Author: scooter
Date: 2012-07-19 19:03:42 -0700 (Thu, 19 Jul 2012)
New Revision: 29934
Modified:
core3/impl/trunk/group-session-restore-shim/pom.xml
core3/impl/trunk/group-session-restore-shim/src/main/java/org/cytoscape/group/session/restore/shim/internal/SessionEventsListener.java
Log:
Update group position information. Still need to transfer settings...
Modified: core3/impl/trunk/group-session-restore-shim/pom.xml
===================================================================
--- core3/impl/trunk/group-session-restore-shim/pom.xml 2012-07-19 23:32:17 UTC
(rev 29933)
+++ core3/impl/trunk/group-session-restore-shim/pom.xml 2012-07-20 02:03:42 UTC
(rev 29934)
@@ -73,6 +73,14 @@
<artifactId>session-api</artifactId>
</dependency>
<dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>viewmodel-api</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>presentation-api</artifactId>
+ </dependency>
+ <dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
Modified:
core3/impl/trunk/group-session-restore-shim/src/main/java/org/cytoscape/group/session/restore/shim/internal/SessionEventsListener.java
===================================================================
---
core3/impl/trunk/group-session-restore-shim/src/main/java/org/cytoscape/group/session/restore/shim/internal/SessionEventsListener.java
2012-07-19 23:32:17 UTC (rev 29933)
+++
core3/impl/trunk/group-session-restore-shim/src/main/java/org/cytoscape/group/session/restore/shim/internal/SessionEventsListener.java
2012-07-20 02:03:42 UTC (rev 29934)
@@ -7,6 +7,7 @@
import org.cytoscape.group.CyGroup;
import org.cytoscape.group.CyGroupFactory;
import org.cytoscape.group.CyGroupManager;
+import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
@@ -21,6 +22,9 @@
import org.cytoscape.session.events.SessionAboutToBeSavedListener;
import org.cytoscape.session.events.SessionLoadedEvent;
import org.cytoscape.session.events.SessionLoadedListener;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.model.View;
+import org.cytoscape.view.presentation.property.BasicVisualLexicon;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -31,6 +35,7 @@
private final CyNetworkManager netMgr;
private final CyRootNetworkManager rootNetMgr;
private final String EXTERNAL_EDGE_ATTRIBUTE="__externalEdges";
+ private final String GROUP_COLLAPSED_ATTRIBUTE="__groupCollapsed";
private static final Logger logger =
LoggerFactory.getLogger(SessionEventsListener.class);
@@ -76,14 +81,35 @@
return;
boolean collapsed = false;
+ boolean cy2group = false;
if (hnRow.isSet("__groupState")) {
Integer grState = hnRow.get("__groupState",
Integer.class); // 2.x metadata
+ cy2group = true;
if (grState.intValue() == 2) collapsed = true;
} else if (dnRow.isSet("__groupState")) {
Integer grState = dnRow.get("__groupState",
Integer.class); // 2.x metadata
+ cy2group = true;
if (grState.intValue() == 2) collapsed = true;
}
+
+ // Check to make sure the column exists
+ if
(rnRow.getTable().getColumn(GROUP_COLLAPSED_ATTRIBUTE) == null) {
+
rnRow.getTable().createListColumn(GROUP_COLLAPSED_ATTRIBUTE, String.class,
true);
+ }
+
+ if (!rnRow.isSet(GROUP_COLLAPSED_ATTRIBUTE)) {
+ // This is a 2.x group. We need to recreate
the 3.x structure
+ List<String> collapsedList =
rnRow.getList(GROUP_COLLAPSED_ATTRIBUTE, String.class);
+ if (collapsedList == null) collapsedList = new
ArrayList<String>();
+
+ String netName =
net.getDefaultNetworkTable().getRow(net.getSUID()).get(CyNetwork.NAME,
String.class);
+ if (netName == null)
+ netName = "(null)";
+
+ collapsedList.add(netName+":"+collapsed);
+ rnRow.set(GROUP_COLLAPSED_ATTRIBUTE,
collapsedList);
+ }
// Create the group
final CyGroup group = groupFactory.createGroup(net, n,
true);
@@ -108,22 +134,35 @@
group.addEdges(externalEdges);
}
+ /*
+ // Disable nested network
+ final boolean nestedNetVisible =
dnRow.get("nested_network_is_visible", Boolean.class, Boolean.FALSE);
+ if
(dnRow.getTable().getColumn("nested_network_is_visible") == null) {
+
dnRow.getTable().createColumn("nested_network_is_visible", Boolean.class,
false);
+ }
+ dnRow.set("nested_network_is_visible", Boolean.FALSE);
+ */
+
// TODO: restore group's settings
- // final boolean nestedNetVisible =
dnRow.get("nested_network_is_visible", Boolean.class, Boolean.FALSE);
-// groupSettings.setUseNestedNetworks(nestedNetVisible,
group);
-
- // So the group node is removed from the network when
it is expanded:
- // TODO: Shouldn't the group factory automatically
remove the provided group node, since the initial state
- // should be the same as expanded?
