Author: scooter
Date: 2010-08-18 20:33:09 -0700 (Wed, 18 Aug 2010)
New Revision: 21466
Added:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNodeManager.java
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodeGroupViewer.java
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodePlugin2.java
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/actions/MetanodeCommandListener.java
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeMenuListener.java
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
Log:
Starting refactoring -- still a *long* ways to go!
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodeGroupViewer.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodeGroupViewer.java
2010-08-19 03:32:26 UTC (rev 21465)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodeGroupViewer.java
2010-08-19 03:33:09 UTC (rev 21466)
@@ -32,13 +32,17 @@
*/
package metaNodePlugin2;
-import java.lang.reflect.Method;
+import java.util.HashMap;
+import java.util.Map;
import cytoscape.CyNetwork;
import cytoscape.CyNode;
import cytoscape.Cytoscape;
import cytoscape.view.CyNetworkView;
+import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandResult;
+
import cytoscape.groups.CyGroup;
import cytoscape.groups.CyGroupChangeEvent;
import cytoscape.groups.CyGroupChangeListener;
@@ -48,6 +52,7 @@
import cytoscape.logger.CyLogger;
import metaNodePlugin2.model.MetaNode;
+import metaNodePlugin2.model.MetaNodeManager;
import metaNodePlugin2.model.MetanodeProperties;
import metaNodePlugin2.ui.MetanodeMenuListener;
import metaNodePlugin2.ui.MetanodeSettingsDialog;
@@ -61,10 +66,11 @@
CyLogger logger = null;
String viewerName = null;
CyGroupViewer namedSelectionViewer = null;
- Method updateMethod = null;
MetanodeSettingsDialog settingsDialog = null;
boolean registeredWithGroupPanel = false;
+ private static String NAMEDSELECTION = "namedselection";
+
public MetaNodeGroupViewer (String viewerName, CyLogger logger) {
this.viewerName = viewerName;
this.logger = logger;
@@ -116,8 +122,8 @@
*/
public void groupCreated(CyGroup group) {
// logger.debug("groupCreated("+group+")");
- if (MetaNode.getMetaNode(group) == null) {
- MetaNode newNode = new MetaNode(group);
+ if (MetaNodeManager.getMetaNode(group) == null) {
+ MetaNode newNode =
MetaNodeManager.createMetaNode(group);
}
// Update the attributes of the group node
logger.info("updating group panel for new group: "+group);
@@ -136,8 +142,8 @@
*/
public void groupCreated(CyGroup group, CyNetworkView myview) {
// logger.debug("groupCreated("+group+", view)");
- if (MetaNode.getMetaNode(group) == null) {
- MetaNode newNode = new MetaNode(group);
+ if (MetaNodeManager.getMetaNode(group) == null) {
+ MetaNode newNode =
MetaNodeManager.createMetaNode(group);
// We need to be a little tricky if we are restoring a
collapsed
// metaNode from XGMML. We essentially need to
"recollapse" it,
@@ -169,14 +175,14 @@
* @param group the CyGroup that will be deleted
*/
public void groupWillBeRemoved(CyGroup group) {
- MetaNode mn = MetaNode.getMetaNode(group);
+ MetaNode mn = MetaNodeManager.getMetaNode(group);
if (mn == null) return;
// Expand the group in any views that it's collapsed
mn.expand(true, null, true);
// Get rid of the MetaNode
logger.info("updating group panel for removed group: "+group);
- MetaNode.removeMetaNode(mn);
+ MetaNodeManager.removeMetaNode(mn);
}
/**
@@ -189,7 +195,7 @@
*/
public void groupChanged(CyGroup group, CyNode node, ChangeType change)
{
- MetaNode mn = MetaNode.getMetaNode(group);
+ MetaNode mn = MetaNodeManager.getMetaNode(group);
if (mn == null) return;
if (change == ChangeType.NODE_ADDED) {
@@ -210,32 +216,33 @@
registerWithGroupPanel();
} else {
try {
- updateMethod.invoke(namedSelectionViewer);
+ Map<String,Object> args = new
HashMap<String,Object>();
+ CyCommandResult result =
CyCommandManager.execute(NAMEDSELECTION, "update", args);
} catch (Exception e) {
- logger.warning(e.getMessage());
+ logger.info(e.getMessage());
+ return;
}
}
return;
}
public void registerWithGroupPanel() {
- namedSelectionViewer =
CyGroupManager.getGroupViewer("namedSelection");
- if (namedSelectionViewer == null)
- return;
-
- if
(namedSelectionViewer.getClass().getName().equals("namedSelection.NamedSelection"))
{
- // Get the addViewerToGroupPanel method
-
- try {
- updateMethod =
namedSelectionViewer.getClass().getMethod("updateGroupPanel");
- Method regMethod =
namedSelectionViewer.getClass().getMethod("addViewerToGroupPanel",
CyGroupViewer.class);
- regMethod.invoke(namedSelectionViewer,
(CyGroupViewer)this);
- registeredWithGroupPanel = true;
- } catch (Exception e) {
- logger.warning(e.getMessage());
+ try {
+ Map<String,Object> args = new HashMap<String,Object>();
+ args.put("viewer",viewerName);
+ CyCommandResult result =
CyCommandManager.execute(NAMEDSELECTION, "add viewer", args);
+ if (result.getErrors() != null &&
result.getErrors().size() > 0) {
+ for (String error: result.getErrors())
+ logger.warning(error);
return;
+ } else if (result.getMessages() != null &&
result.getMessages().size() > 0) {
+ for (String message: result.getMessages())
+ logger.info(message);
}
- // Invoke it
+ } catch (Exception e) {
+ logger.warning(e.getMessage());
+ return;
}
+ registeredWithGroupPanel = true;
}
}
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodePlugin2.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodePlugin2.java
2010-08-19 03:32:26 UTC (rev 21465)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodePlugin2.java
2010-08-19 03:33:09 UTC (rev 21466)
@@ -76,6 +76,7 @@
// our imports
import metaNodePlugin2.model.MetaNode;
+import metaNodePlugin2.model.MetaNodeManager;
import metaNodePlugin2.ui.MetanodeSettingsDialog;
import metaNodePlugin2.ui.MetanodeMenuListener;
@@ -173,13 +174,13 @@
public void propertyChange (PropertyChangeEvent e) {
if (e.getPropertyName() ==
CytoscapeDesktop.NETWORK_VIEW_CREATED) {
((CyNetworkView)e.getNewValue()).addNodeContextMenuListener(this);
- MetaNode.newView((CyNetworkView)e.getNewValue());
+ //
MetaNodeManager.newView((CyNetworkView)e.getNewValue());
((CyNetworkView)e.getNewValue()).addGraphViewChangeListener(this);
groupViewer.getSettingsDialog().updateAttributes();
} else if (e.getPropertyName() ==
