Author: mes
Date: 2012-01-11 17:46:00 -0800 (Wed, 11 Jan 2012)
New Revision: 27992
Modified:
core3/api/trunk/viewmodel-api/src/main/java/org/cytoscape/view/model/CyNetworkViewManager.java
core3/impl/trunk/application-impl/src/main/java/org/cytoscape/application/internal/CyApplicationManagerImpl.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/AbstractNetworkFromSelectionTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewEdit.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/networkobjects/DeleteEdit.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/AbstractSelectTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/DeselectAllEdgesTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/DeselectAllNodesTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/DeselectAllTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/InvertSelectedEdgesTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/InvertSelectedNodesTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectAdjacentEdgesTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectAllEdgesTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectAllNodesTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectAllTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectConnectedNodesTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectFirstNeighborsTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectFromFileListTask.java
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/select/AbstractSelectTaskTester.java
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/cytoscape/MergeNetworkEdit.java
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/NetworkUtil.java
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/IndexAndSearchTask.java
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CysessionFactory.java
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/select/RowsSetViewUpdater.java
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkPanel.java
core3/impl/trunk/viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/CyNetworkViewManagerImpl.java
core3/support/trunk/samples/sample06/src/main/java/org/cytoscape/sample/internal/MyNetworkViewTask.java
Log:
fixes #434 Changes CyNetworkViewManager api to work with networks instead of
network ids.
Modified:
core3/api/trunk/viewmodel-api/src/main/java/org/cytoscape/view/model/CyNetworkViewManager.java
===================================================================
---
core3/api/trunk/viewmodel-api/src/main/java/org/cytoscape/view/model/CyNetworkViewManager.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/api/trunk/viewmodel-api/src/main/java/org/cytoscape/view/model/CyNetworkViewManager.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -33,6 +33,7 @@
import java.util.Set;
import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.model.CyNetwork;
/**
@@ -48,22 +49,22 @@
public Set<CyNetworkView> getNetworkViewSet();
/**
- * Returns the network view corresponding to an ID, if found.
+ * Returns the network view corresponding to the specified network, if
found.
*
- * @param networkId a unique ID that hopefully corresponds to a
network view.
+ * @param network The network we're requesting a view of.
*
* @return null if no network view was found corresponding to
"networkId", else the network view
*/
- public CyNetworkView getNetworkView(long networkId);
+ public CyNetworkView getNetworkView(CyNetwork network);
/**
- * Determines whether a network view corresponding to a certain ID is
known to the network view manager.
+ * Determines whether a network view for the specified network is known
to the network view manager.
*
- * @param networkId a unique ID that may correspond to a network view
+ * @param network The network for which we want to know whether a view
exists.
*
* @return true if a view was found that corresponds to "networkId",
else false
*/
- public boolean viewExists(long networkId);
+ public boolean viewExists(CyNetwork network);
/**
* Destroys a network view.
Modified:
core3/impl/trunk/application-impl/src/main/java/org/cytoscape/application/internal/CyApplicationManagerImpl.java
===================================================================
---
core3/impl/trunk/application-impl/src/main/java/org/cytoscape/application/internal/CyApplicationManagerImpl.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/application-impl/src/main/java/org/cytoscape/application/internal/CyApplicationManagerImpl.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -185,7 +185,7 @@
logger.info("Set current network called. Current
network ID = " + networkId);
currentNetwork = network;
- currentNetworkView =
networkViewManager.getNetworkView(networkId);
+ currentNetworkView =
networkViewManager.getNetworkView(network);
// reset selected networks
selectedNetworks.clear();
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/AbstractNetworkFromSelectionTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/AbstractNetworkFromSelectionTask.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/AbstractNetworkFromSelectionTask.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -96,7 +96,7 @@
