Author: mes
Date: 2011-06-21 15:41:41 -0700 (Tue, 21 Jun 2011)
New Revision: 25864
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/edit/ConnectSelectedNodesTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/networkobjects/DeleteEdit.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/networkobjects/DeleteSelectedNodesAndEdgesTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/CreateSubnetworkTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedEdgesTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedNodesTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFromFileListTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectUtils.java
Log:
updated for event-api changes that rely on payload events instead of
microlisteners
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
2011-06-21 22:41:27 UTC (rev 25863)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
2011-06-21 22:41:41 UTC (rev 25864)
@@ -42,8 +42,6 @@
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableEntry;
-import org.cytoscape.model.events.RowsAboutToChangeEvent;
-import org.cytoscape.model.events.RowsFinishedChangingEvent;
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
@@ -105,12 +103,6 @@
final CyTable nodeTable = newNet.getDefaultNodeTable();
final CyTable edgeTable = newNet.getDefaultEdgeTable();
final CyTable networkTable = newNet.getDefaultNetworkTable();
-
- try {
- // Generate bundled event to avoid too many events
problem.
- eventHelper.fireSynchronousEvent(new
RowsAboutToChangeEvent(this, nodeTable));
- eventHelper.fireSynchronousEvent(new
RowsAboutToChangeEvent(this, edgeTable));
- eventHelper.fireSynchronousEvent(new
RowsAboutToChangeEvent(this, networkTable));
// copy default columns
cloneColumns(origNet.getDefaultNodeTable(), nodeTable);
cloneColumns(origNet.getDefaultEdgeTable(), edgeTable);
@@ -121,10 +113,6 @@
newNet.getCyRow().set(CyTableEntry.NAME,
naming.getSuggestedNetworkTitle(origNet.getCyRow().get(CyTableEntry.NAME,
String.class)));
- } finally {
- eventHelper.fireSynchronousEvent(new
RowsFinishedChangingEvent(this, nodeTable));
- eventHelper.fireSynchronousEvent(new
RowsFinishedChangingEvent(this, edgeTable));
- }
return newNet;
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/edit/ConnectSelectedNodesTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/edit/ConnectSelectedNodesTask.java
2011-06-21 22:41:27 UTC (rev 25863)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/edit/ConnectSelectedNodesTask.java
2011-06-21 22:41:41 UTC (rev 25864)
@@ -10,8 +10,6 @@
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.CyTableUtil;
-import org.cytoscape.model.events.RowsAboutToChangeEvent;
-import org.cytoscape.model.events.RowsFinishedChangingEvent;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
@@ -35,11 +33,6 @@
final CyTable nodeTable = network.getDefaultNodeTable();
final CyTable edgeTable = network.getDefaultEdgeTable();
- try {
- // Generate bundled event to avoid too many events
problem.
- eventHelper.fireSynchronousEvent(new
RowsAboutToChangeEvent(this, nodeTable));
- eventHelper.fireSynchronousEvent(new
RowsAboutToChangeEvent(this, edgeTable));
-
final List<CyNode> selectedNodes =
CyTableUtil.getNodesInState(network, CyNetwork.SELECTED, true);
for (CyNode source : selectedNodes) {
for (CyNode target : selectedNodes) {
@@ -58,10 +51,6 @@
}
}
}
- } finally {
- eventHelper.fireSynchronousEvent(new
RowsFinishedChangingEvent(this, nodeTable));
- eventHelper.fireSynchronousEvent(new
RowsFinishedChangingEvent(this, edgeTable));
- }
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
2011-06-21 22:41:27 UTC (rev 25863)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
2011-06-21 22:41:41 UTC (rev 25864)
@@ -85,10 +85,10 @@
taskMonitor.setProgress(0.0);
taskMonitor.setStatusMessage("Creating Cytoscape Network...");
-
+ System.out.println("inserting generate network task");
insertTasksAfterCurrentTask(viewReader, new
GenerateNetworkViewsTask(name, viewReader, networkManager,
networkViewManager, namingUtil, viewThreshold));
-
+ System.out.println("finished inserting generate network task");
taskMonitor.setProgress(1.0);
}
@@ -129,18 +129,24 @@
