Author: mes
Date: 2012-04-18 14:27:25 -0700 (Wed, 18 Apr 2012)
New Revision: 28880
Removed:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/export/table/ExportEdgeTableTaskFactoryImpl.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/export/table/ExportNodeTableTaskFactoryImpl.java
Modified:
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/export/table/ExportCurrentTableTaskFactory.java
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/table/MapGlobalToLocalTableTaskFactory.java
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/vizmap/ApplyVisualStyleTaskFactory.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/export/table/ExportCurrentTableTaskFactoryImpl.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/vizmap/ApplyVisualStyleTaskFactoryimpl.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ImportAttributeTableReaderTask.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/GeneAssociationReader.java
Log:
cleaned up some core-task-api issues related to ListSingleSelection where it
shouldn't have been used.
Modified:
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/export/table/ExportCurrentTableTaskFactory.java
===================================================================
---
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/export/table/ExportCurrentTableTaskFactory.java
2012-04-18 21:23:43 UTC (rev 28879)
+++
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/export/table/ExportCurrentTableTaskFactory.java
2012-04-18 21:27:25 UTC (rev 28880)
@@ -3,7 +3,6 @@
import org.cytoscape.model.CyTable;
import org.cytoscape.task.TableTaskFactory;
import org.cytoscape.work.TaskIterator;
-import org.cytoscape.work.util.ListSingleSelection;
/**
* This interface provides a task iterator for exporting the current
@@ -17,10 +16,10 @@
* Creates a task iterator for exporting the current table to a
selected table.
* This task will run synchronously in the current thread and it will
not create a
* task monitor.
- * @param table The current table
- * @param selectTable A list of tables to select from.
+ * @param table The table to be exported.
+ * @param format The file format description (e.g. .csv, .tsv)
* @return task iterator
*/
- TaskIterator createTaskIterator(CyTable table,
ListSingleSelection<String> selectTable);
+ TaskIterator createTaskIterator(CyTable table, String format);
}
Modified:
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/table/MapGlobalToLocalTableTaskFactory.java
===================================================================
---
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/table/MapGlobalToLocalTableTaskFactory.java
2012-04-18 21:23:43 UTC (rev 28879)
+++
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/table/MapGlobalToLocalTableTaskFactory.java
2012-04-18 21:27:25 UTC (rev 28880)
@@ -2,7 +2,6 @@
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
-import org.cytoscape.work.util.ListSingleSelection;
/**
@@ -16,9 +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 globalTables A list of global tables with a single table
selected from.
- * @param localTables A list of local tables with a single table
selected from to map to.
+ * @param globalTable The global table name to map from.
+ * @param localTable The local table name to map to.
* @return A task iterator of type {@link TaskIterator}.
*/
- TaskIterator createTaskIterator(final ListSingleSelection<String>
globalTables, final ListSingleSelection<String> localTables);
+ TaskIterator createTaskIterator(final String globalTable, final String
localTable);
}
Modified:
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/vizmap/ApplyVisualStyleTaskFactory.java
===================================================================
---
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/vizmap/ApplyVisualStyleTaskFactory.java
2012-04-18 21:23:43 UTC (rev 28879)
+++
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/vizmap/ApplyVisualStyleTaskFactory.java
2012-04-18 21:27:25 UTC (rev 28880)
@@ -4,7 +4,6 @@
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.vizmap.VisualStyle;
import org.cytoscape.work.TaskIterator;
-import org.cytoscape.work.util.ListSingleSelection;
/**
* This interface provides a task iterator for applying a visual style.
@@ -18,10 +17,8 @@
* The created task will run synchronously in the current thread and
will
* not create a task monitor.
* @param networkView The network view to apply the visual style on.
- * @param styles The set of visual styles.
+ * @param style The visual styles to apply.
* @return a task iterator of type {@link TaskIterator}.
