsed(view))) {
parentCollapsed
= true;
break;
}
@@ -529,7 +536,7 @@
}
if (command == Command.ADD) {
- MetaNode metaNode = null;
+ metaNode = null;
// Are we already in this group?
if ((nodeGroups != null) &&
(nodeGroups.contains(group)))
continue;
@@ -634,7 +641,7 @@
}
MetaNode newNode = new MetaNode(group);
groupCreated(group);
- newNode.collapse(recursive, multipleEdges, true, null);
+ newNode.collapse(recursive, multipleEdges, true,
Cytoscape.getCurrentNetworkView());
}
/**
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
2008-10-31 18:48:48 UTC (rev 15154)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
2008-10-31 20:05:18 UTC (rev 15155)
@@ -33,12 +33,13 @@
package metaNodePlugin2.model;
// System imports
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Iterator;
import java.util.List;
import java.util.ListIterator;
-import java.util.HashMap;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.Collection;
+import java.util.Map;
import java.awt.Dimension;
// giny imports
@@ -78,7 +79,6 @@
public class MetaNode {
// Static variables
private static HashMap<CyNode,MetaNode> metaMap = new HashMap();
- private static HashMap<CyNode,Boolean> hiddenNodes = new HashMap();
private static final boolean DEBUG = false;
public static final String X_HINT_ATTR = "__metanodeHintX";
@@ -100,7 +100,7 @@
private boolean multipleEdges = false;
private boolean recursive = false;
- protected boolean isCollapsed = false;
+ protected Map<CyNetworkView, Boolean> collapsedMap = null;
private CyAttributes edgeAttributes = null;
private CyAttributes nodeAttributes = null;
@@ -169,7 +169,7 @@
CyNetworkView nView = Cytoscape.getCurrentNetworkView();
Collection<MetaNode> metaNodes = metaMap.values();
for (MetaNode mNode: metaNodes) {
- if (mNode.isCollapsed)
+ if (mNode.isCollapsed(nView))
mNode.expand(true, nView, false);
}
// VisualMappingManager vizmapper =
Cytoscape.getVisualMappingManager();
@@ -184,7 +184,7 @@
CyNetworkView nView = Cytoscape.getCurrentNetworkView();
Collection<MetaNode> metaNodes = metaMap.values();
for (MetaNode mNode: metaNodes) {
- if (!mNode.isCollapsed)
+ if (!mNode.isCollapsed(nView))
mNode.collapse(true, true, false, nView);
}
// VisualMappingManager vizmapper =
Cytoscape.getVisualMappingManager();
@@ -192,8 +192,29 @@
nView.updateView();
}
+ /**
+ * Update the collapse/expand information for all metanodes
+ * in the provided view
+ *
+ * @param view the view to update
+ */
+ static public void newView(CyNetworkView view) {
+ CyNetwork net = view.getNetwork();
+ for (MetaNode mn: metaMap.values()) {
+ CyNode groupNode = mn.getCyGroup().getGroupNode();
+ // Is this actually collapsed in this view?
+ if (net.containsNode(groupNode)) {
+ // Yes, mark it as so
+ mn.collapsedMap.put(view, Boolean.TRUE);
+ } else {
+ // No, make it so
+ mn.collapsedMap.put(view, Boolean.FALSE);
+ }
+ }
+ }
+
/*****************************************************************
* Public methods *
****************************************************************/
@@ -208,6 +229,7 @@
groupNode = group.getGroupNode();
metaMap.put(groupNode, this);
metaEdgeMap = new HashMap();
+ collapsedMap = new HashMap();
logger = CyLogger.getLogger(MetaNode.class);
if (DEBUG) logger.debug("Creating meta-group
"+group.getGroupName());
@@ -253,8 +275,7 @@
group.addOuterEdge(edge);
}
}
- // Note that this node is hidden
- hiddenNodes.put(groupNode, Boolean.TRUE);
+ collapsedMap.put(networkView, Boolean.FALSE);
updateAttributes();
if (DEBUG) logger.debug("... done\n\n");
}
@@ -335,7 +356,7 @@
// Finally, if we're collapsed, hide this node (possibly
recursively) and
// update the display
- if (!isCollapsed)
+ if (!isCollapsed(networkView))
return;
// Get the X and Y coordinates of the metaNode
@@ -377,7 +398,7 @@
public void nodeRemoved(CyNode node) {
update(null);
// If we're collapsed, unhide the node
- if (isCollapsed) {
+ if (isCollapsed(networkView)) {
restoreNode(node, null);
}
@@ -396,7 +417,7 @@
if (edge.getTarget() == node ||
edge.getSource() == node) {
// Remove it from this metaEdge
edgeIter.remove();
- if (isCollapsed) {
+ if (isCollapsed(networkView)) {
restoreEdge(edge);
}
}
@@ -422,7 +443,7 @@
// Rats, looks like we need to create metaEdges
for this node
CyEdge metaEdge = createMetaEdge(edge, null,
false);
// If we're expanded, hide it
- if (!isCollapsed) {
+ if (!isCollapsed(networkView)) {
hideEdge(metaEdge);
}
}
@@ -449,7 +470,7 @@
if (newEdgeMap == null)
createMetaEdges();
- isCollapsed = true;
+ collapsedMap.put(view, Boolean.TRUE);
expand(recursive, view, true);
collapse(recursive, multipleEdges, false, view);
}
@@ -465,15 +486,16 @@
*/
public void collapse(boolean recursive, boolean multipleEdges, boolean
updateNetwork,
CyNetworkView view) {
- if (isCollapsed)
+ // Initialize
+ update(view);
+
+ if (isCollapsed(networkView))
return;
if (DEBUG) logger.debug("collapsing "+groupNode);
// Profile prf = new Profile();
// prf.start();
- // Initialize
- update(view);
// prf.done("collapse: Update=");
this.multipleEdges = multipleEdges;
@@ -487,7 +509,7 @@
createMetaEdges();
// prf.done("collapse: createMetaEdges=");
- isCollapsed = true;
+ collapsedMap.put(view, Boolean.TRUE);
// Set our state
metaGroup.setState(MetaNodePlugin2.COLLAPSED);
@@ -506,14 +528,23 @@
* @param update update the display?