throw new NullPointerException("Source network is
null.");
tm.setProgress(0.0);
- final CyNetworkView curView =
networkViewManager.getNetworkView(parentNetwork.getSUID());
+ final CyNetworkView curView =
networkViewManager.getNetworkView(parentNetwork);
tm.setProgress(0.1);
// Get the selected nodes, but only create network if nodes are
actually
@@ -129,7 +129,7 @@
if (curView == null) {
// inserted first, happens second
- final Task setCurrentNetworkView = new
SetCurrentNetworkViewTask(newNet.getSUID());
+ final Task setCurrentNetworkView = new
SetCurrentNetworkViewTask(newNet);
insertTasksAfterCurrentTask(setCurrentNetworkView);
@@ -176,13 +176,13 @@
}
private class SetCurrentNetworkViewTask extends AbstractTask {
- long netId;
- SetCurrentNetworkViewTask(long netId) {
- this.netId = netId;
+ CyNetwork net;
+ SetCurrentNetworkViewTask(CyNetwork net) {
+ this.net = net;
}
public void run(TaskMonitor tm) {
tm.setProgress(0.0);
- CyNetworkView view =
networkViewManager.getNetworkView(netId);
+ CyNetworkView view =
networkViewManager.getNetworkView(net);
tm.setProgress(0.5);
if ( view != null )
appManager.setCurrentNetworkView( view );
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -87,7 +87,7 @@
// Create copied network model
final CyNetwork newNet = cloneNetwork(parentNetwork);
tm.setProgress(0.4);
- final CyNetworkView origView =
networkViewManager.getNetworkView(parentNetwork.getSUID());
+ final CyNetworkView origView =
networkViewManager.getNetworkView(parentNetwork);
networkManager.addNetwork(newNet);
tm.setProgress(0.6);
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewEdit.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewEdit.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewEdit.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -69,7 +69,7 @@
public void undo() {
;
- final CyNetworkView view =
networkViewManager.getNetworkView(network.getSUID());
+ final CyNetworkView view =
networkViewManager.getNetworkView(network);
networkCenterX =
view.getVisualProperty(NETWORK_CENTER_X_LOCATION);
networkCenterY =
view.getVisualProperty(NETWORK_CENTER_Y_LOCATION);
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/networkobjects/DeleteEdit.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/networkobjects/DeleteEdit.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/networkobjects/DeleteEdit.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -66,7 +66,7 @@
// save the positions of the nodes
xPos = new double[nodes.size()];
yPos = new double[nodes.size()];
- CyNetworkView netView =
netViewMgr.getNetworkView(net.getSUID());
+ CyNetworkView netView = netViewMgr.getNetworkView(net);
if (netView != null) {
int i = 0;
for (CyNode n : nodes) {
@@ -84,7 +84,7 @@
net.removeNodes(nodes);
net.removeEdges(edges);
- CyNetworkView netView =
netViewMgr.getNetworkView(net.getSUID());
+ CyNetworkView netView = netViewMgr.getNetworkView(net);
// Manually call update presentation
netView.updateView();
@@ -100,7 +100,7 @@
eventHelper.flushPayloadEvents();
- CyNetworkView netView =
netViewMgr.getNetworkView(net.getSUID());
+ CyNetworkView netView = netViewMgr.getNetworkView(net);
if (netView != null) {
int i = 0;
for (final CyNode node : nodes) {
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/AbstractSelectTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/AbstractSelectTask.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/AbstractSelectTask.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -53,7 +53,7 @@
// This is necessary, otherwise, this does not update
presentation!
eventHelper.flushPayloadEvents();
- final CyNetworkView view =
networkViewManager.getNetworkView(network.getSUID());
+ final CyNetworkView view =
networkViewManager.getNetworkView(network);
if (view != null)
view.updateView();
}
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/DeselectAllEdgesTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/DeselectAllEdgesTask.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/DeselectAllEdgesTask.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -51,7 +51,7 @@
public void run(TaskMonitor tm) {
tm.setProgress(0.0);
- final CyNetworkView view =
networkViewManager.getNetworkView(network.getSUID());
+ final CyNetworkView view =
networkViewManager.getNetworkView(network);
undoSupport.postEdit(
new SelectionEdit(eventHelper, "Deselect All Edges",
network, view,
SelectionEdit.SelectionFilter.EDGES_ONLY));
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/DeselectAllNodesTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/DeselectAllNodesTask.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/DeselectAllNodesTask.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -51,7 +51,7 @@
public void run(final TaskMonitor tm) {
tm.setProgress(0.0);
- final CyNetworkView view =
networkViewManager.getNetworkView(network.getSUID());
+ final CyNetworkView view =
networkViewManager.getNetworkView(network);
undoSupport.postEdit(