CytoscapeDesktop.NETWORK_VIEW_FOCUSED) {
// Load the default aggregation values for this network
groupViewer.getSettingsDialog().updateOverrides(Cytoscape.getCurrentNetwork());
- MetaNode.newView(Cytoscape.getCurrentNetworkView());
+ //
MetaNodeManager.newView(Cytoscape.getCurrentNetworkView());
}
}
@@ -207,7 +208,7 @@
Node[] nodes = event.getSelectedNodes();
// We only care about expanded metanodes
for (int i=0; i < nodes.length; i++) {
- MetaNode n =
MetaNode.getMetaNode((CyNode)nodes[i]);
+ MetaNode n =
MetaNodeManager.getMetaNode((CyNode)nodes[i]);
if (n == null || n.getCyGroup().getState() ==
COLLAPSED) continue;
// OK, so we have selected an expanded
metanode. This means that we are
// not hiding the metanode, so we want to
implicitly select all of the children
@@ -218,7 +219,7 @@
Node[] nodes = event.getUnselectedNodes();
// We only care about expanded metanodes
for (int i=0; i < nodes.length; i++) {
- MetaNode n =
MetaNode.getMetaNode((CyNode)nodes[i]);
+ MetaNode n =
MetaNodeManager.getMetaNode((CyNode)nodes[i]);
if (n == null || n.getCyGroup().getState() ==
COLLAPSED) continue;
// OK, so we have selected an expanded
metanode. This means that we are
// not hiding the metanode, so we want to
implicitly select all of the children
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/actions/MetanodeCommandListener.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/actions/MetanodeCommandListener.java
2010-08-19 03:32:26 UTC (rev 21465)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/actions/MetanodeCommandListener.java
2010-08-19 03:33:09 UTC (rev 21466)
@@ -48,6 +48,7 @@
import cytoscape.groups.CyGroupManager;
import metaNodePlugin2.model.MetaNode;
+import metaNodePlugin2.model.MetaNodeManager;
import metaNodePlugin2.MetaNodeGroupViewer;
import metaNodePlugin2.MetaNodePlugin2;
import metaNodePlugin2.MetaNodePlugin2.Command;
@@ -127,7 +128,7 @@
// Careful! If one of the nodes is an expanded (but not
hidden) metanode,
// we need to collapse it first or this gets messy fast
for (CyNode node: (List<CyNode>)new
ArrayList(network.getSelectedNodes())) {
- MetaNode mn = MetaNode.getMetaNode(node);
+ MetaNode mn = MetaNodeManager.getMetaNode(node);
if (mn == null) continue;
// Is this an expanded metanode?
if (mn.getCyGroup().getState() ==
MetaNodePlugin2.EXPANDED) {
@@ -147,7 +148,7 @@
JOptionPane.ERROR_MESSAGE);
return;
}
- MetaNode newNode = new MetaNode(group);
+ MetaNode newNode = MetaNodeManager.createMetaNode(group);
groupViewer.groupCreated(group);
newNode.collapse(false, false, true,
Cytoscape.getCurrentNetworkView());
}
@@ -205,9 +206,9 @@
* Perform the action associated with a select menu selection
*/
private void collapse() {
- MetaNode mNode = MetaNode.getMetaNode(group);
+ MetaNode mNode = MetaNodeManager.getMetaNode(group);
if (mNode == null) {
- mNode = new MetaNode(group);
+ mNode = MetaNodeManager.createMetaNode(group);
if (mNode == null) return;
groupViewer.groupCreated(group);
}
@@ -218,9 +219,9 @@
* Perform the action associated with an unselect menu selection
*/
private void expand() {
- MetaNode mNode = MetaNode.getMetaNode(group);
+ MetaNode mNode = MetaNodeManager.getMetaNode(group);
if (mNode == null) {
- mNode = new MetaNode(group);
+ mNode = MetaNodeManager.createMetaNode(group);
groupViewer.groupCreated(group);
}
mNode.expand(false, Cytoscape.getCurrentNetworkView(), true);
@@ -230,9 +231,9 @@
* Create a new network from the currently collapsed group
*/
private void createNetworkFromGroup() {
- MetaNode mNode = MetaNode.getMetaNode(group);
+ MetaNode mNode = MetaNodeManager.getMetaNode(group);
if (mNode == null) {
- mNode = new MetaNode(group);
+ mNode = MetaNodeManager.createMetaNode(group);
groupViewer.groupCreated(group);
}
mNode.createNetworkFromGroup();
@@ -242,13 +243,13 @@
* Expand all metanodes
*/
private void expandAll() {
- MetaNode.expandAll();
+ MetaNodeManager.expandAll();
}
/**
* Collapse all metanodes
*/
private void collapseAll() {
- MetaNode.collapseAll();
+ MetaNodeManager.collapseAll();
}
}
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
2010-08-19 03:32:26 UTC (rev 21465)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
2010-08-19 03:33:09 UTC (rev 21466)
@@ -44,7 +44,6 @@
// giny imports
import giny.view.NodeView;
-import ding.view.*;
// Cytoscape imports
import cytoscape.Cytoscape;
@@ -58,7 +57,6 @@
import cytoscape.data.CyAttributes;
import cytoscape.data.Semantics;
import cytoscape.logger.CyLogger;
-import cytoscape.util.CytoscapeAction;
import cytoscape.visual.VisualMappingManager;
import cytoscape.visual.VisualPropertyType;
@@ -79,13 +77,6 @@
* more efficiently
*/
public class MetaNode {
- // Static variables
- private static HashMap<CyNode,MetaNode> metaMap = new HashMap();
- private static final boolean DEBUG = false;
- private static boolean hideMetanodeDefault = true;
- private static double metanodeOpacityDefault = 0.;
- private static boolean sizeToBoundingBoxDefault = true;
-
public static final String X_HINT_ATTR = "__metanodeHintX";
public static final String Y_HINT_ATTR = "__metanodeHintY";
public static final String CHILDREN_ATTR = "NumChildren";
@@ -97,16 +88,14 @@
// newEdgeMap is a map with all of the meta-edges we've created
// and the list of edges they have replaced
- protected HashMap<CyEdge,List<CyEdge>> newEdgeMap = null;
+ protected Map<CyEdge,List<CyEdge>> newEdgeMap = null;
// metaEdgeMap maps the nodes to the edges we've created
- private HashMap<CyNode,CyEdge> metaEdgeMap = null;
+ private Map<CyNode,CyEdge> metaEdgeMap = null;
private List<MetaNode> childMetaNodes = null;
private boolean multipleEdges = false;
private boolean recursive = false;
- protected Map<CyNetworkView, Boolean> collapsedMap = null;
-
private CyAttributes edgeAttributes = null;
private CyAttributes nodeAttributes = null;
private CyNetworkView networkView = null;
@@ -123,183 +112,24 @@
private CyLogger logger = null;
- /*****************************************************************
- * Static methods *
- ****************************************************************/
-
/**
- * Return the MetaNode associated with this group
- *
- * @param metaGroup the CyGroup to use to search for the
- * associated MetaNode.
