Author: rozagh
Date: 2012-09-07 15:28:56 -0700 (Fri, 07 Sep 2012)
New Revision: 30338
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkPanel.java
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/TreeCellRenderer.java
Log:
fixes #1432 showing the title of root network and adding menu items for
renaming and also selecting all of the networks in the collection.
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
2012-09-07 21:48:46 UTC (rev 30337)
+++
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
2012-09-07 22:28:56 UTC (rev 30338)
@@ -117,6 +117,7 @@
import org.cytoscape.task.NetworkViewCollectionTaskFactory;
import org.cytoscape.task.NetworkViewTaskFactory;
import org.cytoscape.task.TableTaskFactory;
+import org.cytoscape.task.edit.EditNetworkTitleTaskFactory;
import org.cytoscape.task.write.SaveSessionAsTaskFactory;
import org.cytoscape.util.swing.FileUtil;
import org.cytoscape.util.swing.OpenBrowser;
@@ -196,6 +197,8 @@
DataSourceManager dsManagerServiceRef = getService(bc,
DataSourceManager.class);
+ EditNetworkTitleTaskFactory editNetworkTitleTFServiceRef =
getService(bc, EditNetworkTitleTaskFactory.class);
+
//////////////
UndoAction undoAction = new UndoAction(undoSupportServiceRef);
RedoAction redoAction = new RedoAction(undoSupportServiceRef);
@@ -229,7 +232,8 @@
cyNetworkViewManagerServiceRef,
birdsEyeViewHandler,
dialogTaskManagerServiceRef,
-
dynamicTaskFactoryProvisionerServiceRef);
+
dynamicTaskFactoryProvisionerServiceRef,
+
editNetworkTitleTFServiceRef);
CytoscapeDesktop cytoscapeDesktop = new
CytoscapeDesktop(cytoscapeMenus,
networkViewManager, networkPanel,
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkPanel.java
===================================================================
---
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkPanel.java
2012-09-07 21:48:46 UTC (rev 30337)
+++
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkPanel.java
2012-09-07 22:28:56 UTC (rev 30338)
@@ -33,6 +33,8 @@
import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.util.ArrayList;
@@ -89,6 +91,7 @@
import org.cytoscape.task.NetworkTaskFactory;
import org.cytoscape.task.NetworkViewCollectionTaskFactory;
import org.cytoscape.task.NetworkViewTaskFactory;
+import org.cytoscape.task.edit.EditNetworkTitleTaskFactory;
import org.cytoscape.util.swing.JTreeTable;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewManager;
@@ -142,6 +145,9 @@
private boolean ignoreTreeSelectionEvents;
+ private final EditNetworkTitleTaskFactory rootNetworkTitleEditor;
+ private final JPopupMenu rootPopupMenu;
+ private CyRootNetwork selectedRoot;
/**
*
* @param appMgr
@@ -155,7 +161,8 @@
final CyNetworkViewManager
netViewMgr,
final BirdsEyeViewHandler bird,
final DialogTaskManager taskMgr,
- DynamicTaskFactoryProvisioner
factoryProvisioner) {
+ DynamicTaskFactoryProvisioner
factoryProvisioner,
+ final
EditNetworkTitleTaskFactory networkTitleEditor) {
super();
this.treeNodeMap = new HashMap<Long, NetworkTreeNode>();
@@ -165,7 +172,8 @@
this.netViewMgr = netViewMgr;
this.taskMgr = taskMgr;
this.factoryProvisioner = factoryProvisioner;
-
+
+
root = new NetworkTreeNode("Network Root", null);
treeTableModel = new NetworkTreeTableModel(this, root);
treeTable = new JTreeTable(treeTableModel);
@@ -181,6 +189,7 @@
nodeEdgeTables = new WeakHashMap<CyTable, CyNetwork>();
this.network2nodeMap = new WeakHashMap<CyNetwork,
NetworkTreeNode>();
+
setNavigator(bird.getBirdsEyeView());
/*
@@ -194,6 +203,30 @@
treeTable.setInputMap(WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, map);
