Author: pwang
Date: 2012-03-26 16:20:35 -0700 (Mon, 26 Mar 2012)
New Revision: 28653
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/DisplayBioPaxXmlTask.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/AttributeUtil.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxVisualStyleUtil.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxDetailsPanel.java
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/ViewNetworkNeighborhoodTask.java
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/cytoscape/BinarySifVisualStyleUtil.java
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/GetParentInteractions.java
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/MergeNetworkTask.java
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/AttributeUtil.java
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/BioPaxUtil.java
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/SelectUtil.java
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DGraphView.java
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/FlagAndSelectionHandler.java
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/AddNodeTask.java
Log:
Fixed bug#810
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
2012-03-26 22:26:13 UTC (rev 28652)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
2012-03-26 23:20:35 UTC (rev 28653)
@@ -192,7 +192,7 @@
AttributeUtil.set(network, network,
BioPaxMapper.BIOPAX_NETWORK, Boolean.TRUE, Boolean.class);
// default Quick Find Index
- AttributeUtil.set(network, network, "quickfind.default_index",
CyNode.NAME, String.class);
+ AttributeUtil.set(network, network, "quickfind.default_index",
CyNetwork.NAME, String.class);
// (converted to L3, processed) RDF/XML data
ByteArrayOutputStream baos = new ByteArrayOutputStream();
@@ -706,7 +706,7 @@
setChemicalModificationAttributes(network, node,
chemicalModificationsWrapper);
}
// update the name (also used for node's label and quick find)
- AttributeUtil.set(network, node, CyNode.NAME, name,
String.class);
+ AttributeUtil.set(network, node, CyNetwork.NAME, name,
String.class);
// traverse to create the rest of attr.
bpeAutoMapper.traverse(element, model);
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/DisplayBioPaxXmlTask.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/DisplayBioPaxXmlTask.java
2012-03-26 22:26:13 UTC (rev 28652)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/DisplayBioPaxXmlTask.java
2012-03-26 23:20:35 UTC (rev 28653)
@@ -7,6 +7,7 @@
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.biopax.internal.util.BioPaxUtil;
import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyRow;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
@@ -36,7 +37,7 @@
CyNode node = nodeView.getModel();
CyRow row = networkView.getModel().getRow(node);
String owlxml = row.get(BioPaxUtil.BIOPAX_DATA, String.class);
- String label = row.get(CyNode.NAME, String.class);
+ String label = row.get(CyNetwork.NAME, String.class);
Component component = cySwingApplication.getJFrame();
JOptionPane.showMessageDialog(component, owlxml, label,
JOptionPane.PLAIN_MESSAGE);
}
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/AttributeUtil.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/AttributeUtil.java
2012-03-26 22:26:13 UTC (rev 28652)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/AttributeUtil.java
2012-03-26 23:20:35 UTC (rev 28653)
@@ -6,16 +6,16 @@
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.model.CyNetwork;
public class AttributeUtil {
- public static void set(CyNetwork network, CyTableEntry entry, String
name, Object value, Class<?> type) {
+ public static void set(CyNetwork network, CyIdentifiable entry, String
name, Object value, Class<?> type) {
set(network, entry, null, name, value, type);
}
- public static void copyAttributes(CyNetwork network, CyTableEntry
source, CyTableEntry target) {
+ public static void copyAttributes(CyNetwork network, CyIdentifiable
source, CyIdentifiable target) {
CyRow sourceRow = network.getRow(source);
for (Entry<String, Object> entry :
sourceRow.getAllValues().entrySet()) {
String key = entry.getKey();
@@ -32,7 +32,7 @@