- * @return the associated MetaNode or null of there is none
- */
- static public MetaNode getMetaNode(CyGroup metaGroup) {
- CyNode groupNode = metaGroup.getGroupNode();
- if (metaMap.containsKey(groupNode))
- return (MetaNode)metaMap.get(groupNode);
- return null;
- }
-
- /**
- * Return the MetaNode associated with this group node
- *
- * @param groupNode the CyNode to use to search for the
- * associated MetaNode.
- * @return the associated MetaNode or null of there is none
- */
- static public MetaNode getMetaNode(CyNode groupNode) {
- if (metaMap.containsKey(groupNode))
- return (MetaNode)metaMap.get(groupNode);
- return null;
- }
-
- /**
- * Remove a MetaNode from our internal map
- *
- * @param groupNode the CyNode that maps to the metaNode
- */
- static public void removeMetaNode(CyNode groupNode) {
- // Remove the metanode
- if (metaMap.containsKey(groupNode))
- metaMap.remove(groupNode);
- }
-
- /**
- * Remove a MetaNode from our internal map
- *
- * @param metaNode the metaNode to remove
- */
- static public void removeMetaNode(MetaNode metaNode) {
- if (metaNode == null) return;
- removeMetaNode(metaNode.getCyGroup().getGroupNode());
- }
-
- /**
- * Expand all MetaNodes
- */
- static public void expandAll() {
- CyNetworkView nView = Cytoscape.getCurrentNetworkView();
- Collection<MetaNode> metaNodes = metaMap.values();
- for (MetaNode mNode: metaNodes) {
- if (mNode.isCollapsed(nView))
- mNode.expand(true, nView, false);
- }
- // VisualMappingManager vizmapper =
Cytoscape.getVisualMappingManager();
- // vizmapper.applyAppearances();
- nView.updateView();
- }
-
- /**
- * Collapse all MetaNodes
- */
- static public void collapseAll() {
- CyNetworkView nView = Cytoscape.getCurrentNetworkView();
- Collection<MetaNode> metaNodes = metaMap.values();
- for (MetaNode mNode: metaNodes) {
- if (!mNode.isCollapsed(nView))
- mNode.collapse(true, true, false, nView);
- }
- // VisualMappingManager vizmapper =
Cytoscape.getVisualMappingManager();
- // vizmapper.applyAppearances();
- 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);
- }
- }
- }
-
- /**
- * Sets whether or not we hide the metnode when we expand the
- * network.
- *
- * @param hide if 'true' we hide the metanode upon expansion
- */
- static public void setHideMetaNodeDefault(boolean hide) {
- MetaNode.hideMetanodeDefault = hide;
- }
-
- /**
- * Sets the opacity of a metanode if we don't hide on expansion.
- *
- * @param opacity the opacity (between 0 and 100)
- */
- static public void setExpandedOpacityDefault(double opacity) {
- MetaNode.metanodeOpacityDefault = 255*opacity/100;
- }
-
- /**
- * Returns 'true' if we hide the metnode when we expand the
- * network.
- *
- * @return 'true' if we hide the metanode upon expansion
- */
- static public boolean getHideMetaNodeDefault() {
- return MetaNode.hideMetanodeDefault;
- }
-
- /**
- * 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.
- *
- * @param hide if 'true' we resize on expansion
- */
- static public void setSizeToBoundingBoxDefault(boolean resize) {
- MetaNode.sizeToBoundingBoxDefault = resize;
- }
-
- /**
- * Returns 'true' if we hide the metnode when we expand the
- * network.
- *
- * @return 'true' if we hide the metanode upon expansion
- */
- static public boolean getSizeToBoundingBoxDefault() {
- return MetaNode.sizeToBoundingBoxDefault;
- }
-
- /*****************************************************************
- * Public methods *
- ****************************************************************/
-
- /**
* Main constructor
*
* @param group the group to wrap the MetaNode around
*/
- public MetaNode(CyGroup group) {
+ protected MetaNode(CyGroup group) {
metaGroup = group;
groupNode = group.getGroupNode();
- metaMap.put(groupNode, this);
metaEdgeMap = new HashMap();
- collapsedMap = new HashMap();
logger = CyLogger.getLogger(MetaNode.class);
- this.hideMetanode = MetaNode.hideMetanodeDefault;
- this.sizeToBoundingBox = MetaNode.sizeToBoundingBoxDefault;
- this.metanodeOpacity = MetaNode.metanodeOpacityDefault;
+ this.hideMetanode = MetaNodeManager.hideMetanodeDefault;
+ this.sizeToBoundingBox =
MetaNodeManager.sizeToBoundingBoxDefault;
+ this.metanodeOpacity = MetaNodeManager.metanodeOpacityDefault;
this.aggregateAttributes = AttributeHandler.getEnable();
- if (DEBUG) logger.debug("Creating meta-group
"+group.getGroupName());
+ // logger.debug("Creating meta-group "+group.getGroupName());
- newEdgeMap = new HashMap();
+ newEdgeMap = new HashMap<CyEdge,List<CyEdge>>();
// TODO: handle special case where all of the nodes in this
group are
// members of an existing metanode. Implicitly, we treat this
as a
@@ -313,10 +143,11 @@
// to be connected to nodes which are now part of a collapsed
// group. If this is the case, some of *our* external edges
// will be meta-edges
- ArrayList<CyEdge>newOuterEdges = new ArrayList();
+ List<CyEdge>newOuterEdges = new ArrayList<CyEdge>();
List<CyEdge>externalEdges = group.getOuterEdges();
+
for (CyEdge edge: externalEdges) {
