Author: mes
Date: 2012-04-25 11:53:35 -0700 (Wed, 25 Apr 2012)
New Revision: 29006
Added:
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/edit/MapTableToNetworkTablesTaskFactory.java
Removed:
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/edit/MapNetworkAttrTaskFactory.java
Modified:
core3/api/trunk/app-api/src/main/java/org/cytoscape/app/CyAppAdapter.java
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/edit/MapGlobalToLocalTableTaskFactory.java
core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/CyActivator.java
core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/CyAppAdapterImpl.java
core3/impl/trunk/app-impl/src/test/java/org/cytoscape/app/internal/CyAppAdapterImplTest.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapGlobalToLocalTableTaskFactoryImpl.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapNetworkAttrTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapNetworkAttrTaskFactoryImpl.java
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/BiomartClient.java
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/CyActivator.java
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportTableTask.java
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/CyActivator.java
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/NCBITableImportClient.java
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/task/ImportTableFromNCBITask.java
core3/samples/trunk/sample11/src/main/java/org/cytoscape/sample/internal/CreateTableTask.java
core3/samples/trunk/sample11/src/main/java/org/cytoscape/sample/internal/CyActivator.java
core3/samples/trunk/sample11/src/main/java/org/cytoscape/sample/internal/Sample11TaskFactory.java
Log:
Renamed task factory to be more consistent with 3.0 naming
Modified:
core3/api/trunk/app-api/src/main/java/org/cytoscape/app/CyAppAdapter.java
===================================================================
--- core3/api/trunk/app-api/src/main/java/org/cytoscape/app/CyAppAdapter.java
2012-04-25 18:45:36 UTC (rev 29005)
+++ core3/api/trunk/app-api/src/main/java/org/cytoscape/app/CyAppAdapter.java
2012-04-25 18:53:35 UTC (rev 29006)
@@ -82,7 +82,7 @@
import org.cytoscape.task.edit.EditNetworkTitleTaskFactory;
import org.cytoscape.task.edit.GroupNodesTaskFactory;
import org.cytoscape.task.edit.MapGlobalToLocalTableTaskFactory;
-import org.cytoscape.task.edit.MapNetworkAttrTaskFactory;
+import org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory;
import org.cytoscape.task.edit.RenameColumnTaskFactory;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.task.TableCellTaskFactory;
@@ -744,9 +744,9 @@
NodeViewTaskFactory get_UnGroupNodesTaskFactory();
/**
- * Returns an instance of {@link MapNetworkAttrTaskFactory}.
- * @return an instance of {@link MapNetworkAttrTaskFactory}.
+ * Returns an instance of {@link MapTableToNetworkTablesTaskFactory}.
+ * @return an instance of {@link MapTableToNetworkTablesTaskFactory}.
*/
- MapNetworkAttrTaskFactory get_MapNetworkAttrTaskFactory();
+ MapTableToNetworkTablesTaskFactory
get_MapTableToNetworkTablesTaskFactory();
}
Modified:
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/edit/MapGlobalToLocalTableTaskFactory.java
===================================================================
---
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/edit/MapGlobalToLocalTableTaskFactory.java
2012-04-25 18:45:36 UTC (rev 29005)
+++
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/edit/MapGlobalToLocalTableTaskFactory.java
2012-04-25 18:53:35 UTC (rev 29006)
@@ -1,5 +1,6 @@
package org.cytoscape.task.edit;
+import org.cytoscape.model.CyTable;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
@@ -14,9 +15,9 @@
* Creates a task iterator for mapping a selected global table to a
selected local table.
* The created task will run synchronously in the current thread and
will not create a
* new task monitor.
- * @param globalTable The global table name to map from.
- * @param localTable The local table name to map to.
+ * @param globalTable The global table to map from.
+ * @param localTable The local table to map to.
* @return A task iterator of type {@link TaskIterator}.
