Author: rozagh
Date: 2012-05-17 18:08:17 -0700 (Thu, 17 May 2012)
New Revision: 29294
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/loaddatatable/AbstractLoadAttributesTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/AddImportedTableTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapTableToNetworkTablesTask.java
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/AttributeBrowserToolBar.java
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/CyActivator.java
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/DefaultTableBrowser.java
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/GlobalTableBrowser.java
Log:
Removing Global Table tab
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
2012-05-17 22:25:29 UTC (rev 29293)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
2012-05-18 01:08:17 UTC (rev 29294)
@@ -298,7 +298,7 @@
Properties mapGlobalProps = new Properties();
-
mapGlobalProps.setProperty(ID,"mapGlobalToLocalTableTaskFactory");
+ /*
mapGlobalProps.setProperty(ID,"mapGlobalToLocalTableTaskFactory");
mapGlobalProps.setProperty(PREFERRED_MENU,"Tools");
mapGlobalProps.setProperty(ACCELERATOR,"cmd m");
mapGlobalProps.setProperty(TITLE, "Map Table to Attributes");
@@ -307,9 +307,9 @@
mapGlobalProps.setProperty(IN_TOOL_BAR,"false");
mapGlobalProps.setProperty(COMMAND,"map-global-to-local");
mapGlobalProps.setProperty(COMMAND_NAMESPACE,"table");
- registerService(bc, mapGlobal, TableTaskFactory.class,
mapGlobalProps);
+ */ registerService(bc, mapGlobal, TableTaskFactory.class,
mapGlobalProps);
registerService(bc, mapGlobal,
MapGlobalToLocalTableTaskFactory.class, mapGlobalProps);
-
+
Properties loadNetworkFileTaskFactoryProps = new Properties();
loadNetworkFileTaskFactoryProps.setProperty(ID,"loadNetworkFileTaskFactory");
loadNetworkFileTaskFactoryProps.setProperty(PREFERRED_MENU,"File.Import.Network");
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/AbstractLoadAttributesTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/AbstractLoadAttributesTask.java
2012-05-17 22:25:29 UTC (rev 29293)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/AbstractLoadAttributesTask.java
2012-05-18 01:08:17 UTC (rev 29294)
@@ -41,7 +41,8 @@
taskMonitor.setStatusMessage("Importing Data Table...");
- insertTasksAfterCurrentTask(reader ,new
AddImportedTableTask(tableMgr, reader), new MapTableToNetworkTablesTask(netMgr,
reader), new FinalStatusMessageUpdateTask(reader));
+ insertTasksAfterCurrentTask(reader , new
MapTableToNetworkTablesTask(netMgr, reader), new AddImportedTableTask(tableMgr,
reader), new FinalStatusMessageUpdateTask(reader));
+
}
}
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/AddImportedTableTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/AddImportedTableTask.java
2012-05-17 22:25:29 UTC (rev 29293)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/AddImportedTableTask.java
2012-05-18 01:08:17 UTC (rev 29294)
@@ -31,6 +31,7 @@
else
logger.warn("No tables in reader!");
}
+
}
}
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapTableToNetworkTablesTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapTableToNetworkTablesTask.java
2012-05-17 22:25:29 UTC (rev 29293)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapTableToNetworkTablesTask.java
2012-05-18 01:08:17 UTC (rev 29294)
@@ -26,7 +26,7 @@
public final class MapTableToNetworkTablesTask extends AbstractTask {
private static enum TableType {
- NODE_ATTR("Node Attributes", CyNode.class), EDGE_ATTR("Edge
Attributes", CyEdge.class), NETWORK_ATTR("Network Attributes",
CyNetwork.class), GLOBAL("Other Tables", CyTable.class);