}
- public static void set(CyNetwork network, CyTableEntry entry, String
tableName, String name, Object value, Class<?> type) {
+ public static void set(CyNetwork network, CyIdentifiable entry, String
tableName, String name, Object value, Class<?> type) {
CyRow row = (tableName==null) ? network.getRow(entry) :
network.getRow(entry,tableName);
CyTable table = row.getTable();
CyColumn column = table.getColumn(name);
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxVisualStyleUtil.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxVisualStyleUtil.java
2012-03-26 22:26:13 UTC (rev 28652)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxVisualStyleUtil.java
2012-03-26 23:20:35 UTC (rev 28653)
@@ -42,7 +42,7 @@
import org.biopax.paxtools.model.level3.ControlType;
import org.biopax.paxtools.model.level3.Interaction;
import org.biopax.paxtools.model.level3.PhysicalEntity;
-import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyNetwork;
import org.cytoscape.view.presentation.property.ArrowShapeVisualProperty;
import org.cytoscape.view.presentation.property.BasicVisualLexicon;
import org.cytoscape.view.presentation.property.NodeShapeVisualProperty;
@@ -266,7 +266,7 @@
private void createNodeLabel(VisualStyle style) {
// create pass through mapper for node labels
style.addVisualMappingFunction(passthroughFactory
- .createVisualMappingFunction(CyNode.NAME,
String.class, null,
+ .createVisualMappingFunction(CyNetwork.NAME,
String.class, null,
BasicVisualLexicon.NODE_LABEL));
}
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxDetailsPanel.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxDetailsPanel.java
2012-03-26 22:26:13 UTC (rev 28652)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxDetailsPanel.java
2012-03-26 23:20:35 UTC (rev 28653)
@@ -169,7 +169,7 @@
CyRow row = network.getRow(node);
// name
- stringRef = row.get(CyNode.NAME, String.class);
+ stringRef = row.get(CyNetwork.NAME, String.class);
buf.append("<h2>" + stringRef + "</h2>");
// type (to the text buffer)
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/ViewNetworkNeighborhoodTask.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/ViewNetworkNeighborhoodTask.java
2012-03-26 22:26:13 UTC (rev 28652)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/ViewNetworkNeighborhoodTask.java
2012-03-26 23:20:35 UTC (rev 28653)
@@ -45,7 +45,7 @@
CyRow nodeRow = network.getRow(cyNode);
String biopaxID = nodeRow.get(BioPaxUtil.BIOPAX_RDF_ID, String.class);
biopaxID = biopaxID.replace("CPATH-", "");
- String neighborhoodParam = "Neighborhood: " + nodeRow.get(CyNode.NAME,
String.class);
+ String neighborhoodParam = "Neighborhood: " +
nodeRow.get(CyNetwork.NAME, String.class);
// encode some parts of the url
try {
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/cytoscape/BinarySifVisualStyleUtil.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/cytoscape/BinarySifVisualStyleUtil.java
2012-03-26 22:26:13 UTC (rev 28652)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/cytoscape/BinarySifVisualStyleUtil.java
2012-03-26 23:20:35 UTC (rev 28653)
@@ -16,6 +16,7 @@
import org.cytoscape.view.vizmap.VisualStyle;
import org.cytoscape.view.vizmap.VisualStyleFactory;
import org.cytoscape.view.vizmap.mappings.DiscreteMapping;
+import org.cytoscape.model.CyNetwork;
/**
* Binary SIF Visual Style.
@@ -170,7 +171,7 @@
private void createNodeLabel(VisualStyle style) {
// create pass through mapper for node labels
style.addVisualMappingFunction(passthroughFactory
- .createVisualMappingFunction(CyNode.NAME,
String.class, null,
+ .createVisualMappingFunction(CyNetwork.NAME,
String.class, null,
BasicVisualLexicon.NODE_LABEL));
}
}
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
2012-03-26 22:26:13 UTC (rev 28652)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
2012-03-26 23:20:35 UTC (rev 28653)
@@ -253,7 +253,7 @@
final CyNetwork cyNetwork = view.getModel();
// Set the Quick Find Default Index
- AttributeUtil.set(cyNetwork, cyNetwork,
"quickfind.default_index", CyNode.NAME, String.class);
+ AttributeUtil.set(cyNetwork, cyNetwork,
"quickfind.default_index", CyNetwork.NAME, String.class);