*/
- TaskIterator createTaskIterator(final String globalTable, final String
localTable);
+ TaskIterator createTaskIterator(final CyTable globalTable, final
CyTable localTable);
}
Deleted:
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/edit/MapNetworkAttrTaskFactory.java
===================================================================
---
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/edit/MapNetworkAttrTaskFactory.java
2012-04-25 18:45:36 UTC (rev 29005)
+++
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/edit/MapNetworkAttrTaskFactory.java
2012-04-25 18:53:35 UTC (rev 29006)
@@ -1,57 +0,0 @@
-package org.cytoscape.task.edit;
-
-import org.cytoscape.model.CyIdentifiable;
-import org.cytoscape.model.CyTable;
-import org.cytoscape.work.TaskFactory;
-import org.cytoscape.work.TaskIterator;
-
-public interface MapNetworkAttrTaskFactory extends TaskFactory {
-
- enum MappingType {
- CURRENT_LOCAL("Only to the current network"),
- CURRENT_SHARED("All networks related to current network"),
- ALL_SHARED("All networks"),
- INDEPENDENT("None (create Global Table w/o mapping)"),
- ;
-
- private final String desc;
- private MappingType(String desc) {
- this.desc = desc;
- }
- public String getDescription(){
- return desc;
- }
- public static MappingType fromDescription(String d) {
- for (MappingType m : values())
- if (m.getDescription().equals(d))
- return m;
- throw new IllegalArgumentException("String " + d + "
doesn't match a known description in MappingType");
- }
- }
- /**
- * This creates a task iterator that will take a specified table and
ask whether
- * the columns in the specified table should become virtual columns in
the node or
- * edge table of the current network, all networks, or no networks.
- * @param type The type of table to map to, either CyNode.class or
CyEdge.class.
- * @param newGlobalTable The table to be mapped.
- * @param mappingKey The column name in the existing table used to join
with the primary key in the new table.
- * @param mappingType The type of mapping to be performed.
- */
- TaskIterator createTaskIterator(final Class<? extends CyIdentifiable>
type,
- final CyTable newGlobalTable,
- String mappingKey,
- MappingType mappingType);
- /**
- * This creates a task iterator that will take a specified table and
ask whether
- * the columns in the specified table should become virtual columns in
the node or
- * edge table of the current network, all networks, or no networks.
The resulting
- * Task will prompt the user to determine which mapping type to choose
via the Tunable
- * user interface.
- * @param type The type of table to map to, either CyNode.class or
CyEdge.class.
- * @param newGlobalTable The table to be mapped.
- * @param mappingKey The column name in the existing table used to join
with the primary key in the new table.
- */
- TaskIterator createTaskIterator(final Class<? extends CyIdentifiable>
type,
- final CyTable newGlobalTable,
- String mappingKey);
-}
Copied:
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/edit/MapTableToNetworkTablesTaskFactory.java
(from rev 29002,
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/edit/MapNetworkAttrTaskFactory.java)
===================================================================
---
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/edit/MapTableToNetworkTablesTaskFactory.java
(rev 0)
+++
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/edit/MapTableToNetworkTablesTaskFactory.java
2012-04-25 18:53:35 UTC (rev 29006)
@@ -0,0 +1,62 @@
+package org.cytoscape.task.edit;
+
+import org.cytoscape.model.CyIdentifiable;
+import org.cytoscape.model.CyTable;
+import org.cytoscape.work.TaskFactory;
+import org.cytoscape.work.TaskIterator;
+
+/**
+ * This interface provides a task factory that maps a global table to various
combinations
+ * of network tables.
+ * @CyAPI.Api.Interface
+ */
+public interface MapTableToNetworkTablesTaskFactory extends TaskFactory {
+
+ enum MappingType {
+ CURRENT_LOCAL("Only to the current network"),
+ CURRENT_SHARED("All networks related to current network"),
+ ALL_SHARED("All networks"),
+ INDEPENDENT("None (create Global Table w/o mapping)"),
+ ;
+
+ private final String desc;
+ private MappingType(String desc) {
+ this.desc = desc;
+ }
+ public String getDescription(){
+ return desc;
+ }
+ public static MappingType fromDescription(String d) {
+ for (MappingType m : values())
+ if (m.getDescription().equals(d))
+ return m;
+ throw new IllegalArgumentException("String " + d + "
doesn't match a known description in MappingType");
+ }
+ }
+ /**
+ * This creates a task iterator that will take a specified table and
ask whether
+ * the columns in the specified table should become virtual columns in
the node or
+ * edge table of the current network, all networks, or no networks.