- if (DEBUG) logger.debug("... outer edge
"+edge.getIdentifier());
+ // logger.debug("... outer edge "+edge.getIdentifier());
if (!isMetaEdge(edge))
continue;
@@ -332,13 +163,12 @@
// OK, now add all of the new outer edges
for (CyEdge edge: newOuterEdges) {
if (!externalEdges.contains(edge)) {
- if (DEBUG) logger.debug("... adding
edge "+edge.getIdentifier());
+ // logger.debug("... adding edge
"+edge.getIdentifier());
group.addOuterEdge(edge);
}
}
- collapsedMap.put(networkView, Boolean.FALSE);
updateAttributes();
- if (DEBUG) logger.debug("... done\n\n");
+ // logger.debug("... done\n\n");
}
/**
@@ -357,16 +187,19 @@
// Initialize
edgeAttributes = Cytoscape.getEdgeAttributes();
nodeAttributes = Cytoscape.getNodeAttributes();
+ this.network = metaGroup.getNetwork();
+ this.networkView =
Cytoscape.getNetworkView(network.getIdentifier());
+
// Initialize our network-related information. This might
// be overwritten by calls to setGroupViewer
- if (view != null) {
- // Override the defaults for networkView and network
- this.networkView = view;
- this.network = view.getNetwork();
- } else {
- this.networkView = Cytoscape.getCurrentNetworkView();
- this.network = Cytoscape.getCurrentNetwork();
- }
+ // if (view != null) {
+ // // Override the defaults for networkView and network
+ // this.networkView = view;
+ // this.network = view.getNetwork();
+ // } else {
+ // this.networkView = Cytoscape.getCurrentNetworkView();
+ // this.network = Cytoscape.getCurrentNetwork();
+ // }
}
/**
@@ -377,7 +210,7 @@
* @param node the CyNode that was added
*/
public void nodeAdded(CyNode node) {
- if (DEBUG) logger.debug(groupNode.getIdentifier()+": adding
node "+node.getIdentifier());
+ // logger.debug(groupNode.getIdentifier()+": adding node
"+node.getIdentifier());
// Adding a node could result in a couple of changes to our
// internal data structures. First, we might have to add new
// metaedges to reflect the connection between this node and
other
@@ -391,7 +224,7 @@
if (metaEdgeMap.containsKey(node)) {
// Get the metaEdge
CyEdge metaEdge = metaEdgeMap.get(node);
- if (DEBUG) logger.debug("... removing edge
"+metaEdge.getIdentifier());
+ // logger.debug("... removing edge
"+metaEdge.getIdentifier());
// Remove it from the network
network.removeEdge(metaEdge.getRootGraphIndex(), true);
// Remove it from our data structures
@@ -404,7 +237,7 @@
// Attach them to the group node
for (CyEdge edge: edges) {
- if (DEBUG) logger.debug("... checking edge
"+edge.getIdentifier());
+ // logger.debug("... checking edge
"+edge.getIdentifier());
// Did we "cause" this edge?
if (edge.getTarget() == node ||
edge.getSource() == node) {
// Yes, we need to create a new
metaEdge, then
@@ -415,7 +248,7 @@
// Finally, if we're collapsed, hide this node (possibly
recursively) and
// update the display
- if (!isCollapsed(networkView))
+ if (!isCollapsed())
return;
// Get the X and Y coordinates of the metaNode
@@ -426,16 +259,15 @@
nv = (NodeView)networkView.getNodeView(node);
double X = nv.getXPosition();
double Y = nv.getYPosition();
- if (DEBUG) logger.debug(node.getIdentifier()+" = ("+X+",
"+Y+")");
+ // logger.debug(node.getIdentifier()+" = ("+X+", "+Y+")");
// Update our attributes
String nodeName = node.getIdentifier();
setXHintAttr(nodeAttributes, nodeName, metaX-X);
setYHintAttr(nodeAttributes, nodeName, metaY-Y);
// Collapse ourselves (if we are a group and we aren't already
collapsed)
- if (metaMap.containsKey(node)) {
- // Yes, recurse down
- MetaNode child = (MetaNode)metaMap.get(node);
+ MetaNode child = MetaNodeManager.getMetaNode(node);
+ if (child != null) {
// If we're already collapsed, this will just return
child.collapse(recursive, multipleEdges, false,
networkView);
}
@@ -457,7 +289,7 @@
public void nodeRemoved(CyNode node) {
update(null);
// If we're collapsed, unhide the node
- if (isCollapsed(networkView)) {
+ if (isCollapsed()) {
restoreNode(node, null);
}
@@ -474,7 +306,7 @@
if (edge.getTarget() == node ||
edge.getSource() == node) {
// Remove it from this metaEdge
edgeIter.remove();
- if (isCollapsed(networkView)) {
+ if (isCollapsed()) {
restoreEdge(edge);
}
}
@@ -497,7 +329,7 @@
// 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(networkView)) {
+ if (!isCollapsed()) {
hideEdge(metaEdge);
}
}
@@ -524,7 +356,6 @@
if (newEdgeMap == null)
createMetaEdges();
- collapsedMap.put(view, Boolean.TRUE);
expand(recursive, view, true);
collapse(recursive, multipleEdges, false, view);
}
@@ -543,10 +374,10 @@
// Initialize
update(view);
- if (isCollapsed(networkView))
+ if (isCollapsed())
return;
- if (DEBUG) logger.debug("collapsing "+groupNode);
+ // logger.debug("collapsing "+groupNode);
// Profile prf = new Profile();
// prf.start();
@@ -563,8 +394,6 @@
createMetaEdges();
// prf.done("collapse: createMetaEdges=");
- collapsedMap.put(view, Boolean.TRUE);
-
// Set our state
metaGroup.setState(MetaNodePlugin2.COLLAPSED);
@@ -584,29 +413,20 @@
* @param update update the display?