+ NODE_ATTR("Node Attributes", CyNode.class), EDGE_ATTR("Edge
Attributes", CyEdge.class), NETWORK_ATTR("Network Attributes", CyNetwork.class);
private final String name;
private final Class<? extends CyIdentifiable> type;
@@ -105,27 +105,28 @@
public void run(TaskMonitor taskMonitor) throws Exception {
TableType tableType = dataTypeOptions.getSelectedValue();
- if (tableType != tableType.GLOBAL ){ //The table has already
been added to the global tables
- List<CyNetwork> networks = new ArrayList<CyNetwork>();
- if (!selectedNetworksOnly)
- networks.addAll(networkManager.getNetworkSet());
- else
- for(String netName:
networkList.getSelectedValues())
-
networks.add(name2NetworkMap.get(netName));
-
- for (CyNetwork network: networks){
- CyTable targetTable = getTable(network,
tableType);
- if (targetTable != null){
- if(byReader){
- if (reader.getTables() != null
&& reader.getTables().length >0){
- for(CyTable sourceTable
: reader.getTables())
-
mapTable(targetTable, sourceTable);
- }
- }else{
- mapTable(targetTable,
globalTable);
+
+ List<CyNetwork> networks = new ArrayList<CyNetwork>();
+
+ if (!selectedNetworksOnly)
+ networks.addAll(networkManager.getNetworkSet());
+ else
+ for(String netName: networkList.getSelectedValues())
+ networks.add(name2NetworkMap.get(netName));
+
+ for (CyNetwork network: networks){
+ CyTable targetTable = getTable(network, tableType);
+ if (targetTable != null){
+ if(byReader){
+ if (reader.getTables() != null &&
reader.getTables().length >0){
+ for(CyTable sourceTable :
reader.getTables())
+ mapTable(targetTable,
sourceTable);
}
- }
+ }else
+ mapTable(targetTable, globalTable);
}
+ }
+ if(!selectedNetworksOnly){ //if table should be mapped to all
of the tables
//add each mapped table to the list for mapping to
networks going to be added later
if(byReader){
if (reader.getTables() != null &&
reader.getTables().length >0)
@@ -145,7 +146,7 @@
return network.getDefaultEdgeTable();
if (tableType == TableType.NETWORK_ATTR)
return network.getDefaultNetworkTable();
- logger.warn("The selected table type is not valie. \nTable
needs to be one of these types: " +TableType.NODE_ATTR +", " +
TableType.EDGE_ATTR + ", "+ TableType.NETWORK_ATTR +" or "+TableType.GLOBAL
+".");
+ logger.warn("The selected table type is not valie. \nTable
needs to be one of these types: " +TableType.NODE_ATTR +", " +
TableType.EDGE_ATTR + "or "+ TableType.NETWORK_ATTR +".");
return null;
}
Modified:
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/AttributeBrowserToolBar.java
===================================================================
---
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/AttributeBrowserToolBar.java
2012-05-17 22:25:29 UTC (rev 29293)
+++
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/AttributeBrowserToolBar.java
2012-05-18 01:08:17 UTC (rev 29294)
@@ -110,8 +110,8 @@
private JButton selectAllAttributesButton = null;
private JButton unselectAllAttributesButton = null;
- private JButton mapGlobalTableButton = null;
- private final MapGlobalToLocalTableTaskFactory
mapGlobalTableTaskFactoryService;
+// private JButton mapGlobalTableButton = null;
+// private final MapGlobalToLocalTableTaskFactory
mapGlobalTableTaskFactoryService;
private final JComboBox tableChooser;
@@ -129,22 +129,22 @@
public AttributeBrowserToolBar(final CyServiceRegistrar
serviceRegistrar, final EquationCompiler compiler,
final DeleteTableTaskFactory
deleteTableTaskFactoryService, DialogTaskManager guiTaskManagerServiceRef,
final JComboBox tableChooser, final Class<? extends
CyIdentifiable> objType,
- final CyApplicationManager appManager,