+ * @param type The type of table to map to, either CyNode.class or
CyEdge.class.
+ * @param newGlobalTable The table to be mapped.
+ * @param mappingKey The column name in the existing table used to join
with the primary key in the new table.
+ * @param mappingType The type of mapping to be performed.
+ */
+ TaskIterator createTaskIterator(final Class<? extends CyIdentifiable>
type,
+ final CyTable newGlobalTable,
+ String mappingKey,
+ MappingType mappingType);
+ /**
+ * This creates a task iterator that will take a specified table and
ask whether
+ * the columns in the specified table should become virtual columns in
the node or
+ * edge table of the current network, all networks, or no networks.
The resulting
+ * Task will prompt the user to determine which mapping type to choose
via the Tunable
+ * user interface.
+ * @param type The type of table to map to, either CyNode.class or
CyEdge.class.
+ * @param newGlobalTable The table to be mapped.
+ * @param mappingKey The column name in the existing table used to join
with the primary key in the new table.
+ */
+ TaskIterator createTaskIterator(final Class<? extends CyIdentifiable>
type,
+ final CyTable newGlobalTable,
+ String mappingKey);
+}
Modified:
core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/CyActivator.java
2012-04-25 18:45:36 UTC (rev 29005)
+++
core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/CyActivator.java
2012-04-25 18:53:35 UTC (rev 29006)
@@ -68,7 +68,7 @@
import org.cytoscape.task.edit.EditNetworkTitleTaskFactory;
import org.cytoscape.task.edit.GroupNodesTaskFactory;
import org.cytoscape.task.edit.MapGlobalToLocalTableTaskFactory;
-import org.cytoscape.task.edit.MapNetworkAttrTaskFactory;
+import org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory;
import org.cytoscape.task.edit.RenameColumnTaskFactory;
import org.cytoscape.task.hide.HideSelectedEdgesTaskFactory;
import org.cytoscape.task.hide.HideSelectedNodesTaskFactory;
@@ -218,7 +218,7 @@
ConnectSelectedNodesTaskFactory
connectSelectedNodesTaskFactory =
getService(bc,ConnectSelectedNodesTaskFactory.class);
MapGlobalToLocalTableTaskFactory mapGlobal =
getService(bc,MapGlobalToLocalTableTaskFactory.class);
ApplyVisualStyleTaskFactory applyVisualStyleTaskFactory =
getService(bc,ApplyVisualStyleTaskFactory.class);
- MapNetworkAttrTaskFactory mapNetworkAttrTaskFactory =
getService(bc,MapNetworkAttrTaskFactory.class);
+ MapTableToNetworkTablesTaskFactory mapNetworkAttrTaskFactory =
getService(bc,MapTableToNetworkTablesTaskFactory.class);
GroupNodesTaskFactory groupNodesTaskFactory =
getService(bc,GroupNodesTaskFactory.class,"title=Group Nodes");
NetworkViewTaskFactory unGroupTaskFactory=
getService(bc,NetworkViewTaskFactory.class,"title=Ungroup Nodes");
Modified:
core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/CyAppAdapterImpl.java
===================================================================
---
core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/CyAppAdapterImpl.java
2012-04-25 18:45:36 UTC (rev 29005)
+++
core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/CyAppAdapterImpl.java
2012-04-25 18:53:35 UTC (rev 29006)
@@ -57,7 +57,7 @@
import org.cytoscape.task.edit.EditNetworkTitleTaskFactory;
import org.cytoscape.task.edit.GroupNodesTaskFactory;
import org.cytoscape.task.edit.MapGlobalToLocalTableTaskFactory;
-import org.cytoscape.task.edit.MapNetworkAttrTaskFactory;
+import org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory;
import org.cytoscape.task.edit.RenameColumnTaskFactory;
import org.cytoscape.task.hide.HideSelectedEdgesTaskFactory;
import org.cytoscape.task.hide.HideSelectedNodesTaskFactory;
@@ -267,7 +267,7 @@
private ConnectSelectedNodesTaskFactory connectSelectedNodesTaskFactory;
private MapGlobalToLocalTableTaskFactory mapGlobal;
private ApplyVisualStyleTaskFactory applyVisualStyleTaskFactory;
- private MapNetworkAttrTaskFactory mapNetworkAttrTaskFactory;
+ private MapTableToNetworkTablesTaskFactory mapNetworkAttrTaskFactory;