taskMonitor.setProgress(0.0);
+ System.out.println("asdf1");
+
final CyNetwork[] networks = viewReader.getCyNetworks();
+ System.out.println("asdf2 " +networks.length);
for (CyNetwork network : networks) {
network.getCyRow().set(CyTableEntry.NAME,
namingUtil.getSuggestedNetworkTitle(name));
+ System.out.println("set name");
networkManager.addNetwork(network);
+ System.out.println("added network)");
final int numGraphObjects = network.getNodeCount() +
network.getEdgeCount();
if (numGraphObjects < viewThreshold) {
final CyNetworkView view =
viewReader.buildCyNetworkView(network);
networkViewManager.addNetworkView(view);
view.fitContent();
+ System.out.println("created view");
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/networkobjects/DeleteEdit.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/networkobjects/DeleteEdit.java
2011-06-21 22:41:27 UTC (rev 25863)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/networkobjects/DeleteEdit.java
2011-06-21 22:41:41 UTC (rev 25864)
@@ -70,10 +70,8 @@
public void redo() {
super.redo();
- for (CyNode n : nodes)
- net.removeNode(n);
- for (CyEdge e : edges)
- net.removeEdge(e);
+ net.removeNodes(nodes);
+ net.removeEdges(edges);
CyNetworkView netView =
netViewMgr.getNetworkView(net.getSUID());
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/networkobjects/DeleteSelectedNodesAndEdgesTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/networkobjects/DeleteSelectedNodesAndEdgesTask.java
2011-06-21 22:41:27 UTC (rev 25863)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/networkobjects/DeleteSelectedNodesAndEdgesTask.java
2011-06-21 22:41:41 UTC (rev 25864)
@@ -73,10 +73,8 @@
new DeleteEdit(network, selectedNodes, selectedEdges, this,
networkViewManager));
// Delete the actual nodes and edges:
- for (CyNode selectedNode : selectedNodes)
- network.removeNode(selectedNode);
- for (CyEdge selectedEdge : selectedEdges)
- network.removeEdge(selectedEdge);
+ network.removeNodes(selectedNodes);
+ network.removeEdges(selectedEdges);
myView.updateView();
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/CreateSubnetworkTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/CreateSubnetworkTask.java
2011-06-21 22:41:27 UTC (rev 25863)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/CreateSubnetworkTask.java
2011-06-21 22:41:41 UTC (rev 25864)
@@ -10,8 +10,6 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableEntry;
-import org.cytoscape.model.events.RowsAboutToChangeEvent;
-import org.cytoscape.model.events.RowsFinishedChangingEvent;
import org.cytoscape.task.internal.quickstart.IDType;
import org.cytoscape.task.internal.select.SelectFirstNeighborsTask;
import org.cytoscape.work.AbstractTask;
@@ -95,8 +93,6 @@
boolean found = false;
- try {
- util.eventHelper.fireSynchronousEvent(new
RowsAboutToChangeEvent(this, nodeTable));
List<CyNode> nodeList = target.getNodeList();
for (final CyNode node : nodeList) {
@@ -117,9 +113,6 @@
node.getCyRow().set(SEARCH_GENE_ATTR_NAME, state.getSearchTerms());
}
}
- } finally {
- util.eventHelper.fireSynchronousEvent(new
RowsFinishedChangingEvent(this, nodeTable));
- }
if (!found) {
logger.error("Query genes were not found in the
interactome.");
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedEdgesTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedEdgesTask.java
2011-06-21 22:41:27 UTC (rev 25863)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedEdgesTask.java
2011-06-21 22:41:41 UTC (rev 25864)
@@ -32,8 +32,6 @@
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.events.RowsAboutToChangeEvent;
-import org.cytoscape.model.events.RowsFinishedChangingEvent;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.work.TaskMonitor;
@@ -47,8 +45,6 @@
}
public void run(TaskMonitor tm) {
- try {
- eventHelper.fireSynchronousEvent(new RowsAboutToChangeEvent(this,
network.getDefaultNodeTable()));
for (final CyEdge e : network.getEdgeList()) {
if (e.getCyRow().get(CyNetwork.SELECTED, Boolean.class))
@@ -56,10 +52,8 @@
else
e.getCyRow().set(CyNetwork.SELECTED, true);
}
- } finally {
- eventHelper.fireSynchronousEvent(new
RowsFinishedChangingEvent(this, network.getDefaultNodeTable()));