new SelectionEdit(eventHelper, "Deselect All Nodes",
network, view,
SelectionEdit.SelectionFilter.NODES_ONLY));
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/DeselectAllTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/DeselectAllTask.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/DeselectAllTask.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -51,7 +51,7 @@
public void run(final TaskMonitor tm) {
tm.setProgress(0.0);
- final CyNetworkView view =
networkViewManager.getNetworkView(network.getSUID());
+ final CyNetworkView view =
networkViewManager.getNetworkView(network);
undoSupport.postEdit(
new SelectionEdit(eventHelper, "Deselect All Nodes and
Edges", network, view,
SelectionEdit.SelectionFilter.NODES_AND_EDGES));
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/InvertSelectedEdgesTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/InvertSelectedEdgesTask.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/InvertSelectedEdgesTask.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -52,7 +52,7 @@
public void run(final TaskMonitor tm) {
tm.setProgress(0.0);
- final CyNetworkView view =
networkViewManager.getNetworkView(network.getSUID());
+ final CyNetworkView view =
networkViewManager.getNetworkView(network);
undoSupport.postEdit(
new SelectionEdit(eventHelper, "Invert Selected Edges",
network, view,
SelectionEdit.SelectionFilter.EDGES_ONLY));
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/InvertSelectedNodesTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/InvertSelectedNodesTask.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/InvertSelectedNodesTask.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -53,7 +53,7 @@
@Override
public void run(final TaskMonitor tm) {
tm.setProgress(0.0);
- final CyNetworkView view =
networkViewManager.getNetworkView(network.getSUID());
+ final CyNetworkView view =
networkViewManager.getNetworkView(network);
undoSupport.postEdit(
new SelectionEdit(eventHelper, "Invert Selected Nodes",
network, view,
SelectionEdit.SelectionFilter.NODES_ONLY));
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectAdjacentEdgesTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectAdjacentEdgesTask.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectAdjacentEdgesTask.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -57,7 +57,7 @@
public void run(final TaskMonitor tm) {
tm.setProgress(0.0);
- final CyNetworkView view =
networkViewManager.getNetworkView(network.getSUID());
+ final CyNetworkView view =
networkViewManager.getNetworkView(network);
undoSupport.postEdit(
new SelectionEdit(eventHelper, "Select Adjacent Edges",
network, view,
SelectionEdit.SelectionFilter.EDGES_ONLY));
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectAllEdgesTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectAllEdgesTask.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectAllEdgesTask.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -51,7 +51,7 @@
public void run(TaskMonitor tm) {
tm.setProgress(0.0);
- final CyNetworkView view =
networkViewManager.getNetworkView(network.getSUID());
+ final CyNetworkView view =
networkViewManager.getNetworkView(network);
undoSupport.postEdit(
new SelectionEdit(eventHelper, "Select All Edges",
network, view,
SelectionEdit.SelectionFilter.EDGES_ONLY));
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectAllNodesTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectAllNodesTask.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectAllNodesTask.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -53,7 +53,7 @@
@Override
public void run(TaskMonitor tm) throws Exception {
tm.setProgress(0.0);
- final CyNetworkView view =
networkViewManager.getNetworkView(network.getSUID());
+ final CyNetworkView view =
networkViewManager.getNetworkView(network);
undoSupport.postEdit(
new SelectionEdit(eventHelper, "Select All Nodes",
network, view,
SelectionEdit.SelectionFilter.NODES_ONLY));
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectAllTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectAllTask.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectAllTask.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -51,7 +51,7 @@
public void run(TaskMonitor monitor) {
monitor.setProgress(0.0);
- final CyNetworkView view =
networkViewManager.getNetworkView(network.getSUID());
+ final CyNetworkView view =
networkViewManager.getNetworkView(network);
undoSupport.postEdit(
new SelectionEdit(eventHelper, "Select All Nodes and
Edges", network, view,
SelectionEdit.SelectionFilter.NODES_AND_EDGES));
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectConnectedNodesTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectConnectedNodesTask.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectConnectedNodesTask.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -59,7 +59,7 @@
public void run(TaskMonitor tm) {
tm.setProgress(0.0);
- final CyNetworkView view =
networkViewManager.getNetworkView(network.getSUID());
+ final CyNetworkView view =
networkViewManager.getNetworkView(network);
