Author: pwang
Date: 2012-03-26 16:26:59 -0700 (Mon, 26 Mar 2012)
New Revision: 28658
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/AttributeSetManager.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewEditorImpl.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewPanelImpl.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/VizMapPropertyBuilder.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/VizMapPropertySheetBuilder.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/bypass/BypassTask.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/EditorManagerImpl.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/mappingeditor/C2CEditor.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/mappingeditor/C2DEditor.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/mappingeditor/GradientEditor.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/propertyeditor/AttributeComboBoxPropertyEditor.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/event/CellEditorEventHandler.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/util/VizMapperUtil.java
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/AbstractApplyHandler.java
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/ApplyToEdgeHandler.java
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/ApplyToNetworkHandler.java
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/ApplyToNodeHandler.java
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleImpl.java
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/ContinuousMappingImpl.java
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/DiscreteMappingImpl.java
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/PassthroughMappingImpl.java
core3/impl/trunk/webservice-impl/src/main/java/org/cytoscape/webservice/internal/task/WebServiceContextMenuTask.java
core3/impl/trunk/webservice-impl/src/main/java/org/cytoscape/webservice/internal/ui/WebServiceContextMenuManager.java
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/ImportTableTask.java
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/rest/EntrezRestClient.java
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/rest/ImportNetworkTask.java
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/task/ImportNetworkFromGeneTask.java
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/mapper/Mitab25Mapper.java
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/task/ImportNetworkFromPSICQUICTask.java
Log:
Fixed bug#810
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/AttributeSetManager.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/AttributeSetManager.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/AttributeSetManager.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -12,7 +12,7 @@
import org.cytoscape.model.CyNetworkTableManager;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.events.ColumnCreatedEvent;
import org.cytoscape.model.events.ColumnCreatedListener;
import org.cytoscape.model.events.ColumnDeletedEvent;
@@ -26,10 +26,10 @@
private static final Logger logger =
LoggerFactory.getLogger(AttributeSetManager.class);
- private static final Set<Class<? extends CyTableEntry>> GRAPH_OBJECTS;
+ private static final Set<Class<? extends CyIdentifiable>> GRAPH_OBJECTS;
static {
- GRAPH_OBJECTS = new HashSet<Class<? extends CyTableEntry>>();
+ GRAPH_OBJECTS = new HashSet<Class<? extends CyIdentifiable>>();
GRAPH_OBJECTS.add(CyNode.class);
GRAPH_OBJECTS.add(CyEdge.class);
GRAPH_OBJECTS.add(CyNetwork.class);
@@ -37,21 +37,21 @@
private final CyNetworkTableManager tableMgr;
- private final Map<CyNetwork, Map<Class<? extends CyTableEntry>,
AttributeSet>> attrSets;
- private final Map<CyNetwork, Map<Class<? extends CyTableEntry>,
Set<CyTable>>> tableSets;
+ private final Map<CyNetwork, Map<Class<? extends CyIdentifiable>,
AttributeSet>> attrSets;
+ private final Map<CyNetwork, Map<Class<? extends CyIdentifiable>,
Set<CyTable>>> tableSets;
public AttributeSetManager(final CyNetworkTableManager tableMgr) {
this.tableMgr = tableMgr;
- this.attrSets = new HashMap<CyNetwork, Map<Class<? extends
CyTableEntry>, AttributeSet>>();
- this.tableSets = new HashMap<CyNetwork, Map<Class<? extends
CyTableEntry>, Set<CyTable>>>();
+ this.attrSets = new HashMap<CyNetwork, Map<Class<? extends
CyIdentifiable>, AttributeSet>>();
+ this.tableSets = new HashMap<CyNetwork, Map<Class<? extends
CyIdentifiable>, Set<CyTable>>>();
}
- public AttributeSet getAttributeSet(final CyNetwork network, final
Class<? extends CyTableEntry> objectType) {
+ public AttributeSet getAttributeSet(final CyNetwork network, final
Class<? extends CyIdentifiable> objectType) {
if (network == null || objectType == null)
throw new NullPointerException("Both parameters should
not be null.");
