Author: mes
Date: 2010-09-09 09:47:12 -0700 (Thu, 09 Sep 2010)
New Revision: 21755
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesEdgesTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesOnlyTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/hide/HideSelectedEdgesTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/hide/HideSelectedNodesTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/hide/HideSelectedTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadDataTableTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadDataTableTaskFactoryImpl.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAdjacentEdgesTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectConnectedNodesTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFirstNeighborsTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/session/OpenSessionTask.java
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
Log:
Changed CyDataTable name to CyTable
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesEdgesTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesEdgesTask.java
2010-09-09 16:47:06 UTC (rev 21754)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesEdgesTask.java
2010-09-09 16:47:12 UTC (rev 21755)
@@ -43,7 +43,7 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyDataTableUtil;
+import org.cytoscape.model.CyTableUtil;
import org.cytoscape.view.model.CyNetworkView;
//import org.cytoscape.vizmap.VisualMappingManager;
//import org.cytoscape.vizmap.VisualStyle;
@@ -70,8 +70,8 @@
if ((current_network == null) || (current_network ==
Cytoscape.getNullNetwork()))
return;
- List<CyNode> nodes =
CyDataTableUtil.getNodesInState(current_network,"selected",true);
- List<CyEdge> edges =
CyDataTableUtil.getEdgesInState(current_network,"selected",true);
+ List<CyNode> nodes =
CyTableUtil.getNodesInState(current_network,"selected",true);
+ List<CyEdge> edges =
CyTableUtil.getEdgesInState(current_network,"selected",true);
CyNetwork new_network = Cytoscape.createNetwork(nodes, edges,
CyNetworkNaming.getSuggestedSubnetworkTitle(current_network, netmgr),
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesOnlyTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesOnlyTask.java
2010-09-09 16:47:06 UTC (rev 21754)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesOnlyTask.java
2010-09-09 16:47:12 UTC (rev 21755)
@@ -46,7 +46,7 @@
import java.util.List;
import java.util.Set;
-import org.cytoscape.model.CyDataTableUtil;
+import org.cytoscape.model.CyTableUtil;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
@@ -95,7 +95,7 @@
.getSUID());
}
- List<CyNode> nodes =
CyDataTableUtil.getNodesInState(current_network,
+ List<CyNode> nodes =
CyTableUtil.getNodesInState(current_network,
"selected", true);
Set<CyEdge> edges = new HashSet<CyEdge>();
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/hide/HideSelectedEdgesTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/hide/HideSelectedEdgesTask.java
2010-09-09 16:47:06 UTC (rev 21754)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/hide/HideSelectedEdgesTask.java
2010-09-09 16:47:12 UTC (rev 21755)
@@ -39,7 +39,7 @@
import org.cytoscape.task.AbstractNetworkViewTask;
import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyDataTableUtil;
+import org.cytoscape.model.CyTableUtil;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.Task;
@@ -56,7 +56,7 @@
public void run(TaskMonitor e) {
final CyNetwork curr = view.getModel();
- final List<CyEdge> selectedEdges =
CyDataTableUtil.getEdgesInState(curr,"selected",true);
+ final List<CyEdge> selectedEdges =
CyTableUtil.getEdgesInState(curr,"selected",true);
HideUtils.setVisibleEdges( selectedEdges, false, view );
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/hide/HideSelectedNodesTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/hide/HideSelectedNodesTask.java
2010-09-09 16:47:06 UTC (rev 21754)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/hide/HideSelectedNodesTask.java
2010-09-09 16:47:12 UTC (rev 21755)
@@ -39,7 +39,7 @@
import java.util.List;
-import org.cytoscape.model.CyDataTableUtil;