undoSupport.postEdit(
new SelectionEdit(eventHelper, "Select Nodes Connected
by Selected Edges",
network, view,
SelectionEdit.SelectionFilter.NODES_ONLY));
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectFirstNeighborsTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectFirstNeighborsTask.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectFirstNeighborsTask.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -62,7 +62,7 @@
@Override
public void run(TaskMonitor tm) {
tm.setProgress(0.0);
- final CyNetworkView view =
networkViewManager.getNetworkView(network.getSUID());
+ final CyNetworkView view =
networkViewManager.getNetworkView(network);
undoSupport.postEdit(
new SelectionEdit(eventHelper, "Select First-Neighbour
Nodes", network, view,
SelectionEdit.SelectionFilter.NODES_ONLY));
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectFromFileListTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectFromFileListTask.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectFromFileListTask.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -74,7 +74,7 @@
if (file == null)
throw new NullPointerException("You must specify a
non-null file to load!");
- final CyNetworkView view =
networkViewManager.getNetworkView(network.getSUID());
+ final CyNetworkView view =
networkViewManager.getNetworkView(network);
final SelectionEdit edit =
new SelectionEdit(eventHelper, "Select Nodes From
File", network, view,
SelectionEdit.SelectionFilter.NODES_ONLY);
Modified:
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/select/AbstractSelectTaskTester.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/select/AbstractSelectTaskTester.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/select/AbstractSelectTaskTester.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -27,7 +27,7 @@
*/
package org.cytoscape.task.internal.select;
-import static org.mockito.Matchers.anyLong;
+import static org.mockito.Matchers.any;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
@@ -70,7 +70,7 @@
when(view.getModel()).thenReturn(net);
networkViewManager = mock(CyNetworkViewManager.class);
- when(networkViewManager.getNetworkView(anyLong())).thenReturn(view);
+
when(networkViewManager.getNetworkView(any(CyNetwork.class))).thenReturn(view);
tm = mock(TaskMonitor.class);
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/cytoscape/MergeNetworkEdit.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/cytoscape/MergeNetworkEdit.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/cytoscape/MergeNetworkEdit.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -91,7 +91,7 @@
this.cyEdges = cyEdges;
this.cyNodes = new HashMap<CyNode, Point2D.Double>();
- CyNetworkView view =
factory.getCyNetworkViewManager().getNetworkView(cyNetwork.getSUID());
+ CyNetworkView view =
factory.getCyNetworkViewManager().getNetworkView(cyNetwork);
if (view != null) {
for (CyNode cyNode : cyNodes) {
View<CyNode> nv = view.getNodeView(cyNode);
@@ -118,7 +118,7 @@
public void redo() {
// get ref to view
- CyNetworkView view =
factory.getCyNetworkViewManager().getNetworkView(cyNetwork.getSUID());
+ CyNetworkView view =
factory.getCyNetworkViewManager().getNetworkView(cyNetwork);
if (view != null) {
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/NetworkUtil.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/NetworkUtil.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/NetworkUtil.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -222,7 +222,7 @@
private void postProcess(final CyNetwork cyNetwork, boolean doLayout) {
// ref to view used below
- CyNetworkView view =
factory.getCyNetworkViewManager().getNetworkView(cyNetwork.getSUID());
+ CyNetworkView view =
factory.getCyNetworkViewManager().getNetworkView(cyNetwork);
// if do layout, do it
// TODO: Port this?
Modified:
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/IndexAndSearchTask.java
===================================================================
---
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/IndexAndSearchTask.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/IndexAndSearchTask.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -118,7 +118,7 @@
* If view(s) exists for the current network, update them.
*/
private void updateView() {
- final CyNetworkView targetView =
viewManager.getNetworkView(network.getSUID());
+ final CyNetworkView targetView =
viewManager.getNetworkView(network);
if(targetView != null)
targetView.updateView();
Modified:
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CysessionFactory.java
===================================================================
---
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CysessionFactory.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CysessionFactory.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -159,7 +159,7 @@
String name =
cyNet.getRow(cyNet).get(CyNetwork.NAME, String.class);
String styleName = DEF_STYLE_NAME;
- CyNetworkView cyNetView =
nvMgr.getNetworkView(cyNet.getSUID());
+ CyNetworkView cyNetView =