*/
public void expand(boolean recursive, CyNetworkView view, boolean
update) {
- 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;
- }
-
// Initialize
update(view);
- if (!isCollapsed(networkView))
+ if (!isCollapsed())
return;
- if (DEBUG) logger.debug("Expanding "+groupNode);
+ // 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);
if (edgeArray != null) {
- if (DEBUG) logger.debug(groupNode.getIdentifier()+" has
"+edgeArray.length+" edges");
+ // logger.debug(groupNode.getIdentifier()+" has
"+edgeArray.length+" edges");
// Now, go through a (hopefully) quick loop to add any
edges we don't already have into
// our edge map
@@ -615,7 +435,7 @@
if (!isMetaEdge(edge)) {
// Not a meta edge. This may be an
additional edge that got created
// to our group node. We want to add
this to our outerEdge list
- if (DEBUG) logger.debug("Adding outer
edge "+edge.getIdentifier()+" to "+groupNode.getIdentifier());
+ // logger.debug("Adding outer edge
"+edge.getIdentifier()+" to "+groupNode.getIdentifier());
metaGroup.addOuterEdge(edge);
if (!this.hideMetanode)
continue;
@@ -669,7 +489,6 @@
updateDisplay();
}
- collapsedMap.put(view, Boolean.FALSE);
metaGroup.setState(MetaNodePlugin2.EXPANDED);
// Now, for any of our nodes that are metaNodes and were
expanded when we
@@ -699,7 +518,7 @@
*/
public CyEdge createMetaEdge(CyEdge edge, CyNode partner, boolean
ignoreCollapsed) {
- if (DEBUG) logger.debug(metaGroup.getGroupName()+": Examining
edge "+edge.getIdentifier());
+ // logger.debug(metaGroup.getGroupName()+": Examining edge
"+edge.getIdentifier());
CyNode source = (CyNode)edge.getSource();
CyNode target = (CyNode)edge.getTarget();
@@ -720,15 +539,15 @@
if (parent == null) {
return null;
}
- if (DEBUG) logger.debug("... parent of
"+partner.getIdentifier()+" is "+parent.metaGroup.getGroupName());
- if (!metaMap.containsKey(parent.groupNode) ||
isNodeHidden(parent.groupNode)) {
- if (DEBUG) logger.debug("... returning edge
"+edge.getIdentifier());
+ // logger.debug("... parent of
"+partner.getIdentifier()+" is "+parent.metaGroup.getGroupName());
+ if (MetaNodeManager.getMetaNode(parent.groupNode) ==
null || isNodeHidden(parent.groupNode)) {
+ // logger.debug("... returning edge
"+edge.getIdentifier());
return null;
}
- if (!multipleEdges &&
metaEdgeMap.containsKey(parent.groupNode) && parent.isCollapsed(networkView)) {
+ if (!multipleEdges &&
metaEdgeMap.containsKey(parent.groupNode) && parent.isCollapsed()) {
// Already seen this?
- if (DEBUG) logger.debug("... returning cached
edge "+metaEdgeMap.get(parent.groupNode).getIdentifier());
+ // logger.debug("... returning cached edge
"+metaEdgeMap.get(parent.groupNode).getIdentifier());
return metaEdgeMap.get(parent.groupNode);
}
@@ -745,8 +564,8 @@
// one edge per partner
// First make sure our partner is not an expanded
metanode
- if (MetaNode.getMetaNode(partner) != null &&
!MetaNode.getMetaNode(partner).isCollapsed(networkView)) {
- if (DEBUG) logger.debug("... returning null ");
+ if (MetaNodeManager.getMetaNode(partner) != null &&
!MetaNodeManager.getMetaNode(partner).isCollapsed()) {
+ // logger.debug("... returning null ");
// skip it
return null;
}
@@ -768,7 +587,7 @@
addMetaEdge(newEdge, partner, edge);
}
}
- if (DEBUG) logger.debug("... returning edge
"+newEdge.getIdentifier());
+ // logger.debug("... returning edge "+newEdge.getIdentifier());
return newEdge;
}
@@ -815,11 +634,10 @@
* @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;
+ public boolean isCollapsed() {
+ if (metaGroup.getState() == MetaNodePlugin2.COLLAPSED)
+ return true;
+ return false;
}
/**
@@ -898,7 +716,7 @@
CyEdge newEdge =
Cytoscape.getCyEdge(source.getIdentifier(),identifier,
target.getIdentifier(),"meta-"+interaction);
- if (DEBUG) logger.debug("Created meta-edge
"+newEdge.getIdentifier());
+ // logger.debug("Created meta-edge "+newEdge.getIdentifier());
return newEdge;
}
@@ -913,7 +731,7 @@
// Attach them to the group node
for (CyEdge edge: edges) {
- if (DEBUG) logger.debug("Outer edge:
"+edge.getIdentifier());
+ // logger.debug("Outer edge: "+edge.getIdentifier());
CyEdge newEdge = createMetaEdge(edge, null, false);
if (newEdge != null) {
network.addEdge(newEdge);
@@ -932,16 +750,16 @@
//
// Restore outer edges
//
- if (DEBUG) logger.debug(metaGroup.getGroupName()+":
restoreEdges");
+ // logger.debug(metaGroup.getGroupName()+": restoreEdges");
for (CyEdge edge: metaGroup.getOuterEdges()) {
// First, see if the partner of this edge is gone
- if (DEBUG) logger.debug("... restoring outer edge
"+edge.getIdentifier());
+ // logger.debug("... restoring outer edge
"+edge.getIdentifier());
String identifier = edge.getIdentifier();
// Get the edge partner
CyNode partner = getPartner(edge);
- if (DEBUG) logger.debug("... partner is
"+partner.getIdentifier());
+ // logger.debug("... partner is
"+partner.getIdentifier());
// Is our partner an expanded metaNode?