*/
- TaskIterator createTaskIterator(final CyNetworkView networkView, final
ListSingleSelection<VisualStyle> styles);
-
-
+ TaskIterator createTaskIterator(final CyNetworkView networkView,
VisualStyle style);
}
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/export/table/ExportCurrentTableTaskFactoryImpl.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/export/table/ExportCurrentTableTaskFactoryImpl.java
2012-04-18 21:23:43 UTC (rev 28879)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/export/table/ExportCurrentTableTaskFactoryImpl.java
2012-04-18 21:27:25 UTC (rev 28880)
@@ -36,11 +36,15 @@
}
@Override
- public TaskIterator createTaskIterator(CyTable table,
- ListSingleSelection<String> selectTable) {
+ public TaskIterator createTaskIterator(CyTable table, String format) {
final Map<String, Object> m = new HashMap<String, Object>();
- m.put("selectTable", selectTable);
- return
tunableSetter.createTaskIterator(this.createTaskIterator(table), m);
+ ListSingleSelection<String> formatSelection = new
ListSingleSelection<String>(format);
+ formatSelection.setSelectedValue(format);
+
+ m.put("options", formatSelection);
+
+ return tunableSetter.createTaskIterator(new TaskIterator(2, new
CyTableWriter(writerManager, table)), m);
+
}
}
Deleted:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/export/table/ExportEdgeTableTaskFactoryImpl.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/export/table/ExportEdgeTableTaskFactoryImpl.java
2012-04-18 21:23:43 UTC (rev 28879)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/export/table/ExportEdgeTableTaskFactoryImpl.java
2012-04-18 21:27:25 UTC (rev 28880)
@@ -1,40 +0,0 @@
-package org.cytoscape.task.internal.export.table;
-
-import java.io.File;
-import java.util.HashMap;
-import java.util.Map;
-
-import org.cytoscape.io.write.CyTableWriterManager;
-import org.cytoscape.model.CyTable;
-import org.cytoscape.task.AbstractNetworkViewTaskFactory;
-import org.cytoscape.task.export.table.ExportEdgeTableTaskFactory;
-import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.work.TaskIterator;
-import org.cytoscape.work.TunableSetter;
-
-public class ExportEdgeTableTaskFactoryImpl extends
AbstractNetworkViewTaskFactory implements ExportEdgeTableTaskFactory{
-
- private final CyTableWriterManager writerManager;
-
- private final TunableSetter tunableSetter;
-
- public ExportEdgeTableTaskFactoryImpl(CyTableWriterManager
writerManager, TunableSetter tunableSetter) {
- this.writerManager = writerManager;
- this.tunableSetter = tunableSetter;
- }
-
- @Override
- public TaskIterator createTaskIterator(CyNetworkView view) {
- CyTable table = view.getModel().getDefaultEdgeTable();
- return new TaskIterator(2, new CyTableWriter(writerManager,
table));
- }
-
- @Override
- public TaskIterator createTaskIterator(CyNetworkView view, File
outputFile) {
- final Map<String, Object> m = new HashMap<String, Object>();
- m.put("OutputFile", outputFile);
-
- return
tunableSetter.createTaskIterator(this.createTaskIterator(view), m);
- }
-
-}
Deleted:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/export/table/ExportNodeTableTaskFactoryImpl.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/export/table/ExportNodeTableTaskFactoryImpl.java
2012-04-18 21:23:43 UTC (rev 28879)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/export/table/ExportNodeTableTaskFactoryImpl.java
2012-04-18 21:27:25 UTC (rev 28880)
@@ -1,23 +0,0 @@
-package org.cytoscape.task.internal.export.table;
-
-import org.cytoscape.io.write.CyTableWriterManager;
-import org.cytoscape.model.CyTable;
-import org.cytoscape.task.AbstractNetworkViewTaskFactory;
-import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.work.TaskIterator;
-
-public class ExportNodeTableTaskFactoryImpl extends
AbstractNetworkViewTaskFactory {
-