private GroupNodesTaskFactory groupNodesTaskFactory;
private NetworkViewTaskFactory unGroupTaskFactory;
@@ -387,7 +387,7 @@
final MapGlobalToLocalTableTaskFactory
mapGlobal,
final ApplyVisualStyleTaskFactory
applyVisualStyleTaskFactory,
- final MapNetworkAttrTaskFactory
mapNetworkAttrTaskFactory,
+ final MapTableToNetworkTablesTaskFactory
mapNetworkAttrTaskFactory,
final GroupNodesTaskFactory
groupNodesTaskFactory,
final NetworkViewTaskFactory unGroupTaskFactory,
@@ -601,5 +601,5 @@
@Override public NodeViewTaskFactory
get_CollapseGroupTaskFactory(){return this.collapseGroupTaskFactory;}
@Override public NodeViewTaskFactory
get_ExpandGroupTaskFactory(){return this.expandGroupTaskFactory;}
@Override public NodeViewTaskFactory
get_UnGroupNodesTaskFactory(){return this.unGroupNodesTaskFactory;}
- @Override public MapNetworkAttrTaskFactory
get_MapNetworkAttrTaskFactory(){ return this.mapNetworkAttrTaskFactory;}
+ @Override public MapTableToNetworkTablesTaskFactory
get_MapTableToNetworkTablesTaskFactory(){ return
this.mapNetworkAttrTaskFactory;}
}
Modified:
core3/impl/trunk/app-impl/src/test/java/org/cytoscape/app/internal/CyAppAdapterImplTest.java
===================================================================
---
core3/impl/trunk/app-impl/src/test/java/org/cytoscape/app/internal/CyAppAdapterImplTest.java
2012-04-25 18:45:36 UTC (rev 29005)
+++
core3/impl/trunk/app-impl/src/test/java/org/cytoscape/app/internal/CyAppAdapterImplTest.java
2012-04-25 18:53:35 UTC (rev 29006)
@@ -47,7 +47,7 @@
import org.cytoscape.task.edit.EditNetworkTitleTaskFactory;
import org.cytoscape.task.edit.GroupNodesTaskFactory;
import org.cytoscape.task.edit.MapGlobalToLocalTableTaskFactory;
-import org.cytoscape.task.edit.MapNetworkAttrTaskFactory;
+import org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory;
import org.cytoscape.task.edit.RenameColumnTaskFactory;
import org.cytoscape.task.hide.HideSelectedEdgesTaskFactory;
import org.cytoscape.task.hide.HideSelectedNodesTaskFactory;
@@ -191,7 +191,7 @@
mock(ConnectSelectedNodesTaskFactory.class),
mock(MapGlobalToLocalTableTaskFactory.class),
mock(ApplyVisualStyleTaskFactory.class),
- mock(MapNetworkAttrTaskFactory.class),
+ mock(MapTableToNetworkTablesTaskFactory.class),
mock(GroupNodesTaskFactory.class),
mock(NetworkViewTaskFactory.class),
mock(NodeViewTaskFactory.class),
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
2012-04-25 18:45:36 UTC (rev 29005)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
2012-04-25 18:53:35 UTC (rev 29006)
@@ -51,7 +51,7 @@
import org.cytoscape.task.edit.EditNetworkTitleTaskFactory;
import org.cytoscape.task.edit.GroupNodesTaskFactory;
import org.cytoscape.task.edit.MapGlobalToLocalTableTaskFactory;
-import org.cytoscape.task.edit.MapNetworkAttrTaskFactory;
+import org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory;
import org.cytoscape.task.edit.RenameColumnTaskFactory;
import org.cytoscape.task.hide.HideSelectedEdgesTaskFactory;
import org.cytoscape.task.hide.HideSelectedNodesTaskFactory;
@@ -950,6 +950,6 @@
MapNetworkAttrTaskFactoryImpl mapNetworkAttrTaskFactory = new
MapNetworkAttrTaskFactoryImpl(cyNetworkManagerServiceRef,
cyApplicationManagerServiceRef,
cyRootNetworkFactoryServiceRef,tunableSetterServiceRef);
Properties mapNetworkAttrTaskFactoryProps = new Properties();
-
registerService(bc,mapNetworkAttrTaskFactory,MapNetworkAttrTaskFactory.class,mapNetworkAttrTaskFactoryProps);
+
registerService(bc,mapNetworkAttrTaskFactory,MapTableToNetworkTablesTaskFactory.class,mapNetworkAttrTaskFactoryProps);
}
}
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapGlobalToLocalTableTaskFactoryImpl.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapGlobalToLocalTableTaskFactoryImpl.java
2012-04-25 18:45:36 UTC (rev 29005)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapGlobalToLocalTableTaskFactoryImpl.java
2012-04-25 18:53:35 UTC (rev 29006)
@@ -4,6 +4,7 @@
import java.util.Map;
import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableManager;