- final Map<Class<? extends CyTableEntry>, AttributeSet>
attrSetMap = this.attrSets.get(network);
+ final Map<Class<? extends CyIdentifiable>, AttributeSet>
attrSetMap = this.attrSets.get(network);
if (attrSetMap == null)
throw new NullPointerException("No such network
registered in this mamager: " + network);
@@ -64,10 +64,10 @@
logger.debug("@@@@@@ Attr Set manager got new network." +
network.getSUID());
- final Map<Class<? extends CyTableEntry>, Set<CyTable>>
object2tableMap = new HashMap<Class<? extends CyTableEntry>, Set<CyTable>>();
- final Map<Class<? extends CyTableEntry>, AttributeSet>
attrSetMap = new HashMap<Class<? extends CyTableEntry>, AttributeSet>();
+ final Map<Class<? extends CyIdentifiable>, Set<CyTable>>
object2tableMap = new HashMap<Class<? extends CyIdentifiable>, Set<CyTable>>();
+ final Map<Class<? extends CyIdentifiable>, AttributeSet>
attrSetMap = new HashMap<Class<? extends CyIdentifiable>, AttributeSet>();
- for (final Class<? extends CyTableEntry> objectType :
GRAPH_OBJECTS) {
+ for (final Class<? extends CyIdentifiable> objectType :
GRAPH_OBJECTS) {
final Map<String, CyTable> tableMap =
tableMgr.getTables(network, objectType);
final Collection<CyTable> tables = tableMap.values();
@@ -95,8 +95,8 @@
final CyTable table = e.getSource();
for (CyNetwork network : tableSets.keySet()) {
- Map<Class<? extends CyTableEntry>, Set<CyTable>> tMap =
tableSets.get(network);
- for (final Class<? extends CyTableEntry> objectType :
GRAPH_OBJECTS) {
+ Map<Class<? extends CyIdentifiable>, Set<CyTable>> tMap
= tableSets.get(network);
+ for (final Class<? extends CyIdentifiable> objectType :
GRAPH_OBJECTS) {
final Set<CyTable> targetTables =
tMap.get(objectType);
if (!targetTables.contains(table))
continue;
@@ -113,8 +113,8 @@
final CyTable table = e.getSource();
for (CyNetwork network : tableSets.keySet()) {
- Map<Class<? extends CyTableEntry>, Set<CyTable>> tMap =
tableSets.get(network);
- for (final Class<? extends CyTableEntry> objectType :
GRAPH_OBJECTS) {
+ Map<Class<? extends CyIdentifiable>, Set<CyTable>> tMap
= tableSets.get(network);
+ for (final Class<? extends CyIdentifiable> objectType :
GRAPH_OBJECTS) {
final Set<CyTable> targetTables =
tMap.get(objectType);
if (!targetTables.contains(table))
continue;
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewEditorImpl.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewEditorImpl.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewEditorImpl.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -60,7 +60,7 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.VisualLexicon;
import org.cytoscape.view.model.VisualLexiconNode;
@@ -110,8 +110,8 @@
private static final int ICON_WIDTH = 48;
private static final int ICON_HEIGHT = 48;
- private final Map<Class<? extends CyTableEntry>,
Set<VisualProperty<?>>> vpSets;
- private final Map<Class<? extends CyTableEntry>, JList> listMap;
+ private final Map<Class<? extends CyIdentifiable>,
Set<VisualProperty<?>>> vpSets;
+ private final Map<Class<? extends CyIdentifiable>, JList> listMap;
private final CyApplicationManager cyApplicationManager;
@@ -160,8 +160,8 @@
this.vmm = vmm;
this.util = util;
this.selectedManager = selectedManager;
- vpSets = new HashMap<Class<? extends CyTableEntry>,
Set<VisualProperty<?>>>();
- listMap = new HashMap<Class<? extends CyTableEntry>, JList>();
+ vpSets = new HashMap<Class<? extends CyIdentifiable>,
Set<VisualProperty<?>>>();
+ listMap = new HashMap<Class<? extends CyIdentifiable>, JList>();
this.cyApplicationManager = cyApplicationManager;
this.setModal(true);
@@ -539,7 +539,7 @@
final VisualLexicon lex = currentEngine.getVisualLexicon();
- for (Class<? extends CyTableEntry> key : vpSets.keySet()) {
+ for (Class<? extends CyIdentifiable> key : vpSets.keySet()) {
final DefaultListModel model = new DefaultListModel();
final JList list = listMap.get(key);
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewPanelImpl.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewPanelImpl.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewPanelImpl.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -51,7 +51,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.presentation.RenderingEngine;
@@ -124,13 +124,13 @@
final CyNode source = dummyNet.addNode();
final CyNode target = dummyNet.addNode();
- dummyNet.getRow(source).set(CyTableEntry.NAME, "Source");
- dummyNet.getRow(target).set(CyTableEntry.NAME, "Target");
+ dummyNet.getRow(source).set(CyNetwork.NAME, "Source");
+ dummyNet.getRow(target).set(CyNetwork.NAME, "Target");
final CyEdge edge = dummyNet.addEdge(source, target, true);
- dummyNet.getRow(edge).set(CyTableEntry.NAME, "Source
(interaction) Target");
+ dummyNet.getRow(edge).set(CyNetwork.NAME, "Source (interaction)
Target");
- dummyNet.getRow(dummyNet).set(CyTableEntry.NAME, "Default