- if (MetaNode.getMetaNode(partner) != null &&
!MetaNode.getMetaNode(partner).isCollapsed(networkView)) {
+ if (MetaNodeManager.getMetaNode(partner) != null &&
!MetaNodeManager.getMetaNode(partner).isCollapsed()) {
// Yes, just continue
continue;
} else if (isNodeHidden(partner)) {
@@ -950,7 +768,7 @@
MetaNode parent = getParent(partner);
if (parent != null) {
// Create the meta-edge
- if (DEBUG) logger.debug("... parent of
"+partner.getIdentifier()+" is "+parent.metaGroup.getGroupName());
+ // logger.debug("... parent of
"+partner.getIdentifier()+" is "+parent.metaGroup.getGroupName());
restoreEdge(parent.createMetaEdge(edge,
getLocalNode(edge), false));
}
} else {
@@ -962,7 +780,7 @@
// Restore inner edges
//
for (CyEdge edge: metaGroup.getInnerEdges()) {
- if (DEBUG) logger.debug("restoreEdges: restoring inner
edge "+edge.getIdentifier());
+ // logger.debug("restoreEdges: restoring inner edge
"+edge.getIdentifier());
restoreEdge(edge);
}
}
@@ -978,13 +796,13 @@
if (edge == null) return;
CyNode partner = getPartner(edge);
if (!isNodeHidden(partner)) {
- if (DEBUG) logger.debug("Restoring edge
"+edge.getIdentifier()+" partner = "+partner.getIdentifier());
+ // logger.debug("Restoring edge
"+edge.getIdentifier()+" partner = "+partner.getIdentifier());
network.restoreEdge(edge);
if (networkView != null && networkView !=
Cytoscape.getNullNetworkView());
networkView.applyVizMap(edge);
} else {
- if (DEBUG) logger.debug("Not restoring edge
"+edge.getIdentifier()+". "+
- partner.getIdentifier()+" is
hidden");
+ // logger.debug("Not restoring edge
"+edge.getIdentifier()+". "+
+ // partner.getIdentifier()+" is hidden");
}
}
@@ -995,7 +813,7 @@
* @param edge the edge we want to hide
*/
private void hideEdge(CyEdge edge) {
- if (DEBUG) logger.debug("Hiding edge "+edge.getIdentifier());
+ // logger.debug("Hiding edge "+edge.getIdentifier());
network.hideEdge(edge);
}
@@ -1063,10 +881,10 @@
for (int i = 0; i < nodes.size(); i++) {
CyNode node = nodes.get(i);
// Check and see if this is a group
- if (metaMap.containsKey(node)) {
+ MetaNode child = MetaNodeManager.getMetaNode(node);
+ if (child != null) {
// Yes, recurse down
- MetaNode child = (MetaNode)metaMap.get(node);
- if (!child.isCollapsed(networkView)) {
+ if (!child.isCollapsed()) {
if (childMetaNodes == null) {
childMetaNodes = new
ArrayList<MetaNode>();
}
@@ -1135,7 +953,7 @@
* @param node the node to hide
*/
private void hideNode(CyNode node) {
- if (DEBUG) logger.debug("Hiding node "+node.getIdentifier());
+ // logger.debug("Hiding node "+node.getIdentifier());
network.hideNode(node);
}
@@ -1147,7 +965,7 @@
* @param node the node to restore
*/
private void restoreNode(CyNode node, Dimension center) {
- if (DEBUG) logger.debug("Restoring node "+node.getIdentifier());
+ // logger.debug("Restoring node "+node.getIdentifier());
network.restoreNode(node);
@@ -1215,11 +1033,11 @@
private List<CyEdge> getPartnerEdgeList(CyEdge metaEdge) {
CyNode partner = getPartner(metaEdge);
// We have the partner node -- get the group
- if (!metaMap.containsKey(partner)) {
+ MetaNode metaPartner = MetaNodeManager.getMetaNode(partner);
+ if (metaPartner == null) {
// Shouldn't happen!
return new ArrayList<CyEdge>(0);
}
- MetaNode metaPartner = metaMap.get(partner);
return metaPartner.newEdgeMap.get(metaEdge);
}
@@ -1236,9 +1054,9 @@
if (groupList == null) return null;
for (CyGroup group: groupList) {
- if (metaMap.containsKey(group.getGroupNode())) {
- MetaNode meta =
metaMap.get(group.getGroupNode());
- if (meta != this &&
meta.isCollapsed(networkView)) return meta;
+ MetaNode meta =
MetaNodeManager.getMetaNode(group.getGroupNode());
+ if (meta != null) {
+ if (meta != this && meta.isCollapsed()) return
meta;
}
}
return null;
@@ -1261,10 +1079,10 @@
* Update the display
*/
private void updateDisplay() {
- // VisualMappingManager vizmapper =
Cytoscape.getVisualMappingManager();
- // vizmapper.applyAppearances();
- networkView.updateView();
- // networkView.redrawGraph(false,true);
+ VisualMappingManager vizmapper =
Cytoscape.getVisualMappingManager();
+ vizmapper.applyAppearances();
+ // networkView.updateView();
+ networkView.redrawGraph(false,true);
}
/**
@@ -1282,8 +1100,8 @@
// We need to update all of our contained metanode attributes
// first or we'll wind up adding extra attributes
for (CyNode node: metaGroup.getNodes()) {
- if (metaMap.containsKey(node)) {
- MetaNode mn = metaMap.get(node);
+ MetaNode mn = MetaNodeManager.getMetaNode(node);
+ if (mn != null) {
if (mn.getCyGroup().getState() ==
MetaNodePlugin2.COLLAPSED) {
mn.updateAttributes();
}
@@ -1292,9 +1110,9 @@
// OK, now handle
for (CyNode node: metaGroup.getNodes()) {
- if (metaMap.containsKey(node)) {
+ MetaNode mn = MetaNodeManager.getMetaNode(node);
+ if (mn != null) {
// This node is a metaNode
- MetaNode mn = metaMap.get(node);
if (mn.getCyGroup().getState() ==
MetaNodePlugin2.COLLAPSED) {
nDescendents +=
mn.getDescendentCount()-1;
aggregateAttributes(nodeAttributes,
"node", node.getIdentifier(), mn);
@@ -1303,7 +1121,7 @@
aggregateAttributes(nodeAttributes, "node",
node.getIdentifier(), null);
}
}
- if (DEBUG) logger.debug("Assigning attributes for node
"+groupNode.getIdentifier());
+ // logger.debug("Assigning attributes for node
"+groupNode.getIdentifier());
assignAttributes(nodeAttributes, "node",
groupNode.getIdentifier());
// Update our "special" attributes
@@ -1438,8 +1256,8 @@
}
for (CyNode node: recurse.getCyGroup().getNodes()) {
- if (metaMap.containsKey(node)) {
- MetaNode mn = metaMap.get(node);
+ MetaNode mn = MetaNodeManager.getMetaNode(node);
+ if (mn != null) {
aggregateAttribute(attrMap, handler, null, mn);
} else {
aggregateAttribute(attrMap, handler,
node.getIdentifier(), null);
Added:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNodeManager.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNodeManager.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNodeManager.java
2010-08-19 03:33:09 UTC (rev 21466)
@@ -0,0 +1,202 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2007 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package metaNodePlugin2.model;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.groups.CyGroup;
+import cytoscape.view.CyNetworkView;
+
+
+/**
+ * The MetaNode class provides a wrapper for a CyGroup that
+ * maintains the additional state information we want to keep
+ * to allow the MetaNode abstraction (expand/contract) to work
+ * more efficiently
+ */
+public class MetaNodeManager {
+ // Static variables
+ private static Map<CyNode,MetaNode> metaMap = new HashMap<CyNode,
MetaNode>();
+ protected static boolean hideMetanodeDefault = true;
+ protected static double metanodeOpacityDefault = 0.;
+ protected static boolean sizeToBoundingBoxDefault = true;
+
+ public static final String X_HINT_ATTR = "__metanodeHintX";
+ public static final String Y_HINT_ATTR = "__metanodeHintY";
+ public static final String CHILDREN_ATTR = "NumChildren";
+ public static final String DESCENDENTS_ATTR = "NumDescendents";
+
+ /*****************************************************************
+ * Static methods *
+ ****************************************************************/
+
+ /**
+ * Return the MetaNode associated with this group
+ *
+ * @param metaGroup the CyGroup to use to search for the
+ * associated MetaNode.