+import org.cytoscape.model.CyTableUtil;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.task.AbstractNetworkViewTask;
@@ -55,7 +55,7 @@
public void run(TaskMonitor e) {
final CyNetwork curr = view.getModel();
- final List<CyNode> selectedNodes =
CyDataTableUtil.getNodesInState(curr,"selected",true);
+ final List<CyNode> selectedNodes =
CyTableUtil.getNodesInState(curr,"selected",true);
HideUtils.setVisibleNodes( selectedNodes, false, view );
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/hide/HideSelectedTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/hide/HideSelectedTask.java
2010-09-09 16:47:06 UTC (rev 21754)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/hide/HideSelectedTask.java
2010-09-09 16:47:12 UTC (rev 21755)
@@ -39,7 +39,7 @@
import java.util.List;
-import org.cytoscape.model.CyDataTableUtil;
+import org.cytoscape.model.CyTableUtil;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
@@ -56,8 +56,8 @@
public void run(TaskMonitor e) {
final CyNetwork curr = view.getModel();
- final List<CyNode> selectedNodes =
CyDataTableUtil.getNodesInState(curr,"selected",true);
- final List<CyEdge> selectedEdges =
CyDataTableUtil.getEdgesInState(curr,"selected",true);
+ final List<CyNode> selectedNodes =
CyTableUtil.getNodesInState(curr,"selected",true);
+ final List<CyEdge> selectedEdges =
CyTableUtil.getEdgesInState(curr,"selected",true);
HideUtils.setVisibleNodes( selectedNodes, false, view );
HideUtils.setVisibleEdges( selectedEdges, false, view );
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadDataTableTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadDataTableTask.java
2010-09-09 16:47:06 UTC (rev 21754)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadDataTableTask.java
2010-09-09 16:47:12 UTC (rev 21755)
@@ -6,9 +6,9 @@
import java.io.File;
import java.util.Properties;
-import org.cytoscape.model.CyDataTable;
-import org.cytoscape.io.read.CyDataTableReaderManager;
-import org.cytoscape.io.read.CyDataTableReader;
+import org.cytoscape.model.CyTable;
+import org.cytoscape.io.read.CyTableReaderManager;
+import org.cytoscape.io.read.CyTableReader;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
@@ -19,10 +19,10 @@
@Tunable(description = "Data table file to load", flags = {
Param.attributes })
public File file;
- private CyDataTableReader reader;
- private final CyDataTableReaderManager mgr;
+ private CyTableReader reader;
+ private final CyTableReaderManager mgr;
- public LoadDataTableTask(final CyDataTableReaderManager mgr) {
+ public LoadDataTableTask(final CyTableReaderManager mgr) {
this.mgr = mgr;
}
@@ -50,14 +50,14 @@
class FinalStatusMessageUpdateTask extends AbstractTask {
- private final CyDataTableReader reader;
+ private final CyTableReader reader;
- FinalStatusMessageUpdateTask(final CyDataTableReader reader) {
+ FinalStatusMessageUpdateTask(final CyTableReader reader) {
this.reader = reader;
}
public void run(final TaskMonitor taskMonitor) throws Exception {
- for (CyDataTable table : reader.getCyDataTables())
+ for (CyTable table : reader.getCyDataTables())
taskMonitor.setStatusMessage("Successfully loaded data
table: " + table.getTitle());
taskMonitor.setProgress(1.0);
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadDataTableTaskFactoryImpl.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadDataTableTaskFactoryImpl.java
2010-09-09 16:47:06 UTC (rev 21754)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadDataTableTaskFactoryImpl.java
2010-09-09 16:47:12 UTC (rev 21755)
@@ -1,15 +1,15 @@
package org.cytoscape.task.internal.loaddatatable;
-import org.cytoscape.io.read.CyDataTableReaderManager;
+import org.cytoscape.io.read.CyTableReaderManager;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.TaskFactory;
public class LoadDataTableTaskFactoryImpl implements TaskFactory {
- private CyDataTableReaderManager mgr;
+ private CyTableReaderManager mgr;
- public LoadDataTableTaskFactoryImpl(CyDataTableReaderManager mgr) {
+ public LoadDataTableTaskFactoryImpl(CyTableReaderManager mgr) {
this.mgr = mgr;