import org.cytoscape.task.edit.MapGlobalToLocalTableTaskFactory;
import org.cytoscape.work.AbstractTaskFactory;
@@ -31,16 +32,16 @@
}
@Override
- public TaskIterator createTaskIterator(String globalTable,
- String localTable) {
+ public TaskIterator createTaskIterator(CyTable globalTable,
+ CyTable localTable) {
final Map<String, Object> m = new HashMap<String, Object>();
- ListSingleSelection<String> globalTables = new
ListSingleSelection<String>(globalTable);
- globalTables.setSelectedValue(globalTable);
+ ListSingleSelection<String> globalTables = new
ListSingleSelection<String>(globalTable.getTitle());
+ globalTables.setSelectedValue(globalTable.getTitle());
- ListSingleSelection<String> localTables = new
ListSingleSelection<String>(localTable);
- localTables.setSelectedValue(localTable);
+ ListSingleSelection<String> localTables = new
ListSingleSelection<String>(localTable.getTitle());
+ localTables.setSelectedValue(localTable.getTitle());
m.put("globalTables", globalTables);
m.put("localTables", localTables);
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapNetworkAttrTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapNetworkAttrTask.java
2012-04-25 18:45:36 UTC (rev 29005)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapNetworkAttrTask.java
2012-04-25 18:53:35 UTC (rev 29006)
@@ -16,9 +16,9 @@
import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.model.subnetwork.CyRootNetwork;
-import org.cytoscape.task.edit.MapNetworkAttrTaskFactory.MappingType;
+import org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory.MappingType;
-import static org.cytoscape.task.edit.MapNetworkAttrTaskFactory.MappingType.*;
+import static
org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory.MappingType.*;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.ProvidesTitle;
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapNetworkAttrTaskFactoryImpl.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapNetworkAttrTaskFactoryImpl.java
2012-04-25 18:45:36 UTC (rev 29005)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapNetworkAttrTaskFactoryImpl.java
2012-04-25 18:53:35 UTC (rev 29006)
@@ -5,7 +5,7 @@
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyTable;
import org.cytoscape.model.subnetwork.CyRootNetworkManager;
-import org.cytoscape.task.edit.MapNetworkAttrTaskFactory;
+import org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory;
import org.cytoscape.work.AbstractTaskFactory;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.TunableSetter;
@@ -13,7 +13,7 @@
import java.util.Map;
import java.util.HashMap;
-public class MapNetworkAttrTaskFactoryImpl extends AbstractTaskFactory
implements MapNetworkAttrTaskFactory {
+public class MapNetworkAttrTaskFactoryImpl extends AbstractTaskFactory
implements MapTableToNetworkTablesTaskFactory {
private final CyNetworkManager networkManager;
private final CyApplicationManager applicationManager;
Modified:
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/BiomartClient.java
===================================================================
---
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/BiomartClient.java
2012-04-25 18:45:36 UTC (rev 29005)
+++
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/BiomartClient.java
2012-04-25 18:53:35 UTC (rev 29006)
@@ -41,7 +41,7 @@
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.model.CyTableManager;
import org.cytoscape.model.subnetwork.CyRootNetworkManager;
-import org.cytoscape.task.edit.MapNetworkAttrTaskFactory;
+import org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory;
import org.cytoscape.work.TaskIterator;
import org.osgi.framework.ServiceException;
@@ -57,7 +57,7 @@
private ImportTableTask importTask;
private final CySwingApplication app;
private final CyTableManager tableManager;
- private final MapNetworkAttrTaskFactory mapNetworkAttrTF;
+ private final MapTableToNetworkTablesTaskFactory mapNetworkAttrTF;
/**
* Creates a new Biomart Client object.