+ * @return the associated MetaNode or null of there is none
+ */
+ static public MetaNode getMetaNode(CyGroup metaGroup) {
+ CyNode groupNode = metaGroup.getGroupNode();
+ if (metaMap.containsKey(groupNode))
+ return (MetaNode)metaMap.get(groupNode);
+ return null;
+ }
+
+ static public MetaNode createMetaNode(CyGroup metaGroup) {
+ MetaNode mn = new MetaNode(metaGroup);
+ metaMap.put(metaGroup.getGroupNode(), mn);
+ return mn;
+ }
+
+ /**
+ * Return the MetaNode associated with this group node
+ *
+ * @param groupNode the CyNode to use to search for the
+ * associated MetaNode.
+ * @return the associated MetaNode or null of there is none
+ */
+ static public MetaNode getMetaNode(CyNode groupNode) {
+ if (metaMap.containsKey(groupNode))
+ return (MetaNode)metaMap.get(groupNode);
+ return null;
+ }
+
+ /**
+ * Remove a MetaNode from our internal map
+ *
+ * @param groupNode the CyNode that maps to the metaNode
+ */
+ static public void removeMetaNode(CyNode groupNode) {
+ // Remove the metanode
+ if (metaMap.containsKey(groupNode))
+ metaMap.remove(groupNode);
+ }
+
+ /**
+ * Remove a MetaNode from our internal map
+ *
+ * @param metaNode the metaNode to remove
+ */
+ static public void removeMetaNode(MetaNode metaNode) {
+ if (metaNode == null) return;
+ removeMetaNode(metaNode.getCyGroup().getGroupNode());
+ }
+
+ /**
+ * Expand all MetaNodes
+ */
+ static public void expandAll() {
+ CyNetworkView nView = Cytoscape.getCurrentNetworkView();
+ Collection<MetaNode> metaNodes = metaMap.values();
+ for (MetaNode mNode: metaNodes) {
+ if (mNode.isCollapsed())
+ mNode.expand(true, nView, false);
+ }
+ // VisualMappingManager vizmapper =
Cytoscape.getVisualMappingManager();
+ // vizmapper.applyAppearances();
+ nView.updateView();
+ }
+
+ /**
+ * Collapse all MetaNodes
+ */
+ static public void collapseAll() {
+ CyNetworkView nView = Cytoscape.getCurrentNetworkView();
+ Collection<MetaNode> metaNodes = metaMap.values();
+ for (MetaNode mNode: metaNodes) {
+ if (!mNode.isCollapsed())
+ mNode.collapse(true, true, false, nView);
+ }
+ // VisualMappingManager vizmapper =
Cytoscape.getVisualMappingManager();
+ // vizmapper.applyAppearances();
+ nView.updateView();
+ }
+
+ /**
+ * Sets whether or not we hide the metnode when we expand the
+ * network.
+ *
+ * @param hide if 'true' we hide the metanode upon expansion
+ */
+ static public void setHideMetaNodeDefault(boolean hide) {
+ MetaNodeManager.hideMetanodeDefault = hide;
+ }
+
+ /**
+ * Sets the opacity of a metanode if we don't hide on expansion.
+ *
+ * @param opacity the opacity (between 0 and 100)
+ */
+ static public void setExpandedOpacityDefault(double opacity) {
+ MetaNodeManager.metanodeOpacityDefault = 255*opacity/100;
+ }
+
+ /**
+ * Returns 'true' if we hide the metnode when we expand the
+ * network.
+ *
+ * @return 'true' if we hide the metanode upon expansion
+ */
+ static public boolean getHideMetaNodeDefault() {
+ return MetaNodeManager.hideMetanodeDefault;
+ }
+
+ /**
+ * 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.
+ *
+ * @param hide if 'true' we resize on expansion
+ */
+ static public void setSizeToBoundingBoxDefault(boolean resize) {
+ MetaNodeManager.sizeToBoundingBoxDefault = resize;
+ }
+
+ /**
+ * Returns 'true' if we hide the metnode when we expand the
+ * network.