- /*
- group.collapse(net);
+ // Some special handling for cy2 groups. We need to
restore the X,Y coordinates of the nodes
+ // if we're collapsed.
+ if (cy2group) {
+ // Copy all of the tables for the group
+ copyTables(netPointer, net, n);
- if (!collapsed) {
- // Expanded...
- group.expand(net);
+ // If the group is collapsed, we need to
provide the location information so
+ // we can expand it
+ if (collapsed) {
+
updateGroupNodeLocation(getNetworkView(sess, net), n);
+ }
}
- */
}
+
+ // TODO: If this is a 2.x group, clean up
+ if (net.getDefaultNodeTable().getColumn("__groupState") != null)
+ net.getDefaultNodeTable().deleteColumn("__groupState");
+ if (net.getDefaultNodeTable().getColumn("__groupIsLocal") !=
null)
+
net.getDefaultNodeTable().deleteColumn("__groupIsLocal");
}
public void handleEvent(SessionAboutToBeSavedEvent e) {
@@ -162,4 +201,80 @@
}
}
}
+
+ private void copyTables(CyNetwork netPointer, CyNetwork net, CyNode
groupNode) {
+ // Copy the tables from the subnetwork
+ CyTable subTable = netPointer.getDefaultNodeTable();
+ CyTable nodeTable = net.getDefaultNodeTable();
+
+ CyTable hiddenSubTable = netPointer.getTable(CyNode.class,
CyNetwork.HIDDEN_ATTRS);
+ CyTable hiddenTable = net.getTable(CyNode.class,
CyNetwork.HIDDEN_ATTRS);
+
+ // The group code stores location information in the root table
+ CyRootNetwork rootNetwork =
((CySubNetwork)net).getRootNetwork();
+ CyTable hiddenRootTable = rootNetwork.getTable(CyNode.class,
CyNetwork.HIDDEN_ATTRS);
+
+ for (CyNode child: netPointer.getNodeList()) {
+ CyRow row = netPointer.getRow(child);
+ CyRow nodeRow = nodeTable.getRow(child.getSUID());
+ for (CyColumn col: subTable.getColumns()) {
+ String name = col.getName();
+ if (nodeTable.getColumn(name) != null &&
+
!nodeTable.getColumn(name).getVirtualColumnInfo().isVirtual()) {
+ nodeRow.set(col.getName(),
row.get(name, col.getType()));
+ }
+ }
+
+ CyRow hiddenRow = hiddenTable.getRow(child.getSUID());
+ CyRow hiddenSubRow =
hiddenSubTable.getRow(child.getSUID());
+ CyRow hiddenRootRow =
hiddenRootTable.getRow(child.getSUID());
+ for (CyColumn col: hiddenSubTable.getColumns()) {
+ String name = col.getName();
+ // Look for child node location information
+ if (name.equals("__metanodeHintX")) {
+ Double offset = hiddenSubRow.get(name,
Double.class);
+ createColumn(hiddenRootRow,
"__xOffset", Double.class);
+ hiddenRootRow.set("__xOffset", offset);
+ } else if (name.equals("__metanodeHintY")) {
+ Double offset = hiddenSubRow.get(name,
Double.class);
+ createColumn(hiddenRootRow,
"__yOffset", Double.class);
+ hiddenRootRow.set("__yOffset", offset);
+ } else if (hiddenTable.getColumn(name) != null
&&
+
!hiddenTable.getColumn(name).getVirtualColumnInfo().isVirtual()) {
+ hiddenSubRow.set(col.getName(),
hiddenRow.get(name, col.getType()));
+ }
+ }
+ }
+ }
+
+ private CyNetworkView getNetworkView(CySession sess, CyNetwork net) {
+ for (CyNetworkView view: sess.getNetworkViews()) {
+ if (view.getModel().equals(net)) {
+ return view;
+ }
+ }
+ return null;
+ }
+
+ private void updateGroupNodeLocation(CyNetworkView view, CyNode
groupNode) {
+ if (view == null) return;
+
+ CyRootNetwork rootNetwork =
((CySubNetwork)view.getModel()).getRootNetwork();
+ View<CyNode> nView = view.getNodeView(groupNode);
+ double x =
nView.getVisualProperty(BasicVisualLexicon.NODE_X_LOCATION);
+ double y =
nView.getVisualProperty(BasicVisualLexicon.NODE_Y_LOCATION);
+ // Save it
+ CyRow hRow = rootNetwork.getRow(groupNode,
CyNetwork.HIDDEN_ATTRS);
+ createColumn(hRow, "__xLocation", Double.class);
+ createColumn(hRow, "__yLocation", Double.class);
+ hRow.set("__xLocation", new Double(x));
+ hRow.set("__yLocation", new Double(y));
+ }
+
+ private void createColumn(CyRow row, String column, Class type) {
+ CyTable table = row.getTable();
+ if (table.getColumn(column) == null) {
+ table.createColumn(column, type, false);
+ }
+ }
}
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