Appearance");
+ dummyNet.getRow(dummyNet).set(CyNetwork.NAME, "Default
Appearance");
final CyNetworkView dummyview = cyNetworkViewFactory
.createNetworkView(dummyNet);
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/VizMapPropertyBuilder.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/VizMapPropertyBuilder.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/VizMapPropertyBuilder.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -48,7 +48,7 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.CyTableManager;
import org.cytoscape.view.model.VisualProperty;
import org.cytoscape.view.vizmap.VisualMappingFunction;
@@ -147,13 +147,13 @@
final Set<CyNetwork> networks =
cyNetworkManager.getNetworkSet();
- final Map<CyNetwork,Set<CyTableEntry>> graphObjectSet = new
HashMap<CyNetwork,Set<CyTableEntry>>();
+ final Map<CyNetwork,Set<CyIdentifiable>> graphObjectSet = new
HashMap<CyNetwork,Set<CyIdentifiable>>();
for (CyNetwork targetNetwork : networks) {
- Iterator<? extends CyTableEntry> it = null;
- graphObjectSet.put(targetNetwork, new
HashSet<CyTableEntry>());
+ Iterator<? extends CyIdentifiable> it = null;
+ graphObjectSet.put(targetNetwork, new
HashSet<CyIdentifiable>());
((PropertyEditorRegistry)
propertySheetPanel.getTable().getEditorFactory()).registerEditor(topProperty,
-
editorManager.getDataTableComboBoxEditor((Class<? extends CyTableEntry>)
vp.getTargetDataType()));
+
editorManager.getDataTableComboBoxEditor((Class<? extends CyIdentifiable>)
vp.getTargetDataType()));
if (vp.getTargetDataType().equals(CyNode.class)) {
it = targetNetwork.getNodeList().iterator();
} else if (vp.getTargetDataType().equals(CyEdge.class))
{
@@ -177,7 +177,7 @@
final SortedSet<K> attrSet = new TreeSet<K>();
for (CyNetwork net : graphObjectSet.keySet()) {
- for (CyTableEntry go : graphObjectSet.get(net))
{
+ for (CyIdentifiable go :
graphObjectSet.get(net)) {
final CyRow row = net.getRow(go);
final CyTable table = row.getTable();
final CyColumn column =
table.getColumn(attrName);
@@ -244,15 +244,15 @@
String stringVal;
for (CyNetwork net : graphObjectSet.keySet()) {
- for (CyTableEntry go : graphObjectSet.get(net)) {
+ for (CyIdentifiable go : graphObjectSet.get(net)) {
CyColumn column =
net.getRow(go).getTable().getColumn(attrName);
if (column != null) {
Class<?> attrClass = column.getType();
- id =
net.getRow(go).get(CyTableEntry.NAME, String.class);
+ id = net.getRow(go).get(CyNetwork.NAME,
String.class);
- if (attrName.equals(CyTableEntry.SUID))
+ if
(attrName.equals(CyIdentifiable.SUID))
value = go.getSUID();
else if
(attrClass.isAssignableFrom(List.class))
value =
net.getRow(go).getList(attrName, column.getListElementType());
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/VizMapPropertySheetBuilder.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/VizMapPropertySheetBuilder.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/VizMapPropertySheetBuilder.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -17,7 +17,7 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.CyTableManager;
import org.cytoscape.view.model.VisualLexicon;
import org.cytoscape.view.model.VisualLexiconNode;
@@ -238,7 +238,7 @@
((PropertyEditorRegistry)
this.propertySheetPanel
.getTable().getEditorFactory())
.registerEditor(calculatorTypeProp, editorManager
-
.getDataTableComboBoxEditor((Class<? extends CyTableEntry>)
targetVP.getTargetDataType()));
+
.getDataTableComboBoxEditor((Class<? extends CyIdentifiable>)
targetVP.getTargetDataType()));
}
props.add(calculatorTypeProp);
}
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/bypass/BypassTask.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/bypass/BypassTask.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/bypass/BypassTask.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -4,7 +4,7 @@
import javax.swing.SwingUtilities;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
import org.cytoscape.view.model.VisualProperty;
@@ -18,7 +18,7 @@
*
* @param <T>
*/
-public class BypassTask<T extends CyTableEntry> extends AbstractTask {
+public class BypassTask<T extends CyIdentifiable> extends AbstractTask {
// Target view object. Node or Edge.
private final View<T> view;
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/EditorManagerImpl.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/EditorManagerImpl.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/EditorManagerImpl.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -51,7 +51,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkTableManager;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.model.ContinuousRange;
import org.cytoscape.view.model.DiscreteRange;
import org.cytoscape.view.model.Range;
@@ -245,7 +245,7 @@
* Editor name is NODE, EDGE, or NETWORK.