- final MapGlobalToLocalTableTaskFactory
mapGlobalTableTaskFactoryService) {
+ final CyApplicationManager appManager){//,
+ //final MapGlobalToLocalTableTaskFactory
mapGlobalTableTaskFactoryService) {
this(serviceRegistrar, compiler, deleteTableTaskFactoryService,
guiTaskManagerServiceRef, tableChooser,
- new JToggleButton(), objType, appManager,
mapGlobalTableTaskFactoryService);
+ new JToggleButton(), objType, appManager);//,
mapGlobalTableTaskFactoryService);
}
public AttributeBrowserToolBar(final CyServiceRegistrar
serviceRegistrar, final EquationCompiler compiler,
final DeleteTableTaskFactory
deleteTableTaskFactoryService, DialogTaskManager guiTaskManagerServiceRef,
final JComboBox tableChooser, final JToggleButton
selectionModeButton,
- Class<? extends CyIdentifiable> objType, final
CyApplicationManager appManager,
- final MapGlobalToLocalTableTaskFactory
mapGlobalTableTaskFactoryService) {
+ Class<? extends CyIdentifiable> objType, final
CyApplicationManager appManager){//,
+ // final MapGlobalToLocalTableTaskFactory
mapGlobalTableTaskFactoryService) {
this.compiler = compiler;
this.selectionModeButton = selectionModeButton;
this.appManager = appManager;
- this.mapGlobalTableTaskFactoryService =
mapGlobalTableTaskFactoryService;
+// this.mapGlobalTableTaskFactoryService =
mapGlobalTableTaskFactoryService;
this.tableChooser = tableChooser;
this.deleteTableTaskFactoryService =
deleteTableTaskFactoryService;
@@ -170,10 +170,10 @@
if(browserTableModel != null && objType != null) {
deleteTableButton.setEnabled(false);
- mapGlobalTableButton.setEnabled(false);
+// mapGlobalTableButton.setEnabled(false);
} else {
deleteTableButton.setEnabled(browserTableModel != null);
- mapGlobalTableButton.setEnabled(browserTableModel !=
null);
+// mapGlobalTableButton.setEnabled(browserTableModel !=
null);
}
formulaBuilderButton.setEnabled(browserTableModel != null);
@@ -488,8 +488,8 @@
.addPreferredGap(ComponentPlacement.UNRELATED)
.addComponent(getFunctionBuilderButton())
.addPreferredGap(ComponentPlacement.UNRELATED)
-
.addComponent(getMapGlobalTableButton())
-
.addPreferredGap(ComponentPlacement.UNRELATED)
+//
.addComponent(getMapGlobalTableButton())
+//
.addPreferredGap(ComponentPlacement.UNRELATED)
.addComponent(this.tableChooser)));
buttonBarLayout.setVerticalGroup(buttonBarLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(selectionModeButton, javax.swing.GroupLayout.Alignment.CENTER,
@@ -523,10 +523,10 @@
javax.swing.GroupLayout.Alignment.CENTER,
javax.swing.GroupLayout.DEFAULT_SIZE,
27,
Short.MAX_VALUE)
-
.addComponent(mapGlobalTableButton,
-
javax.swing.GroupLayout.Alignment.CENTER,
-
javax.swing.GroupLayout.DEFAULT_SIZE,
- 27,
Short.MAX_VALUE)
+//
.addComponent(mapGlobalTableButton,
+//
javax.swing.GroupLayout.Alignment.CENTER,
+//
javax.swing.GroupLayout.DEFAULT_SIZE,
+// 27,
Short.MAX_VALUE)
.addComponent(tableChooser,
javax.swing.GroupLayout.Alignment.CENTER,
javax.swing.GroupLayout.DEFAULT_SIZE,
@@ -830,6 +830,7 @@
return createNewAttributeButton;
}
+ /*
private JButton getMapGlobalTableButton() {
if (mapGlobalTableButton == null) {
mapGlobalTableButton = new JButton();
@@ -850,7 +851,7 @@
return mapGlobalTableButton;
}
-
+ */
private void createNewAttribute(final String type, boolean isShared) {
final String[] existingAttrs = getAttributeArray();
Modified:
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/CyActivator.java
2012-05-17 22:25:29 UTC (rev 29293)
+++
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/CyActivator.java
2012-05-18 01:08:17 UTC (rev 29294)
@@ -46,23 +46,23 @@
DialogTaskManager guiTaskManagerServiceRef =