}
}
+
+
+ this.rootNetworkTitleEditor = networkTitleEditor;
+ rootPopupMenu = new JPopupMenu();
+ JMenuItem editRootNetworTitle = new JMenuItem("Rename Network
Collection...");
+ editRootNetworTitle.addActionListener(new ActionListener() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+
+ taskMgr.execute(
rootNetworkTitleEditor.createTaskIterator(selectedRoot));
+ }
+ });
+ rootPopupMenu.add(editRootNetworTitle);
+
+ JMenuItem selectAllSubNetsMenuItem = new JMenuItem("Select All
Networks");
+ selectAllSubNetsMenuItem.addActionListener(new ActionListener()
{
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ selectAllSubnetwork();
+ }
+ });
+ rootPopupMenu.add(selectAllSubNetsMenuItem);
}
protected void initialize() {
@@ -538,8 +571,11 @@
parentTreeNode =
this.treeNodeMap.get(parentNetwork.getSUID());
}
- if (parentTreeNode == null)
- parentTreeNode = new NetworkTreeNode("", null);
+ if (parentTreeNode == null){
+ parentTreeNode = new
NetworkTreeNode(parentNetwork.getRow(parentNetwork).get(CyNetwork.NAME,
String.class) , parentNetwork);
+
nameTables.put(parentNetwork.getDefaultNetworkTable(), parentNetwork);
+ network2nodeMap.put(parentNetwork,
parentTreeNode);
+ }
// Actual tree node for this network
String netName =
network.getRow(network).get(CyNetwork.NAME, String.class);
@@ -627,12 +663,13 @@
CyNetwork cn = node.getNetwork();
final List<CyNetwork> selectedNetworks = new
LinkedList<CyNetwork>();
-
- if (cn == null) {
+
+ /*
+ if (cn instanceof CyRootNetwork) {
// This is a "network set" node...
// When selecting root node, all of the subnetworks are
selected.
- CyRootNetwork root = ((CySubNetwork) ((NetworkTreeNode)
node.getFirstChild()).getNetwork())
- .getRootNetwork();
+ CyRootNetwork root = (CyRootNetwork) cn;
+ //((NetworkTreeNode)
node.getFirstChild()).getNetwork()).getRootNetwork();
// Creates a list of all selected networks
List<CySubNetwork> subNetworks =
root.getSubNetworkList();
@@ -645,7 +682,7 @@
// Determine the current network
if (!selectedNetworks.isEmpty())
cn = ((NetworkTreeNode)
node.getFirstChild()).getNetwork();
- } else {
+ } else { */
// Regular multiple networks selection...
try {
// Create a list of all selected networks
@@ -658,8 +695,62 @@
} catch (Exception ex) {
logger.error("Error creating the list of
selected networks", ex);
}
+ // }
+
+ final List<CyNetworkView> selectedViews = new
ArrayList<CyNetworkView>();
+
+ for (final CyNetwork n : selectedNetworks) {
+ final Collection<CyNetworkView> views =
netViewMgr.getNetworkViews(n);
+
+ if (!views.isEmpty())
+ selectedViews.addAll(views);
}
+ // No need to set the same network again. It should prevent
infinite loops.
+ // Also check if the network still exists (it could have been
removed by another thread).
+ if (cn == null || netMgr.networkExists(cn.getSUID())) {
+ if (cn == null ||
!cn.equals(appMgr.getCurrentNetwork()))
+ appMgr.setCurrentNetwork(cn);
+
+ CyNetworkView cv = null;
+
+ // Try to get the first view of the current network
+ final Collection<CyNetworkView> cnViews = cn != null ?
netViewMgr.getNetworkViews(cn) : null;
+ cv = (cnViews == null || cnViews.isEmpty()) ? null :
cnViews.iterator().next();
+
+ if (cv == null ||
!cv.equals(appMgr.getCurrentNetworkView()))
+ appMgr.setCurrentNetworkView(cv);
+
+ appMgr.setSelectedNetworks(selectedNetworks);
+ appMgr.setSelectedNetworkViews(selectedViews);
+ }
+ }
+
+ private void selectAllSubnetwork(){
+
+ final List<CyNetwork> selectedNetworks = new
LinkedList<CyNetwork>();
+
+ // This is a "network set" node...