*/
@Override
- public PropertyEditor getDataTableComboBoxEditor(final Class<? extends
CyTableEntry> targetObjectType) {
+ public PropertyEditor getDataTableComboBoxEditor(final Class<? extends
CyIdentifiable> targetObjectType) {
final ListEditor editor =
attrComboBoxEditors.get(targetObjectType);
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/mappingeditor/C2CEditor.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/mappingeditor/C2CEditor.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/mappingeditor/C2CEditor.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -4,7 +4,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkTableManager;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.gui.SelectedVisualStyleManager;
import org.cytoscape.view.vizmap.gui.editor.EditorManager;
@@ -28,7 +28,7 @@
// TODO: error chekcing
mapping = (ContinuousMapping<Number, Number>) value;
@SuppressWarnings("unchecked")
- Class<? extends CyTableEntry> type = (Class<? extends
CyTableEntry>) mapping.getVisualProperty().getTargetDataType();
+ Class<? extends CyIdentifiable> type = (Class<? extends
CyIdentifiable>) mapping.getVisualProperty().getTargetDataType();
final CyTable attr =
manager.getTable(appManager.getCurrentNetwork(), type, CyNetwork.DEFAULT_ATTRS);
this.editorPanel = new
C2CMappingEditorPanel(selectedManager.getCurrentVisualStyle(), mapping, attr,
appManager, vmm);
}
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/mappingeditor/C2DEditor.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/mappingeditor/C2DEditor.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/mappingeditor/C2DEditor.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -4,7 +4,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkTableManager;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.gui.SelectedVisualStyleManager;
import org.cytoscape.view.vizmap.gui.editor.EditorManager;
@@ -32,7 +32,7 @@
// TODO: error chekcing
mapping = (ContinuousMapping<Number, V>) value;
@SuppressWarnings("unchecked")
- Class<? extends CyTableEntry> type = (Class<? extends
CyTableEntry>) mapping.getVisualProperty()
+ Class<? extends CyIdentifiable> type = (Class<? extends
CyIdentifiable>) mapping.getVisualProperty()
.getTargetDataType();
final CyTable attr =
manager.getTable(appManager.getCurrentNetwork(), type, CyNetwork.DEFAULT_ATTRS);
this.editorPanel = new
C2DMappingEditorPanel(selectedManager.getCurrentVisualStyle(), mapping, attr,
appManager,
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/mappingeditor/GradientEditor.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/mappingeditor/GradientEditor.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/mappingeditor/GradientEditor.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -7,7 +7,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkTableManager;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.gui.SelectedVisualStyleManager;
import org.cytoscape.view.vizmap.gui.editor.EditorManager;
@@ -34,7 +34,7 @@
mapping = (ContinuousMapping<Double, Color>) value;
@SuppressWarnings("unchecked")
- Class<? extends CyTableEntry> type = (Class<? extends
CyTableEntry>) mapping.getVisualProperty()
+ Class<? extends CyIdentifiable> type = (Class<? extends
CyIdentifiable>) mapping.getVisualProperty()
.getTargetDataType();
final CyTable attr =
manager.getTable(appManager.getCurrentNetwork(), type, CyNetwork.DEFAULT_ATTRS);
this.editorPanel = new
GradientEditorPanel(selectedManager.getCurrentVisualStyle(), mapping, attr,
appManager,
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/propertyeditor/AttributeComboBoxPropertyEditor.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/propertyeditor/AttributeComboBoxPropertyEditor.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/propertyeditor/AttributeComboBoxPropertyEditor.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -12,7 +12,7 @@
import org.cytoscape.application.events.SetCurrentNetworkViewEvent;
import org.cytoscape.application.events.SetCurrentNetworkViewListener;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.vizmap.gui.editor.ListEditor;
import org.cytoscape.view.vizmap.gui.internal.AttributeSet;
@@ -31,11 +31,11 @@
private static final Logger logger =
LoggerFactory.getLogger(AttributeComboBoxPropertyEditor.class);
- private final Class<? extends CyTableEntry> type;
+ private final Class<? extends CyIdentifiable> type;
private final AttributeSetManager attrManager;
- public AttributeComboBoxPropertyEditor(final Class<? extends
CyTableEntry> type,
+ public AttributeComboBoxPropertyEditor(final Class<? extends
CyIdentifiable> type,
final AttributeSetManager attrManager, final
CyApplicationManager appManager) {
super();
this.attrManager = attrManager;
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/event/CellEditorEventHandler.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/event/CellEditorEventHandler.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/event/CellEditorEventHandler.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -38,7 +38,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkTableManager;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.model.VisualProperty;
import org.cytoscape.view.model.Visualizable;
import org.cytoscape.view.vizmap.VisualMappingFunction;
@@ -249,7 +249,7 @@
* Ignore if not compatible.
*/
@SuppressWarnings("unchecked")
- Class<? extends CyTableEntry> type = (Class<? extends
CyTableEntry>) editor.getTargetObjectType();
+ Class<? extends CyIdentifiable> type = (Class<? extends
CyIdentifiable>) editor.getTargetObjectType();
final CyTable attrForTest =
tableMgr.getTable(applicationManager.getCurrentNetwork(), type,
CyNetwork.DEFAULT_ATTRS);
final Class<K> dataType =
(Class<K>)attrForTest.getColumn(ctrAttrName).getType();
@@ -307,7 +307,7 @@
+ newMapping.getMappingColumnName() + ", "
+ vp.getDisplayName());
- final VisualProperty<Visualizable> category =
util.getCategory((Class<? extends CyTableEntry>) vp.getTargetDataType());
+ final VisualProperty<Visualizable> category =
util.getCategory((Class<? extends CyIdentifiable>) vp.getTargetDataType());
VizMapperProperty<VisualProperty<V>, String, ?> newRootProp =
vizMapPropertySheetBuilder
.getPropertyBuilder().buildProperty(newMapping,
category.getDisplayName(),
propertySheetPanel, factory);
@@ -335,7 +335,7 @@
// This is the currently selected Visual Style.