getService(bc,DialogTaskManager.class);
CyApplicationManager cyApplicationManagerServiceRef =
getService(bc,CyApplicationManager.class);
CyNetworkTableManager cyNetworkTableManagerServiceRef =
getService(bc,CyNetworkTableManager.class);
- MapGlobalToLocalTableTaskFactory
mapGlobalTableTaskFactoryServiceRef =
getService(bc,MapGlobalToLocalTableTaskFactory.class);
+ //MapGlobalToLocalTableTaskFactory
mapGlobalTableTaskFactoryServiceRef =
getService(bc,MapGlobalToLocalTableTaskFactory.class);
CyEventHelper cyEventHelperServiceRef =
getService(bc,CyEventHelper.class);
PopupMenuHelper popupMenuHelper = new
PopupMenuHelper(guiTaskManagerServiceRef);
- AbstractTableBrowser nodeTableBrowser = new
DefaultTableBrowser("Node Attributes", CyNode.class,
cyTableManagerServiceRef,cyNetworkTableManagerServiceRef,cyServiceRegistrarServiceRef,compilerServiceRef,openBrowserServiceRef,cyNetworkManagerServiceRef,deleteTableTaskFactoryService,guiTaskManagerServiceRef,popupMenuHelper,cyApplicationManagerServiceRef,
cyEventHelperServiceRef, mapGlobalTableTaskFactoryServiceRef);
- AbstractTableBrowser edgeTableBrowser = new
DefaultTableBrowser("Edge Attributes", CyEdge.class,
cyTableManagerServiceRef,cyNetworkTableManagerServiceRef,cyServiceRegistrarServiceRef,compilerServiceRef,openBrowserServiceRef,cyNetworkManagerServiceRef,deleteTableTaskFactoryService,guiTaskManagerServiceRef,popupMenuHelper,cyApplicationManagerServiceRef,
cyEventHelperServiceRef, mapGlobalTableTaskFactoryServiceRef);
- AbstractTableBrowser networkTableBrowser = new
DefaultTableBrowser("Network Attributes", CyNetwork.class,
cyTableManagerServiceRef,cyNetworkTableManagerServiceRef,cyServiceRegistrarServiceRef,compilerServiceRef,openBrowserServiceRef,cyNetworkManagerServiceRef,deleteTableTaskFactoryService,guiTaskManagerServiceRef,popupMenuHelper,cyApplicationManagerServiceRef,
cyEventHelperServiceRef, mapGlobalTableTaskFactoryServiceRef);
+ AbstractTableBrowser nodeTableBrowser = new
DefaultTableBrowser("Node Attributes", CyNode.class,
cyTableManagerServiceRef,cyNetworkTableManagerServiceRef,cyServiceRegistrarServiceRef,compilerServiceRef,openBrowserServiceRef,cyNetworkManagerServiceRef,deleteTableTaskFactoryService,guiTaskManagerServiceRef,popupMenuHelper,cyApplicationManagerServiceRef,
cyEventHelperServiceRef);//, mapGlobalTableTaskFactoryServiceRef);
+ AbstractTableBrowser edgeTableBrowser = new
DefaultTableBrowser("Edge Attributes", CyEdge.class,
cyTableManagerServiceRef,cyNetworkTableManagerServiceRef,cyServiceRegistrarServiceRef,compilerServiceRef,openBrowserServiceRef,cyNetworkManagerServiceRef,deleteTableTaskFactoryService,guiTaskManagerServiceRef,popupMenuHelper,cyApplicationManagerServiceRef,
cyEventHelperServiceRef);//, mapGlobalTableTaskFactoryServiceRef);
+ AbstractTableBrowser networkTableBrowser = new
DefaultTableBrowser("Network Attributes", CyNetwork.class,
cyTableManagerServiceRef,cyNetworkTableManagerServiceRef,cyServiceRegistrarServiceRef,compilerServiceRef,openBrowserServiceRef,cyNetworkManagerServiceRef,deleteTableTaskFactoryService,guiTaskManagerServiceRef,popupMenuHelper,cyApplicationManagerServiceRef,
cyEventHelperServiceRef);//, mapGlobalTableTaskFactoryServiceRef);
- AbstractTableBrowser globalTableBrowser = new
GlobalTableBrowser("Other Tables",
cyTableManagerServiceRef,cyNetworkTableManagerServiceRef,cyServiceRegistrarServiceRef,compilerServiceRef,openBrowserServiceRef,cyNetworkManagerServiceRef,deleteTableTaskFactoryService,guiTaskManagerServiceRef,popupMenuHelper,cyApplicationManagerServiceRef,
cyEventHelperServiceRef, mapGlobalTableTaskFactoryServiceRef);