- private final CyTableWriterManager writerManager;
-
- public ExportNodeTableTaskFactoryImpl(CyTableWriterManager
writerManager) {
- this.writerManager = writerManager;
- }
-
- @Override
- public TaskIterator createTaskIterator(CyNetworkView view) {
- CyTable table = view.getModel().getDefaultNodeTable();
- return new TaskIterator(2,new CyTableWriter(writerManager,
table));
- }
-
-}
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
2012-04-18 21:23:43 UTC (rev 28879)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapGlobalToLocalTableTaskFactoryImpl.java
2012-04-18 21:27:25 UTC (rev 28880)
@@ -31,10 +31,17 @@
}
@Override
- public TaskIterator createTaskIterator(
- ListSingleSelection<String> globalTables,
- ListSingleSelection<String> localTables) {
+ public TaskIterator createTaskIterator(String globalTable,
+ String localTable) {
+
final Map<String, Object> m = new HashMap<String, Object>();
+
+ ListSingleSelection<String> globalTables = new
ListSingleSelection<String>(globalTable);
+ globalTables.setSelectedValue(globalTable);
+
+ ListSingleSelection<String> localTables = new
ListSingleSelection<String>(localTable);
+ localTables.setSelectedValue(localTable);
+
m.put("globalTables", globalTables);
m.put("localTables", localTables);
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/vizmap/ApplyVisualStyleTaskFactoryimpl.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/vizmap/ApplyVisualStyleTaskFactoryimpl.java
2012-04-18 21:23:43 UTC (rev 28879)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/vizmap/ApplyVisualStyleTaskFactoryimpl.java
2012-04-18 21:27:25 UTC (rev 28880)
@@ -29,9 +29,12 @@
}
@Override
- public TaskIterator createTaskIterator(final CyNetworkView networkView,
- ListSingleSelection<VisualStyle> styles) {
+ public TaskIterator createTaskIterator(final CyNetworkView networkView,
VisualStyle style) {
final Map<String, Object> m = new HashMap<String, Object>();
+
+ ListSingleSelection<VisualStyle> styles = new
ListSingleSelection<VisualStyle>(style);
+ styles.setSelectedValue(style);
+
m.put("styles", styles);
return
tunableSetter.createTaskIterator(this.createTaskIterator(networkView), m);
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ImportAttributeTableReaderTask.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ImportAttributeTableReaderTask.java
2012-04-18 21:23:43 UTC (rev 28879)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ImportAttributeTableReaderTask.java
2012-04-18 21:27:25 UTC (rev 28880)
@@ -27,7 +27,6 @@
import org.cytoscape.tableimport.internal.reader.TextTableReader.ObjectType;
import org.cytoscape.tableimport.internal.ui.ImportTablePanel;
import org.cytoscape.tableimport.internal.util.CytoscapeServices;
-import org.cytoscape.task.MapNetworkAttrTask;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.vizmap.VisualStyle;
import org.cytoscape.work.AbstractTask;
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/GeneAssociationReader.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/GeneAssociationReader.java
2012-04-18 21:23:43 UTC (rev 28879)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/GeneAssociationReader.java
2012-04-18 21:27:25 UTC (rev 28880)
@@ -29,7 +29,6 @@
import org.cytoscape.model.CyTableManager;
import org.cytoscape.tableimport.internal.util.OntologyDAGManager;
import org.cytoscape.tableimport.internal.util.OntologyUtil;
-import org.cytoscape.task.MapNetworkAttrTask;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
import org.slf4j.Logger;
@@ -265,10 +264,6 @@
tableManager.addTable(table);
- // Map terms to existing networks
- // if (netMgr.getNetworkSet().size() > 0)
- // super.insertTasksAfterCurrentTask(new
- // MapNetworkAttrTask(CyNode.class, table, netMgr, appMgr));
}
private void createColumns() {
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