@@ -69,7 +69,7 @@
final BiomartRestClient restClient, final
CyTableFactory tableFactory,
final CySwingApplication app, final CyTableManager
tableManager,
final BiomartAttrMappingPanel
gui,
- final
MapNetworkAttrTaskFactory mapNetworkAttrTF)
+ final
MapTableToNetworkTablesTaskFactory mapNetworkAttrTF)
{
super(restClient.getBaseURL(), displayName, description);
Modified:
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/CyActivator.java
===================================================================
---
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/CyActivator.java
2012-04-25 18:45:36 UTC (rev 29005)
+++
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/CyActivator.java
2012-04-25 18:53:35 UTC (rev 29006)
@@ -11,7 +11,7 @@
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.model.CyTableManager;
import org.cytoscape.service.util.AbstractCyActivator;
-import org.cytoscape.task.edit.MapNetworkAttrTaskFactory;
+import org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory;
import org.cytoscape.work.swing.DialogTaskManager;
import org.osgi.framework.BundleContext;
@@ -30,7 +30,7 @@
CyTableManager cyTableManagerServiceRef =
getService(bc,CyTableManager.class);
CyApplicationManager cyApplicationManagerServiceRef =
getService(bc,CyApplicationManager.class);
CyTableFactory cyTableFactoryServiceRef =
getService(bc,CyTableFactory.class);
- MapNetworkAttrTaskFactory mapNetworkAttrTFServiceRef =
getService(bc,MapNetworkAttrTaskFactory.class);
+ MapTableToNetworkTablesTaskFactory mapNetworkAttrTFServiceRef =
getService(bc,MapTableToNetworkTablesTaskFactory.class);
BiomartRestClient biomartRestClient = new
BiomartRestClient("http://www.biomart.org/biomart/martservice";);
BiomartAttrMappingPanel biomartAttrMappingPanel = new
BiomartAttrMappingPanel(taskManagerServiceRef,cyApplicationManagerServiceRef,cyTableManagerServiceRef,cyNetworkManagerServiceRef);
Modified:
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportTableTask.java
===================================================================
---
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportTableTask.java
2012-04-25 18:45:36 UTC (rev 29005)
+++
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportTableTask.java
2012-04-25 18:53:35 UTC (rev 29006)
@@ -21,7 +21,7 @@
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.model.CyTableManager;
-import org.cytoscape.task.edit.MapNetworkAttrTaskFactory;
+import org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.TaskMonitor;
@@ -42,13 +42,13 @@
private final Window parent;
private final CyTableManager tableManager;
- private final MapNetworkAttrTaskFactory mapNetworkAttrTF;
+ private final MapTableToNetworkTablesTaskFactory mapNetworkAttrTF;
public ImportTableTask(final BiomartRestClient client, final
BiomartQuery query,
final CyTableFactory tableFactory,
final Window parent,
final CyTableManager tableManager,
- final MapNetworkAttrTaskFactory
mapNetworkAttrTF)
+ final MapTableToNetworkTablesTaskFactory
mapNetworkAttrTF)
{
this.client = client;
this.query = query;
Modified:
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/CyActivator.java
===================================================================
---
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/CyActivator.java
2012-04-25 18:45:36 UTC (rev 29005)
+++
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/CyActivator.java
2012-04-25 18:53:35 UTC (rev 29006)
@@ -20,7 +20,7 @@
import org.osgi.framework.BundleContext;
import org.cytoscape.service.util.AbstractCyActivator;
-import org.cytoscape.task.edit.MapNetworkAttrTaskFactory;
+import org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory;
import java.util.Properties;
@@ -39,7 +39,7 @@