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAdjacentEdgesTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAdjacentEdgesTask.java
2010-09-09 16:47:06 UTC (rev 21754)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAdjacentEdgesTask.java
2010-09-09 16:47:12 UTC (rev 21755)
@@ -40,7 +40,7 @@
import java.util.HashSet;
import java.util.Set;
-import org.cytoscape.model.CyDataTableUtil;
+import org.cytoscape.model.CyTableUtil;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
@@ -60,7 +60,7 @@
final Set<CyEdge> edgeSet = new HashSet<CyEdge>();
// Get the list of selected nodes
- for (CyNode node:
CyDataTableUtil.getNodesInState(network,"selected",true)) {
+ for (CyNode node:
CyTableUtil.getNodesInState(network,"selected",true)) {
// Get the list of edges connected to this node
edgeSet.addAll(
network.getAdjacentEdgeList(node,CyEdge.Type.ANY) );
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectConnectedNodesTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectConnectedNodesTask.java
2010-09-09 16:47:06 UTC (rev 21754)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectConnectedNodesTask.java
2010-09-09 16:47:12 UTC (rev 21755)
@@ -41,7 +41,7 @@
import java.util.List;
import java.util.Set;
-import org.cytoscape.model.CyDataTableUtil;
+import org.cytoscape.model.CyTableUtil;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
@@ -58,7 +58,7 @@
public void run(TaskMonitor tm) {
final CyNetwork currentNetwork = netmgr.getCurrentNetwork();
final CyNetworkView v =
netmgr.getNetworkView(currentNetwork.getSUID());
- final List<CyEdge> selectedEdges =
CyDataTableUtil.getEdgesInState(
+ final List<CyEdge> selectedEdges = CyTableUtil.getEdgesInState(
currentNetwork, "selected", true);
final Set<CyNode> nodes = new HashSet<CyNode>();
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFirstNeighborsTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFirstNeighborsTask.java
2010-09-09 16:47:06 UTC (rev 21754)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFirstNeighborsTask.java
2010-09-09 16:47:12 UTC (rev 21755)
@@ -35,7 +35,7 @@
import java.util.List;
import java.util.Set;
-import org.cytoscape.model.CyDataTableUtil;
+import org.cytoscape.model.CyTableUtil;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
@@ -54,7 +54,7 @@
final CyNetwork currentNetwork = netmgr.getCurrentNetwork();
final CyNetworkView view = netmgr.getNetworkView(currentNetwork
.getSUID());
- final List<CyNode> selectedNodes =
CyDataTableUtil.getNodesInState(
+ final List<CyNode> selectedNodes = CyTableUtil.getNodesInState(
currentNetwork, "selected", true);
final Set<CyNode> nodes = new HashSet<CyNode>();
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/session/OpenSessionTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/session/OpenSessionTask.java
2010-09-09 16:47:06 UTC (rev 21754)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/session/OpenSessionTask.java
2010-09-09 16:47:12 UTC (rev 21755)
@@ -35,7 +35,7 @@
import org.cytoscape.work.Tunable;
import org.cytoscape.session.CySessionManager;
import org.cytoscape.io.read.CyNetworkViewReaderManager;
-import org.cytoscape.io.read.CyDataTableReader;
+import org.cytoscape.io.read.CyTableReader;
import org.cytoscape.io.DataCategory;
import java.io.File;
@@ -76,7 +76,7 @@
taskMonitor.setStatusMessage("Opening Session File.\n\nIt may
take a while.\nPlease wait...");
taskMonitor.setProgress(0.0);
- CyDataTableReader sr;
+ CyTableReader sr;
try {
//sr = factory.getReader(file.toURI(),
DataCategory.SESSION);
Modified:
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2010-09-09 16:47:06 UTC (rev 21754)
+++
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2010-09-09 16:47:12 UTC (rev 21755)
@@ -22,7 +22,7 @@
interface="org.cytoscape.io.read.CyNetworkViewReaderManager" />
<osgi:reference id="cyDataTableReaderManagerServiceRef"
- interface="org.cytoscape.io.read.CyDataTableReaderManager" />
+ interface="org.cytoscape.io.read.CyTableReaderManager" />
<osgi:reference id="visualMappingManagerServiceRef"
interface="org.cytoscape.view.vizmap.VisualMappingManager" />
--
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.