+ *
+ * @return 'true' if we hide the metanode upon expansion
+ */
+ static public boolean getSizeToBoundingBoxDefault() {
+ return MetaNodeManager.sizeToBoundingBoxDefault;
+ }
+}
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeMenuListener.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeMenuListener.java
2010-08-19 03:32:26 UTC (rev 21465)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeMenuListener.java
2010-08-19 03:33:09 UTC (rev 21466)
@@ -46,6 +46,7 @@
import metaNodePlugin2.actions.MetanodeCommandListener;
import metaNodePlugin2.model.MetaNode;
+import metaNodePlugin2.model.MetaNodeManager;
import metaNodePlugin2.MetaNodeGroupViewer;
import metaNodePlugin2.MetaNodePlugin2;
import metaNodePlugin2.MetaNodePlugin2.Command;
@@ -187,15 +188,15 @@
// Get the groups this group is a member of
CyGroup group =
CyGroupManager.findGroup(contextNode.getIdentifier());
// Get the MetaNode
- MetaNode metaNode =
MetaNode.getMetaNode(group.getGroupNode());
- if (metaNode.isCollapsed(view)) {
+ MetaNode metaNode =
MetaNodeManager.getMetaNode(group.getGroupNode());
+ if (metaNode.isCollapsed()) {
addSubMenu(menu, label+"
"+group.getGroupName(),
command, group, contextNode);
}
} else if (CyGroupManager.isaGroup(contextNode) && command ==
Command.EXPANDNEW) {
CyGroup group =
CyGroupManager.findGroup(contextNode.getIdentifier());
- MetaNode metaNode =
MetaNode.getMetaNode(group.getGroupNode());
- if (metaNode.isCollapsed(view)) {
+ MetaNode metaNode =
MetaNodeManager.getMetaNode(group.getGroupNode());
+ if (metaNode.isCollapsed()) {
addSubMenu(menu, "Expand metanode
"+group.getGroupName()+" into new network",
command, group, contextNode);
}
@@ -279,16 +280,16 @@
CyNode groupNode = group.getGroupNode();
List<CyGroup> parents = groupNode.getGroups();
if (group.getViewer() != null &&
group.getViewer().equals(MetaNodePlugin2.viewerName)) {
- MetaNode metaNode =
MetaNode.getMetaNode(group.getGroupNode());
+ MetaNode metaNode =
MetaNodeManager.getMetaNode(group.getGroupNode());
- // Make sure we have a metnode object for this
group
+ // Make sure we have a metanode object for this
group
if (metaNode == null) {
- metaNode = new MetaNode(group);
+ metaNode =
MetaNodeManager.createMetaNode(group);
}
// Only present reasonable choices to the user
- if ((command == Command.COLLAPSE &&
metaNode.isCollapsed(view)) ||
- (command == Command.EXPAND &&
!metaNode.isCollapsed(view)))
+ if ((command == Command.COLLAPSE &&
metaNode.isCollapsed()) ||
+ (command == Command.EXPAND &&
!metaNode.isCollapsed()))
continue;
// If command is expand and we're a child of a
group that isn't
@@ -296,8 +297,8 @@
if ((command == Command.EXPAND) && (parents !=
null) && (parents.size() > 0)) {
boolean parentCollapsed = false;
for (CyGroup parent: parents) {
- MetaNode metaParent =
MetaNode.getMetaNode(parent.getGroupNode());
- if (groupList.contains(parent)
&& (metaParent.isCollapsed(view))) {
+ MetaNode metaParent =
MetaNodeManager.getMetaNode(parent.getGroupNode());
+ if (groupList.contains(parent)
&& (metaParent.isCollapsed())) {
parentCollapsed = true;
break;
}
@@ -311,7 +312,7 @@
if ((nodeGroups != null) &&
(nodeGroups.contains(group)))
continue;
// Are we this group?
- if (((metaNode =
MetaNode.getMetaNode(node)) != null) &&
+ if (((metaNode =
MetaNodeManager.getMetaNode(node)) != null) &&
(metaNode.getCyGroup() == group)) {
continue;
}
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
2010-08-19 03:32:26 UTC (rev 21465)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
2010-08-19 03:33:09 UTC (rev 21466)
@@ -39,6 +39,7 @@
package metaNodePlugin2.ui;
import metaNodePlugin2.model.MetaNode;
+import metaNodePlugin2.model.MetaNodeManager;
import metaNodePlugin2.model.MetanodeProperties;
import metaNodePlugin2.model.AttributeHandler;
import metaNodePlugin2.model.AttributeHandler.AttributeHandlingType;
@@ -309,21 +310,21 @@
t = metanodeProperties.get("hideMetanodes");
if ((t != null) && (t.valueChanged() || force)) {
hideMetaNode = ((Boolean) t.getValue()).booleanValue();
- MetaNode.setHideMetaNodeDefault(hideMetaNode);
+ MetaNodeManager.setHideMetaNodeDefault(hideMetaNode);
metanodeProperties.setProperty(t.getName(),
t.getValue().toString());
}
t = metanodeProperties.get("sizeToBoundingBox");
if ((t != null) && (t.valueChanged() || force)) {
sizeToBoundingBox = ((Boolean) t.getValue()).booleanValue();
- MetaNode.setSizeToBoundingBoxDefault(sizeToBoundingBox);
+
MetaNodeManager.setSizeToBoundingBoxDefault(sizeToBoundingBox);
metanodeProperties.setProperty(t.getName(),
t.getValue().toString());
}
t = metanodeProperties.get("metanodeOpacity");
if ((t != null) && (t.valueChanged() || force)) {
metanodeOpacity = ((Double) t.getValue()).doubleValue();
- MetaNode.setExpandedOpacityDefault(metanodeOpacity);
+
MetaNodeManager.setExpandedOpacityDefault(metanodeOpacity);
metanodeProperties.setProperty(t.getName(),
t.getValue().toString());
}
@@ -431,7 +432,7 @@
// Get all selected nodes
Set<CyNode> nodeList =
Cytoscape.getCurrentNetwork().getSelectedNodes();
for (CyNode node: nodeList) {
- MetaNode mn = MetaNode.getMetaNode(node);
+ MetaNode mn = MetaNodeManager.getMetaNode(node);
if (mn != null) {
mn.setHideMetaNode(hideMetaNode);
mn.setSizeToBoundingBox(sizeToBoundingBox);
@@ -446,7 +447,7 @@
List<CyGroup> groupList =
CyGroupManager.getGroupList(groupViewer);
// Update them
for (CyGroup group: groupList) {
- MetaNode mn = MetaNode.getMetaNode(group);
+ MetaNode mn =
MetaNodeManager.getMetaNode(group);
if (mn != null) {
mn.setHideMetaNode(hideMetaNode);
mn.setSizeToBoundingBox(sizeToBoundingBox);
@@ -465,7 +466,7 @@
sizeToBoundingBoxTunable.setImmutable(true);
else
sizeToBoundingBoxTunable.setImmutable(false);
- MetaNode.setHideMetaNodeDefault(hideMetanode);
+ MetaNodeManager.setHideMetaNodeDefault(hideMetanode);
} else if (t.getName().equals("sizeToBoundingBox")) {
boolean sizeToBoundingBox = ((Boolean) t.getValue()).booleanValue();
if (sizeToBoundingBox) {
@@ -473,10 +474,10 @@
modifyVizMap();
} else
opacityTunable.setImmutable(true);
- MetaNode.setSizeToBoundingBoxDefault(sizeToBoundingBox);
+
MetaNodeManager.setSizeToBoundingBoxDefault(sizeToBoundingBox);
} else if (t.getName().equals("metanodeOpacity")) {
double opacity = ((Double) t.getValue()).doubleValue();
- MetaNode.setExpandedOpacityDefault(opacity);
+ MetaNodeManager.setExpandedOpacityDefault(opacity);
} else if (t.getName().equals("enableHandling")) {
enableHandling = ((Boolean) t.getValue()).booleanValue();
AttributeHandler.setEnable(enableHandling);
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