nvMgr.getNetworkView(cyNet);
if (cyNetView != null) {
org.cytoscape.view.vizmap.VisualStyle
style = vmMgr.getVisualStyle(cyNetView);
@@ -170,7 +170,7 @@
net.setId(name);
net.setFilename(name + ".xgmml");
net.setVisualStyle(styleName);
-
net.setViewAvailable(nvMgr.getNetworkView(cyNet.getSUID()) != null);
+
net.setViewAvailable(nvMgr.getNetworkView(cyNet) != null);
net.setVisualStyle(styleName);
if (cyNet instanceof CySubNetwork) {
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/select/RowsSetViewUpdater.java
===================================================================
---
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/select/RowsSetViewUpdater.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/select/RowsSetViewUpdater.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -59,7 +59,7 @@
if ( network == null )
return;
- CyNetworkView networkView =
vm.getNetworkView(network.getSUID());
+ CyNetworkView networkView = vm.getNetworkView(network);
if ( networkView == null )
return;
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
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkPanel.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -465,7 +465,7 @@
if (parentNetwork != null)
this.treeNodeMap.put(parentNetwork.getSUID(),
parentTreeNode);
- if(networkViewManager.viewExists(network_id))
+ if(networkViewManager.viewExists(network))
dmtn.setNodeColor(Color.black);
this.treeNodeMap.put(network.getSUID(), dmtn);
Modified:
core3/impl/trunk/viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/CyNetworkViewManagerImpl.java
===================================================================
---
core3/impl/trunk/viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/CyNetworkViewManagerImpl.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/impl/trunk/viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/CyNetworkViewManagerImpl.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -54,7 +54,7 @@
public class CyNetworkViewManagerImpl implements CyNetworkViewManager,
NetworkAboutToBeDestroyedListener {
private static final Logger logger =
LoggerFactory.getLogger(CyNetworkViewManagerImpl.class);
- private final Map<Long, CyNetworkView> networkViewMap;
+ private final Map<CyNetwork, CyNetworkView> networkViewMap;
private final CyEventHelper cyEventHelper;
/**
@@ -62,7 +62,7 @@
* @param cyEventHelper
*/
public CyNetworkViewManagerImpl(final CyEventHelper cyEventHelper) {
- networkViewMap = new HashMap<Long, CyNetworkView>();
+ networkViewMap = new HashMap<CyNetwork, CyNetworkView>();
this.cyEventHelper = cyEventHelper;
}
@@ -73,9 +73,9 @@
@Override
public synchronized void handleEvent(final
NetworkAboutToBeDestroyedEvent event) {
- final long networkId = event.getNetwork().getSUID();
- if (viewExists(networkId))
- destroyNetworkView(networkViewMap.get(networkId));
+ final CyNetwork network = event.getNetwork();
+ if (viewExists(network))
+ destroyNetworkView(networkViewMap.get(network));
}
@Override
@@ -84,13 +84,13 @@
}
@Override
- public synchronized CyNetworkView getNetworkView(long networkId) {
- return networkViewMap.get(networkId);
+ public synchronized CyNetworkView getNetworkView(CyNetwork network) {
+ return networkViewMap.get(network);
}
@Override
- public synchronized boolean viewExists(long networkId) {
- return networkViewMap.containsKey(networkId);
+ public synchronized boolean viewExists(CyNetwork network) {
+ return networkViewMap.containsKey(network);
}
@Override
@@ -126,11 +126,11 @@
throw new NullPointerException("CyNetworkView is null");
final CyNetwork network = view.getModel();
- long networkId = network.getSUID();
+
synchronized (this) {
- logger.debug("Adding new Network View Model: Model ID =
" + networkId);
- networkViewMap.put(networkId, view);
+ logger.debug("Adding new Network View Model: Model ID =
" + network.getSUID());
+ networkViewMap.put(network, view);
}
logger.debug("Firing event: NetworkViewAddedEvent");
Modified:
core3/support/trunk/samples/sample06/src/main/java/org/cytoscape/sample/internal/MyNetworkViewTask.java
===================================================================
---
core3/support/trunk/samples/sample06/src/main/java/org/cytoscape/sample/internal/MyNetworkViewTask.java
2012-01-12 00:46:26 UTC (rev 27991)
+++
core3/support/trunk/samples/sample06/src/main/java/org/cytoscape/sample/internal/MyNetworkViewTask.java
2012-01-12 01:46:00 UTC (rev 27992)
@@ -30,7 +30,7 @@
return;
}
- if(networkViewManager.getNetworkView(currNet.getSUID())
== null){
+ if(networkViewManager.getNetworkView(currNet) == null){
// create a new view for current network
CyNetworkView myView =
cnvf.createNetworkView(currNet);
networkViewManager.addNetworkView(myView);
@@ -44,7 +44,7 @@
if(destroyView)
{
CyNetwork currNetwork =
appMgr.getCurrentNetwork();
- CyNetworkView view =
networkViewManager.getNetworkView(currNetwork.getSUID());
+ CyNetworkView view =
networkViewManager.getNetworkView(currNetwork);
networkViewManager.destroyNetworkView(view);
}
}
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