final VisualStyle style = manager.getCurrentVisualStyle();
- final VisualProperty<Visualizable> startVP =
util.getCategory((Class<? extends CyTableEntry>) vp.getTargetDataType());
+ final VisualProperty<Visualizable> startVP =
util.getCategory((Class<? extends CyIdentifiable>) vp.getTargetDataType());
final VisualMappingFunction<?, ?> currentMapping =
style.getVisualMappingFunction(vp);
logger.debug("Current Mapping for " + vp.getDisplayName() + "
is: " + currentMapping);
@@ -348,7 +348,7 @@
// Mapping does not exist. Need to create new one.
final AttributeSet attrSet =
attrManager.getAttributeSet(applicationManager.getCurrentNetwork(),
- (Class<? extends CyTableEntry>)
vp.getTargetDataType());
+ (Class<? extends CyIdentifiable>)
vp.getTargetDataType());
final Class<?> attributeDataType =
attrSet.getAttrMap().get(controllingAttrName);
if (factory.getMappingFunctionType() ==
ContinuousMapping.class) {
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/util/VizMapperUtil.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/util/VizMapperUtil.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/util/VizMapperUtil.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -13,7 +13,7 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.model.VisualLexicon;
import org.cytoscape.view.model.VisualProperty;
import org.cytoscape.view.model.Visualizable;
@@ -29,9 +29,9 @@
*/
public class VizMapperUtil {
- private static final Map<Class<? extends CyTableEntry>,
VisualProperty<Visualizable>> TARGET_TYPE_MAP;
+ private static final Map<Class<? extends CyIdentifiable>,
VisualProperty<Visualizable>> TARGET_TYPE_MAP;
static {
- TARGET_TYPE_MAP = new HashMap<Class<? extends CyTableEntry>,
VisualProperty<Visualizable>>();
+ TARGET_TYPE_MAP = new HashMap<Class<? extends CyIdentifiable>,
VisualProperty<Visualizable>>();
TARGET_TYPE_MAP.put(CyNode.class, BasicVisualLexicon.NODE);
TARGET_TYPE_MAP.put(CyEdge.class, BasicVisualLexicon.EDGE);
TARGET_TYPE_MAP.put(CyNetwork.class,
BasicVisualLexicon.NETWORK);
@@ -94,7 +94,7 @@
}
}
- public VisualProperty<Visualizable> getCategory(Class<? extends
CyTableEntry> targetDataType) {
+ public VisualProperty<Visualizable> getCategory(Class<? extends
CyIdentifiable> targetDataType) {
return TARGET_TYPE_MAP.get(targetDataType);
}
Modified:
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/AbstractApplyHandler.java
===================================================================
---
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/AbstractApplyHandler.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/AbstractApplyHandler.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -2,7 +2,7 @@
import java.util.Collection;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.model.View;
import org.cytoscape.view.model.VisualProperty;
import org.cytoscape.view.vizmap.VisualMappingFunction;
@@ -19,7 +19,7 @@
}
- protected void applyValues(final View<? extends CyTableEntry> view,
final Collection<VisualProperty<?>> vps) {
+ protected void applyValues(final View<? extends CyIdentifiable> view,
final Collection<VisualProperty<?>> vps) {
for (VisualProperty<?> vp : vps) {
// check mapping exists or not
@@ -39,7 +39,7 @@
}
}
- protected void applyMappedValue(final View<? extends CyTableEntry>
nodeView, final VisualProperty<?> vp,
+ protected void applyMappedValue(final View<? extends CyIdentifiable>
nodeView, final VisualProperty<?> vp,
final VisualMappingFunction<?, ?> mapping) {}
}
Modified:
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/ApplyToEdgeHandler.java
===================================================================
---
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/ApplyToEdgeHandler.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/ApplyToEdgeHandler.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -5,7 +5,7 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.model.View;
import org.cytoscape.view.model.VisualProperty;
import org.cytoscape.view.vizmap.VisualMappingFunction;
@@ -28,7 +28,7 @@
* {@inheritDoc}
*/
@Override
- protected void applyMappedValue(final View<? extends CyTableEntry>
edgeView, final VisualProperty<?> vp,
+ protected void applyMappedValue(final View<? extends CyIdentifiable>
edgeView, final VisualProperty<?> vp,
final VisualMappingFunction<?, ?> mapping) {
final View<CyEdge> view = (View<CyEdge>) edgeView;
Modified:
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/ApplyToNetworkHandler.java
===================================================================
---
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/ApplyToNetworkHandler.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/ApplyToNetworkHandler.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -6,7 +6,7 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
import org.cytoscape.view.model.VisualProperty;
@@ -67,7 +67,7 @@
final CyNetwork net = networkView.getModel();
for (View<?> v : views) {
- View<? extends CyTableEntry> view = (View<?