+ //AbstractTableBrowser globalTableBrowser = new
GlobalTableBrowser("Other Tables",
cyTableManagerServiceRef,cyNetworkTableManagerServiceRef,cyServiceRegistrarServiceRef,compilerServiceRef,openBrowserServiceRef,cyNetworkManagerServiceRef,deleteTableTaskFactoryService,guiTaskManagerServiceRef,popupMenuHelper,cyApplicationManagerServiceRef,
cyEventHelperServiceRef, mapGlobalTableTaskFactoryServiceRef);
registerAllServices(bc,nodeTableBrowser, new Properties());
registerAllServices(bc,edgeTableBrowser, new Properties());
registerAllServices(bc,networkTableBrowser, new Properties());
- registerAllServices(bc,globalTableBrowser, new Properties());
+ //registerAllServices(bc,globalTableBrowser, new Properties());
registerServiceListener(bc,popupMenuHelper,"addTableColumnTaskFactory","removeTableColumnTaskFactory",TableColumnTaskFactory.class);
registerServiceListener(bc,popupMenuHelper,"addTableCellTaskFactory","removeTableCellTaskFactory",TableCellTaskFactory.class);
Modified:
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/DefaultTableBrowser.java
===================================================================
---
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/DefaultTableBrowser.java
2012-05-17 22:25:29 UTC (rev 29293)
+++
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/DefaultTableBrowser.java
2012-05-18 01:08:17 UTC (rev 29294)
@@ -61,7 +61,7 @@
CyNetworkTableManager networkTableManager,
CyServiceRegistrar serviceRegistrar, EquationCompiler compiler,
OpenBrowser openBrowser, CyNetworkManager
networkManager, DeleteTableTaskFactory deleteTableTaskFactoryService,
DialogTaskManager guiTaskManagerServiceRef,
PopupMenuHelper popupMenuHelper,
- CyApplicationManager applicationManager, final
CyEventHelper eventHelper, final MapGlobalToLocalTableTaskFactory
mapGlobalTableTaskFactoryService) {
+ CyApplicationManager applicationManager, final
CyEventHelper eventHelper){//, final MapGlobalToLocalTableTaskFactory
mapGlobalTableTaskFactoryService) {
super(tabTitle, tableManager, networkTableManager,
serviceRegistrar, compiler, openBrowser, networkManager,
deleteTableTaskFactoryService,
guiTaskManagerServiceRef, popupMenuHelper, applicationManager, eventHelper);
@@ -91,7 +91,7 @@
});
this.attributeBrowserToolBar = new
AttributeBrowserToolBar(serviceRegistrar, compiler,
- deleteTableTaskFactoryService,
guiTaskManagerServiceRef, networkChooser, selectionModeButton, objType,
applicationManager, mapGlobalTableTaskFactoryService);
+ deleteTableTaskFactoryService,
guiTaskManagerServiceRef, networkChooser, selectionModeButton, objType,
applicationManager);//, mapGlobalTableTaskFactoryService);
add(attributeBrowserToolBar, BorderLayout.NORTH);
}
Modified:
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/GlobalTableBrowser.java
===================================================================
---
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/GlobalTableBrowser.java
2012-05-17 22:25:29 UTC (rev 29293)
+++
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/GlobalTableBrowser.java
2012-05-18 01:08:17 UTC (rev 29294)
@@ -54,7 +54,7 @@
tableChooser.setEnabled(false);
attributeBrowserToolBar = new
AttributeBrowserToolBar(serviceRegistrar, compiler,
- deleteTableTaskFactoryService,
guiTaskManagerServiceRef, tableChooser, null, applicationManager,
mapGlobalTableTaskFactoryService);
+ deleteTableTaskFactoryService,
guiTaskManagerServiceRef, tableChooser, null, applicationManager);//,
mapGlobalTableTaskFactoryService);
add(attributeBrowserToolBar, BorderLayout.NORTH);
}
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