*/
public void expand(boolean recursive, CyNetworkView view, boolean
update) {
- if (!isCollapsed)
+ if (view == null) {
+ // Special case. We're probably going away, so we need
to expand ourselves
+ // in *every* view
+ for (CyNetworkView nView: collapsedMap.keySet()) {
+ expand(recursive, nView, update);
+ }
return;
+ }
- if (DEBUG) logger.debug("Expanding "+groupNode);
-
// Initialize
update(view);
+ if (!isCollapsed(networkView))
+ return;
+
+ if (DEBUG) logger.debug("Expanding "+groupNode);
+
// First, find all of our edges. This will include any
metaEdges as well
// as any edges that were created by external applications
int [] edgeArray =
network.getAdjacentEdgeIndicesArray(groupNode.getRootGraphIndex(),true,true,true);
@@ -546,7 +577,7 @@
updateDisplay();
}
- isCollapsed = false;
+ collapsedMap.put(view, Boolean.FALSE);
metaGroup.setState(MetaNodePlugin2.EXPANDED);
// Now, for any of our nodes that are metaNodes and were
expanded when we
@@ -603,7 +634,7 @@
return null;
}
- if (!multipleEdges &&
metaEdgeMap.containsKey(parent.groupNode) && parent.isCollapsed) {
+ if (!multipleEdges &&
metaEdgeMap.containsKey(parent.groupNode) && parent.isCollapsed(networkView)) {
// Already seen this?
if (DEBUG) logger.debug("... returning cached
edge "+metaEdgeMap.get(parent.groupNode).getIdentifier());
return metaEdgeMap.get(parent.groupNode);
@@ -622,7 +653,7 @@
// one edge per partner
// First make sure our partner is not an expanded
metanode
- if (MetaNode.getMetaNode(partner) != null &&
!MetaNode.getMetaNode(partner).isCollapsed) {
+ if (MetaNode.getMetaNode(partner) != null &&
!MetaNode.getMetaNode(partner).isCollapsed(networkView)) {
if (DEBUG) logger.debug("... returning null ");
// skip it
return null;
@@ -678,6 +709,19 @@
new_view.fitContent();
}
+ /**
+ * Determine if this metanode is collapsed in this view
+ *
+ * @param view the network view to check
+ * @return True if it is collapsed, False otherwise
+ */
+ public boolean isCollapsed(CyNetworkView view) {
+ if (collapsedMap.containsKey(view)) {
+ return collapsedMap.get(view).booleanValue();
+ } else
+ return false;
+ }
+
/*****************************************************************
* Private methods *
****************************************************************/
@@ -736,7 +780,7 @@
CyNode partner = getPartner(edge);
if (DEBUG) logger.debug("... partner is
"+partner.getIdentifier());
// Is our partner an expanded metaNode?
- if (MetaNode.getMetaNode(partner) != null &&
!MetaNode.getMetaNode(partner).isCollapsed) {
+ if (MetaNode.getMetaNode(partner) != null &&
!MetaNode.getMetaNode(partner).isCollapsed(networkView)) {
// Yes, just continue
continue;
} else if (isNodeHidden(partner)) {
@@ -820,7 +864,7 @@
Dimension d = new Dimension();
d.setSize(xValue, yValue);
// Is this already visible?
- if (hiddenNodes.containsKey(node) &&
hiddenNodes.get(node) == Boolean.FALSE)
+ if (network.containsNode(node))
continue;
restoreNode(node, d);
}
@@ -862,7 +906,7 @@
if (metaMap.containsKey(node)) {
// Yes, recurse down
MetaNode child = (MetaNode)metaMap.get(node);
- if (!child.isCollapsed) {
+ if (!child.isCollapsed(networkView)) {
if (childMetaNodes == null) {
childMetaNodes = new
ArrayList<MetaNode>();
}
@@ -916,7 +960,6 @@
private void hideNode(CyNode node) {
if (DEBUG) logger.debug("Hiding node "+node.getIdentifier());
network.hideNode(node);
- hiddenNodes.put(node, Boolean.TRUE);
}
/**
@@ -930,7 +973,6 @@
if (DEBUG) logger.debug("Restoring node "+node.getIdentifier());
network.restoreNode(node);
- hiddenNodes.put(node, Boolean.FALSE);
if (center != null) {
// Get the nodeView
@@ -954,12 +996,7 @@
* @return true if the node is hidden, false otherwise
*/
private boolean isNodeHidden(CyNode node) {
- if (hiddenNodes.containsKey(node) &&
- hiddenNodes.get(node) == Boolean.TRUE) {
- return true;
- }
-
- return false;
+ return (!network.containsNode(node));
}
/**
@@ -1024,7 +1061,7 @@
for (CyGroup group: groupList) {
if (metaMap.containsKey(group.getGroupNode())) {
MetaNode meta =
metaMap.get(group.getGroupNode());
- if (meta != this && meta.isCollapsed) return
meta;
+ if (meta != this &&
meta.isCollapsed(networkView)) return meta;
}
}
return null;
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