extends CyTableEntry>) v;
+ View<? extends CyIdentifiable> view = (View<?
extends CyIdentifiable>) v;
mapping.apply(net.getRow(view.getModel()),
view);
if (view.getVisualProperty(vp) == vpDefault)
Modified:
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/ApplyToNodeHandler.java
===================================================================
---
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/ApplyToNodeHandler.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/ApplyToNodeHandler.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -4,7 +4,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.model.View;
import org.cytoscape.view.model.VisualProperty;
import org.cytoscape.view.vizmap.VisualMappingFunction;
@@ -30,7 +30,7 @@
* @param vp
*/
@Override
- protected void applyMappedValue(final View<? extends CyTableEntry>
nodeView, final VisualProperty<?> vp,
+ protected void applyMappedValue(final View<? extends CyIdentifiable>
nodeView, final VisualProperty<?> vp,
final VisualMappingFunction<?, ?> mapping) {
final View<CyNode> view = (View<CyNode>) nodeView;
Modified:
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleImpl.java
===================================================================
---
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleImpl.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleImpl.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -41,7 +41,7 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
import org.cytoscape.view.model.VisualProperty;
@@ -63,7 +63,7 @@
private final VisualLexiconManager lexManager;
- private final Map<Class<? extends CyTableEntry>, ApplyHandler>
applyHandlersMap;
+ private final Map<Class<? extends CyIdentifiable>, ApplyHandler>
applyHandlersMap;
private String title;
@@ -88,7 +88,7 @@
styleDefaults = new HashMap<VisualProperty<?>, Object>();
// Init Apply handlers for node, egde and network.
- this.applyHandlersMap = new HashMap<Class<? extends
CyTableEntry>, ApplyHandler>();
+ this.applyHandlersMap = new HashMap<Class<? extends
CyIdentifiable>, ApplyHandler>();
applyHandlersMap.put(CyNetwork.class, new
ApplyToNetworkHandler(this, lexManager));
applyHandlersMap.put(CyNode.class, new ApplyToNodeHandler(this,
lexManager));
applyHandlersMap.put(CyEdge.class, new ApplyToEdgeHandler(this,
lexManager));
@@ -143,7 +143,7 @@
* {@inheritDoc}
*/
@Override
- public void apply(final View<? extends CyTableEntry> view) {
+ public void apply(final View<? extends CyIdentifiable> view) {
if (view == null) {
logger.warn("Tried to apply Visual Style to null view");
return;
@@ -171,7 +171,7 @@
// * {@inheritDoc}
// */
// @Override
-// public void apply(final View<? extends CyTableEntry> view) {
+// public void apply(final View<? extends CyIdentifiable> view) {
// if (view == null) {
// logger.warn("Tried to apply Visual Style to null view");
// return;
@@ -211,7 +211,7 @@
final CyNetwork net = networkView.getModel();
for (View<?> v : views) {
- View<? extends CyTableEntry> view = (View<?
extends CyTableEntry>)v;
+ View<? extends CyIdentifiable> view = (View<?
extends CyIdentifiable>)v;
mapping.apply( net.getRow( view.getModel() ),
view);
if (view.getVisualProperty(vp) == vpDefault)
Modified:
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/ContinuousMappingImpl.java
===================================================================
---
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/ContinuousMappingImpl.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/ContinuousMappingImpl.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -37,7 +37,7 @@
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.model.View;
import org.cytoscape.view.model.VisualProperty;
import
org.cytoscape.view.vizmap.internal.mappings.interpolators.FlatInterpolator;
@@ -142,7 +142,7 @@
* @see
org.cytoscape.view.vizmap.mappings.ContinuousMapping#apply(org.cytoscape.view.model.View)
*/
@Override
- public void apply(final CyRow row, final View<? extends CyTableEntry>
view) {
+ public void apply(final CyRow row, final View<? extends CyIdentifiable>
view) {
if (row == null)
return;
@@ -171,7 +171,7 @@
* @param <V>
* the type-parameter of the View
*/
- private void doMap(final CyRow row, final View<? extends CyTableEntry>
view) {
+ private void doMap(final CyRow row, final View<? extends
CyIdentifiable> view) {
if (row.isSet(attrName)) {
// skip Views where source attribute is not defined;
Modified:
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/DiscreteMappingImpl.java
===================================================================
---
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/DiscreteMappingImpl.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/DiscreteMappingImpl.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -36,7 +36,7 @@