DialogTaskManager taskManagerServiceRef =
getService(bc,DialogTaskManager.class);
CyTableManager cyTableManagerServiceRef =
getService(bc,CyTableManager.class);
CyTableFactory cyDataTableFactoryServiceRef =
getService(bc,CyTableFactory.class);
- MapNetworkAttrTaskFactory mapNetworkAttrTFServiceRef =
getService(bc,MapNetworkAttrTaskFactory.class);
+ MapTableToNetworkTablesTaskFactory mapNetworkAttrTFServiceRef =
getService(bc,MapTableToNetworkTablesTaskFactory.class);
NCBIWebServiceClient ncbiClient = new
NCBIWebServiceClient("http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/eutils.wsdl","NCBI
Network Import Client","REST version of NCBI Web Service
Client.",cyNetworkFactoryServiceRef,cyDataTableFactoryServiceRef,cyNetworkManagerServiceRef,cyTableManagerServiceRef);
NCBITableImportClient ncbiTableImportClient = new
NCBITableImportClient("http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/eutils.wsdl","NCBI
Table Import Client","REST version of NCBI Web Service Client for importing
tables.",cyDataTableFactoryServiceRef,cyTableManagerServiceRef,mapNetworkAttrTFServiceRef);
Modified:
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/NCBITableImportClient.java
===================================================================
---
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/NCBITableImportClient.java
2012-04-25 18:45:36 UTC (rev 29005)
+++
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/NCBITableImportClient.java
2012-04-25 18:53:35 UTC (rev 29006)
@@ -6,7 +6,7 @@
import org.cytoscape.io.webservice.client.AbstractWebServiceClient;
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.model.CyTableManager;
-import org.cytoscape.task.edit.MapNetworkAttrTaskFactory;
+import org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory;
import org.cytoscape.webservice.ncbi.task.ImportTableFromNCBITask;
import org.cytoscape.work.TaskIterator;
@@ -15,13 +15,13 @@
private final CyTableFactory tableFactory;
private final CyTableManager tableManager;
- private final MapNetworkAttrTaskFactory mapNetworkAttrTF;
+ private final MapTableToNetworkTablesTaskFactory mapNetworkAttrTF;
public NCBITableImportClient(final String uri, final String displayName,
final String description,
final CyTableFactory tableFactory,
final CyTableManager tableManager,
- final
MapNetworkAttrTaskFactory mapNetworkAttrTF)
+ final
MapTableToNetworkTablesTaskFactory mapNetworkAttrTF)
{
super(uri, displayName, description);
Modified:
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/task/ImportTableFromNCBITask.java
===================================================================
---
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/task/ImportTableFromNCBITask.java
2012-04-25 18:45:36 UTC (rev 29005)
+++
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/task/ImportTableFromNCBITask.java
2012-04-25 18:53:35 UTC (rev 29006)
@@ -8,7 +8,7 @@
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.model.CyTableManager;
-import org.cytoscape.task.edit.MapNetworkAttrTaskFactory;
+import org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory;
import org.cytoscape.webservice.ncbi.rest.EntrezRestClient;
import org.cytoscape.webservice.ncbi.ui.AnnotationCategory;
import org.cytoscape.work.AbstractTask;
@@ -25,12 +25,12 @@
private final Set<String> idList;
private final Set<AnnotationCategory> category;
private final CyTableManager tableManager;
- private final MapNetworkAttrTaskFactory mapNetworkAttrTF;
+ private final MapTableToNetworkTablesTaskFactory mapNetworkAttrTF;
public ImportTableFromNCBITask(final CyTableFactory tableFactory, final
Set<String> idList,
final Set<AnnotationCategory> category,
final CyTableManager tableManager,
- final