+ // When selecting root node, all of the subnetworks are
selected.
+ CyRootNetwork root = selectedRoot;
+
+ final NetworkTreeNode node = this.network2nodeMap.get(root);
+
+ // Creates a list of all selected networks
+ List<CySubNetwork> subNetworks = root.getSubNetworkList();
+
+ for (CySubNetwork sn : subNetworks) {
+ if (netMgr.networkExists(sn.getSUID()))
+ selectedNetworks.add(sn);
+ }
+
+ CyNetwork cn = root;
+
+ // Determine the current network
+ if (!selectedNetworks.isEmpty())
+ cn = ((NetworkTreeNode)
node.getFirstChild()).getNetwork();
+
+
final List<CyNetworkView> selectedViews = new
ArrayList<CyNetworkView>();
for (final CyNetwork n : selectedNetworks) {
@@ -713,7 +804,7 @@
* display the popup
*/
private final void maybeShowPopup(final MouseEvent e) {
-
+
// Ignore if not valid trigger.
if (!e.isPopupTrigger())
return;
@@ -725,15 +816,24 @@
final JTree tree = treeTable.getTree();
final TreePath treePath = tree.getPathForRow(row);
-
+ CyNetwork rootnetwork;
+
Long networkID = -1L;
try {
- networkID = ((NetworkTreeNode)
treePath.getLastPathComponent()).getNetwork().getSUID();
+ rootnetwork = ((NetworkTreeNode)
treePath.getLastPathComponent()).getNetwork();
+ networkID = rootnetwork.getSUID();
} catch (NullPointerException nullExp) {
// The tree root does not represent a network,
ignore it.
return;
}
+ if (rootnetwork instanceof CyRootNetwork)
+ {
+ selectedRoot = (CyRootNetwork) rootnetwork;
+ rootPopupMenu.show(e.getComponent(), e.getX(),
e.getY());
+ return;
+ }
+
final CyNetwork network = netMgr.getNetwork(networkID);
if (network != null) {
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/TreeCellRenderer.java
===================================================================
---
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/TreeCellRenderer.java
2012-09-07 21:48:46 UTC (rev 30337)
+++
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/TreeCellRenderer.java
2012-09-07 22:28:56 UTC (rev 30338)
@@ -12,6 +12,8 @@
import javax.swing.tree.DefaultTreeCellRenderer;
import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.subnetwork.CyRootNetwork;
+import org.cytoscape.model.subnetwork.CySubNetwork;
import org.cytoscape.util.swing.JTreeTable;
final class TreeCellRenderer extends DefaultTreeCellRenderer {
@@ -23,6 +25,7 @@
private static final Font TABLE_FONT = new Font("SansSerif",
Font.PLAIN, 12);
private static final Font TABLE_FONT_SELECTED = new Font("SansSerif",
Font.BOLD, 12);
+ private static final Font TABLE_FONT_ROOT = new Font("SansSerif",
Font.ITALIC, 12);
private static final Dimension CELL_SIZE = new Dimension(1200, 40);
@@ -63,17 +66,19 @@
if (selected) {
this.setFont(TABLE_FONT_SELECTED);
- this.setBackgroundSelectionColor(Color.lightGray);
+ this.setBackgroundSelectionColor( new Color(0, 100,
255, 40));
}
else {
this.setFont(TABLE_FONT);
this.setBackgroundNonSelectionColor(Color.white);
}
- if(treeNode.getNetwork() == null) {
+ if(treeNode.getNetwork() == null || (treeNode.getNetwork()
instanceof CyRootNetwork) ) {
setForeground(treeTable.getForeground());
+ this.setFont(TABLE_FONT_ROOT);
return this;
}
+
setForeground(treeNode.getNodeColor());
try {
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