import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.model.View;
import org.cytoscape.view.model.VisualProperty;
import org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction;
@@ -79,7 +79,7 @@
* @see
org.cytoscape.view.vizmap.mappings.DiscreteMapping#apply(org.cytoscape.view.model.View)
*/
@Override
- public void apply(CyRow row, View<? extends CyTableEntry> view) {
+ public void apply(CyRow row, View<? extends CyIdentifiable> view) {
if ( row == null )
return;
@@ -105,11 +105,11 @@
* @param <V>
* the type-parameter of the View
*/
- private void applyDiscreteMapping(final CyRow row, final View<? extends
CyTableEntry> view) {
+ private void applyDiscreteMapping(final CyRow row, final View<? extends
CyIdentifiable> view) {
V value = null;
- if(attrName.equals(CyTableEntry.SUID)) {
+ if(attrName.equals(CyIdentifiable.SUID)) {
// Special case: SUID
Object key = Long.valueOf(view.getModel().getSUID());
if (key != null)
Modified:
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/PassthroughMappingImpl.java
===================================================================
---
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/PassthroughMappingImpl.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/PassthroughMappingImpl.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -33,7 +33,7 @@
import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.model.View;
import org.cytoscape.view.model.VisualProperty;
import org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction;
@@ -66,14 +66,14 @@
* @see
org.cytoscape.view.vizmap.mappings.PassthroughMapping#apply(org.cytoscape.view.model.View)
*/
@Override
- public void apply(final CyRow row, final View<? extends CyTableEntry>
view) {
+ public void apply(final CyRow row, final View<? extends CyIdentifiable>
view) {
if ( row == null )
return;
if (view == null)
return; // empty list, nothing to do
- if(attrName.equals(CyTableEntry.SUID)) {
+ if(attrName.equals(CyIdentifiable.SUID)) {
// Special case: SUID
view.setVisualProperty(vp,
(V)Long.valueOf(view.getModel().getSUID()));
} else if (row.isSet(attrName)) {
Modified:
core3/impl/trunk/webservice-impl/src/main/java/org/cytoscape/webservice/internal/task/WebServiceContextMenuTask.java
===================================================================
---
core3/impl/trunk/webservice-impl/src/main/java/org/cytoscape/webservice/internal/task/WebServiceContextMenuTask.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/webservice-impl/src/main/java/org/cytoscape/webservice/internal/task/WebServiceContextMenuTask.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -1,11 +1,11 @@
package org.cytoscape.webservice.internal.task;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.model.View;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
-public class WebServiceContextMenuTask<T extends CyTableEntry> extends
AbstractTask {
+public class WebServiceContextMenuTask<T extends CyIdentifiable> extends
AbstractTask {
private final View<T> view;
Modified:
core3/impl/trunk/webservice-impl/src/main/java/org/cytoscape/webservice/internal/ui/WebServiceContextMenuManager.java
===================================================================
---
core3/impl/trunk/webservice-impl/src/main/java/org/cytoscape/webservice/internal/ui/WebServiceContextMenuManager.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/webservice-impl/src/main/java/org/cytoscape/webservice/internal/ui/WebServiceContextMenuManager.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -39,7 +39,7 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.model.View;
@@ -80,7 +80,7 @@
addMenu(edgeView, menu);
}
- private void addMenu(View<? extends CyTableEntry> view, JPopupMenu
menu) {
+ private void addMenu(View<? extends CyIdentifiable> view, JPopupMenu
menu) {
if (menu == null)
menu = new JPopupMenu();
else {
Modified:
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/ImportTableTask.java
===================================================================
---
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/ImportTableTask.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/ImportTableTask.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -15,7 +15,7 @@
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.webservice.ncbi.rest.EntrezRestClient;
import org.cytoscape.webservice.ncbi.ui.AnnotationCategory;
import org.slf4j.Logger;
@@ -23,6 +23,7 @@
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
+import org.cytoscape.model.CyNetwork;
public class ImportTableTask implements Callable<Double> {
@@ -148,7 +149,7 @@
// Create row
final CyRow row = table.getRow(geneID);
- row.set(CyTableEntry.NAME, geneID);
+ row.set(CyNetwork.NAME, geneID);
// First, extract general information. This will be imported
always.