- }
+
updateView();
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedNodesTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedNodesTask.java
2011-06-21 22:41:27 UTC (rev 25863)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedNodesTask.java
2011-06-21 22:41:41 UTC (rev 25864)
@@ -32,35 +32,28 @@
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.events.RowsAboutToChangeEvent;
-import org.cytoscape.model.events.RowsFinishedChangingEvent;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.work.TaskMonitor;
public class InvertSelectedNodesTask extends AbstractSelectTask {
- private final CyEventHelper eventHelper;
+ private final CyEventHelper eventHelper;
- public InvertSelectedNodesTask(final CyNetwork net, final
CyNetworkViewManager networkViewManager,
- final CyEventHelper eventHelper) {
- super(net, networkViewManager, eventHelper);
- this.eventHelper = eventHelper;
- }
+ public InvertSelectedNodesTask(final CyNetwork net,
+ final CyNetworkViewManager networkViewManager, final
CyEventHelper eventHelper) {
+ super(net, networkViewManager, eventHelper);
+ this.eventHelper = eventHelper;
+ }
- @Override
- public void run(final TaskMonitor tm) {
- try {
- eventHelper.fireSynchronousEvent(new RowsAboutToChangeEvent(this,
network.getDefaultNodeTable()));
+ @Override
+ public void run(final TaskMonitor tm) {
- for (final CyNode n : network.getNodeList()) {
- if (n.getCyRow().get(CyNetwork.SELECTED, Boolean.class))
- n.getCyRow().set(CyNetwork.SELECTED, false);
- else
- n.getCyRow().set(CyNetwork.SELECTED, true);
- }
- } finally {
- eventHelper.fireSynchronousEvent(new
RowsFinishedChangingEvent(this, network.getDefaultNodeTable()));
- }
+ for (final CyNode n : network.getNodeList()) {
+ if (n.getCyRow().get(CyNetwork.SELECTED, Boolean.class))
+ n.getCyRow().set(CyNetwork.SELECTED, false);
+ else
+ n.getCyRow().set(CyNetwork.SELECTED, true);
+ }
- updateView();
- }
+ updateView();
+ }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFromFileListTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFromFileListTask.java
2011-06-21 22:41:27 UTC (rev 25863)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFromFileListTask.java
2011-06-21 22:41:41 UTC (rev 25864)
@@ -40,8 +40,6 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTableEntry;
-import org.cytoscape.model.events.RowsAboutToChangeEvent;
-import org.cytoscape.model.events.RowsFinishedChangingEvent;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
@@ -77,8 +75,6 @@
fin.close();
- try {
- eventHelper.fireSynchronousEvent(new
RowsAboutToChangeEvent(this, network.getDefaultNodeTable()));
// loop through all the node of the graph selecting those in the
// file
@@ -87,10 +83,8 @@
if
(fileNodes.contains(node.getCyRow().get(CyTableEntry.NAME, String.class)))
node.getCyRow().set("selected", true);
}
- } finally {
- eventHelper.fireSynchronousEvent(new
RowsFinishedChangingEvent(this, network.getDefaultNodeTable()));
- }
+
updateView();
} catch (Exception e) {
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectUtils.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectUtils.java
2011-06-21 22:41:27 UTC (rev 25863)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectUtils.java
2011-06-21 22:41:41 UTC (rev 25864)
@@ -45,8 +45,6 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableEntry;
-import org.cytoscape.model.events.RowsAboutToChangeEvent;
-import org.cytoscape.model.events.RowsFinishedChangingEvent;
final class SelectUtils {
@@ -68,13 +66,8 @@
private void setSelected(final Collection<? extends CyTableEntry>
objects, final boolean select) {
final CyTable table =
objects.iterator().next().getCyRow().getTable();
- try {
- eventHelper.fireSynchronousEvent(new
RowsAboutToChangeEvent(eventSource, table));
- for (final CyTableEntry nodeOrEdge : objects)
- nodeOrEdge.getCyRow().set(CyNetwork.SELECTED,
select);
- } finally {
- eventHelper.fireSynchronousEvent(new
RowsFinishedChangingEvent(eventSource, table));
- }
+ for (final CyTableEntry nodeOrEdge : objects)
+ nodeOrEdge.getCyRow().set(CyNetwork.SELECTED, select);
}
}
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