MapNetworkAttrTaskFactory mapNetworkAttrTF)
+ final
MapTableToNetworkTablesTaskFactory mapNetworkAttrTF)
{
this.tableFactory = tableFactory;
this.idList = idList;
Modified:
core3/samples/trunk/sample11/src/main/java/org/cytoscape/sample/internal/CreateTableTask.java
===================================================================
---
core3/samples/trunk/sample11/src/main/java/org/cytoscape/sample/internal/CreateTableTask.java
2012-04-25 18:45:36 UTC (rev 29005)
+++
core3/samples/trunk/sample11/src/main/java/org/cytoscape/sample/internal/CreateTableTask.java
2012-04-25 18:53:35 UTC (rev 29006)
@@ -8,7 +8,7 @@
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.CyTableFactory;
-import org.cytoscape.task.edit.MapNetworkAttrTaskFactory;
+import org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
@@ -17,9 +17,9 @@
private static int numImports = 0;
private CyTableFactory tableFactory;
- private MapNetworkAttrTaskFactory mapNetworkAttrTF;
+ private MapTableToNetworkTablesTaskFactory mapNetworkAttrTF;
- public CreateTableTask(CyTableFactory tableFactory,
MapNetworkAttrTaskFactory mapNetworkAttrTF){
+ public CreateTableTask(CyTableFactory tableFactory,
MapTableToNetworkTablesTaskFactory mapNetworkAttrTF){
this.tableFactory = tableFactory;
this.mapNetworkAttrTF = mapNetworkAttrTF;
}
Modified:
core3/samples/trunk/sample11/src/main/java/org/cytoscape/sample/internal/CyActivator.java
===================================================================
---
core3/samples/trunk/sample11/src/main/java/org/cytoscape/sample/internal/CyActivator.java
2012-04-25 18:45:36 UTC (rev 29005)
+++
core3/samples/trunk/sample11/src/main/java/org/cytoscape/sample/internal/CyActivator.java
2012-04-25 18:53:35 UTC (rev 29006)
@@ -10,7 +10,7 @@
import org.osgi.framework.BundleContext;
import org.cytoscape.service.util.AbstractCyActivator;
-import org.cytoscape.task.edit.MapNetworkAttrTaskFactory;
+import org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory;
import java.util.Properties;
@@ -25,7 +25,7 @@
public void start(BundleContext bc) {
CyTableFactory cyDataTableFactoryServiceRef =
getService(bc,CyTableFactory.class);
- MapNetworkAttrTaskFactory mapNetworkAttrTFServiceRef =
getService(bc,MapNetworkAttrTaskFactory.class);
+ MapTableToNetworkTablesTaskFactory mapNetworkAttrTFServiceRef =
getService(bc,MapTableToNetworkTablesTaskFactory.class);
Sample11TaskFactory sample11TaskFactory = new
Sample11TaskFactory(cyDataTableFactoryServiceRef,mapNetworkAttrTFServiceRef);
Modified:
core3/samples/trunk/sample11/src/main/java/org/cytoscape/sample/internal/Sample11TaskFactory.java
===================================================================
---
core3/samples/trunk/sample11/src/main/java/org/cytoscape/sample/internal/Sample11TaskFactory.java
2012-04-25 18:45:36 UTC (rev 29005)
+++
core3/samples/trunk/sample11/src/main/java/org/cytoscape/sample/internal/Sample11TaskFactory.java
2012-04-25 18:53:35 UTC (rev 29006)
@@ -1,17 +1,17 @@
package org.cytoscape.sample.internal;
import org.cytoscape.model.CyTableFactory;
-import org.cytoscape.task.edit.MapNetworkAttrTaskFactory;
+import org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory;
import org.cytoscape.work.AbstractTaskFactory;
import org.cytoscape.work.TaskIterator;
public class Sample11TaskFactory extends AbstractTaskFactory {
private CyTableFactory tableFactory;
- private MapNetworkAttrTaskFactory mapNetworkAttrTF;
+ private MapTableToNetworkTablesTaskFactory mapNetworkAttrTF;
public Sample11TaskFactory(CyTableFactory tableFactory,
- MapNetworkAttrTaskFactory mapNetworkAttrTF){
+ MapTableToNetworkTablesTaskFactory mapNetworkAttrTF){
this.tableFactory = tableFactory;
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