Modified:
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/rest/EntrezRestClient.java
===================================================================
---
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/rest/EntrezRestClient.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/rest/EntrezRestClient.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -24,7 +24,7 @@
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.model.CyTableManager;
import org.cytoscape.webservice.ncbi.ImportTableTask;
@@ -166,7 +166,7 @@
logger.debug("Table Import Executor initialized.");
final Date currentDate = new Date();
final CyTable table = tableFactory.createTable("NCBI Global
Table: " + currentDate.toString(),
- CyTableEntry.NAME, String.class, true, true);
+ CyNetwork.NAME, String.class, true, true);
int group = 0;
int buketNum = 10;
Modified:
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/rest/ImportNetworkTask.java
===================================================================
---
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/rest/ImportNetworkTask.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/rest/ImportNetworkTask.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -17,7 +17,7 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.work.TaskMonitor;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -78,7 +78,7 @@
// This is the center of spokes
final CyNode centerNode = network.addNode();
- network.getRow(centerNode).set(CyTableEntry.NAME, geneIDString);
+ network.getRow(centerNode).set(CyNetwork.NAME, geneIDString);
this.nodeName2CyNodeMap.put(geneIDString, centerNode);
final NodeList ids =
result.getElementsByTagName("Gene-commentary");
@@ -154,14 +154,14 @@
nodeName2CyNodeMap.put(id,
targetNode);
}
-
network.getRow(targetNode).set(CyTableEntry.NAME, id);
+
network.getRow(targetNode).set(CyNetwork.NAME, id);
logger.debug("New Node Name = " + id);
final CyEdge newEdge =
network.addEdge(centerNode, targetNode, false);
network.getRow(newEdge).set(
- CyTableEntry.NAME,
-
network.getRow(centerNode).get(CyTableEntry.NAME, String.class) + " ("
+ CyNetwork.NAME,
+
network.getRow(centerNode).get(CyNetwork.NAME, String.class) + " ("
+
processor.getInteractionType() + ") "
- +
network.getRow(targetNode).get(CyTableEntry.NAME, String.class));
+ +
network.getRow(targetNode).get(CyNetwork.NAME, String.class));
}
}
}
Modified:
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/task/ImportNetworkFromGeneTask.java
===================================================================
---
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/task/ImportNetworkFromGeneTask.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/task/ImportNetworkFromGeneTask.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -6,7 +6,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyNetworkManager;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.model.CyTableManager;
import org.cytoscape.webservice.ncbi.rest.EntrezRestClient;
@@ -61,7 +61,7 @@
newNetwork = restClient.importNetwork(searchResult,
taskMonitor);
// Register it
- newNetwork.getRow(newNetwork).set(CyTableEntry.NAME, "NCBI");
+ newNetwork.getRow(newNetwork).set(CyNetwork.NAME, "NCBI");
manager.addNetwork(newNetwork);
}
Modified:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/mapper/Mitab25Mapper.java
===================================================================
---
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/mapper/Mitab25Mapper.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/mapper/Mitab25Mapper.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -9,7 +9,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
/**
* Map minimal set of information from MITAB25.
@@ -96,14 +96,14 @@
source = nodeMap.get(sourceID[0]);
if(source == null) {
source = network.addNode();
- network.getRow(source).set(CyTableEntry.NAME,
sourceIDHalf);
+ network.getRow(source).set(CyNetwork.NAME,
sourceIDHalf);
network.getRow(source).set(DATABASE_UNIQUE_ID,
sourceID[0]);
nodeMap.put(sourceID[0], source);
}
target = nodeMap.get(targetID[0]);
if (target == null) {
target = network.addNode();
- network.getRow(target).set(CyTableEntry.NAME,
targetIDHalf);
+ network.getRow(target).set(CyNetwork.NAME,
targetIDHalf);
network.getRow(target).set(DATABASE_UNIQUE_ID,
targetID[0]);
nodeMap.put(targetID[0], target);
}
@@ -134,9 +134,9 @@
interactionType = entry[11].split(SEPARATOR);
e = network.addEdge(source, target, true);
network.getRow(e).set(
- CyTableEntry.NAME,
- network.getRow(source).get(CyTableEntry.NAME,
String.class) + " (" + interactionID[0] + ") "
- +
network.getRow(target).get(CyTableEntry.NAME, String.class));
+ CyNetwork.NAME,
+ network.getRow(source).get(CyNetwork.NAME,
String.class) + " (" + interactionID[0] + ") "
+ +
network.getRow(target).get(CyNetwork.NAME, String.class));
network.getRow(e).set(CyEdge.INTERACTION, interactionID[0]);
// setEdgeListAttribute(edgeAttr, e.getIdentifier(),
interactionType, INTERACTION_TYPE);
Modified:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/task/ImportNetworkFromPSICQUICTask.java
===================================================================
---
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/task/ImportNetworkFromPSICQUICTask.java
2012-03-26 23:26:20 UTC (rev 28657)
+++
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/task/ImportNetworkFromPSICQUICTask.java
2012-03-26 23:26:59 UTC (rev 28658)
@@ -11,7 +11,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.task.NetworkTaskFactory;
import org.cytoscape.webservice.psicquic.PSICQUICRestClient;
import org.cytoscape.webservice.psicquic.PSICQUICRestClient.SearchMode;
@@ -107,7 +107,7 @@
final Set<CyNetwork> networks = new HashSet<CyNetwork>();
for (String sourceURL : result.keySet()) {
final CyNetwork network = result.get(sourceURL);
- network.getRow(network).set(CyTableEntry.NAME,
registryManager.getSource2NameMap().get(sourceURL) + " " + suffix);
+ network.getRow(network).set(CyNetwork.NAME,
registryManager.getSource2NameMap().get(sourceURL) + " " + suffix);
addNetworkData(network);
manager.addNetwork(network);
networks.add(network);
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