// Specify that this is a BINARY_NETWORK
AttributeUtil.set(cyNetwork, cyNetwork, "BIOPAX_NETWORK",
Boolean.TRUE, Boolean.class);
@@ -352,13 +352,13 @@
for (CyNode node : cyNetwork.getNodeList()) {
CyNode newNode = mergedNetwork.addNode();
AttributeUtil.copyAttributes(mergedNetwork, node,
newNode);
- String name = cyNetwork.getRow(node).get(CyNode.NAME,
String.class);
+ String name =
cyNetwork.getRow(node).get(CyNetwork.NAME, String.class);
nodes.put(name, newNode);
}
Set<CyEdge> edges = new HashSet<CyEdge>();
for (CyEdge edge : cyNetwork.getEdgeList()) {
- String sourceName =
cyNetwork.getRow(edge.getSource()).get(CyNode.NAME, String.class);
- String targetName =
cyNetwork.getRow(edge.getTarget()).get(CyNode.NAME, String.class);
+ String sourceName =
cyNetwork.getRow(edge.getSource()).get(CyNetwork.NAME, String.class);
+ String targetName =
cyNetwork.getRow(edge.getTarget()).get(CyNetwork.NAME, String.class);
CyNode source = nodes.get(sourceName);
CyNode target = nodes.get(targetName);
CyEdge newEdge = mergedNetwork.addEdge(source, target,
true);
@@ -420,7 +420,7 @@
Map<String, CyNode> nodes = new HashMap<String,
CyNode>();
for (int j = 0; j < currentList.size(); j++) {
CyNode node = currentList.get(j);
- String name =
cyNetwork.getRow(node).get(CyNode.NAME, String.class);
+ String name =
cyNetwork.getRow(node).get(CyNetwork.NAME, String.class);
// 'name' is actually a CPATH-ID (for SIF
imports)
nodes.put(name, node);
ids[j] = Long.valueOf(name);
@@ -475,7 +475,7 @@
int counter = 0;
for (CyNode node : cyNetwork.getNodeList()) {
CyRow row = cyNetwork.getRow(node);
- String label = row.get(CyNode.NAME, String.class);
+ String label = row.get(CyNetwork.NAME, String.class);
if (label != null) {
currentList.add(node);
counter++;
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/GetParentInteractions.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/GetParentInteractions.java
2012-03-26 22:26:13 UTC (rev 28652)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/GetParentInteractions.java
2012-03-26 23:20:35 UTC (rev 28653)
@@ -28,7 +28,7 @@
public GetParentInteractions (CyNetwork network, CyNode node,
CPath2Factory factory) {
// TODO: Debug, investigate this cPath1 (Pathway Commons, BioPAX Level2
webservice specific code...)
- String cpathId = network.getRow(node).get(CyNode.NAME, String.class);
// TODO actually, - must be from "shared name" virtual attr. column
+ String cpathId = network.getRow(node).get(CyNetwork.NAME,
String.class); // TODO actually, - must be from "shared name" virtual attr.
column
// this.cpathId = node.getSUID();
this.cpathId = Integer.parseInt(cpathId); //well, well
this.node = node;
@@ -54,7 +54,7 @@
CySwingApplication application = factory.getCySwingApplication();
JDialog dialog = new JDialog(application.getJFrame());
- String nodeLabel = network.getRow(node).get(CyNode.NAME,
String.class);
+ String nodeLabel = network.getRow(node).get(CyNetwork.NAME,
String.class);
if (nodeLabel != null) {
dialog.setTitle(nodeLabel);
} else {
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/MergeNetworkTask.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/MergeNetworkTask.java
2012-03-26 22:26:13 UTC (rev 28652)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/MergeNetworkTask.java
2012-03-26 23:20:35 UTC (rev 28653)
@@ -121,12 +121,12 @@
for (CyNode node : network.getNodeList()) {
CyNode mergedNode = mergedNetwork.addNode();
AttributeUtil.copyAttributes(mergedNetwork, node, mergedNode);
- String name = network.getRow(mergedNode).get(CyNode.NAME,
String.class);
+ String name = network.getRow(mergedNode).get(CyNetwork.NAME,
String.class);
newNodes.put(name, mergedNode);
}
for (CyEdge edge : network.getEdgeList()) {
- String sourceName =
network.getRow(edge.getSource()).get(CyNode.NAME, String.class);
- String targetName =
network.getRow(edge.getTarget()).get(CyNode.NAME, String.class);
+ String sourceName =
network.getRow(edge.getSource()).get(CyNetwork.NAME, String.class);
+ String targetName =
network.getRow(edge.getTarget()).get(CyNetwork.NAME, String.class);
CyNode source = newNodes.get(sourceName);
CyNode target = newNodes.get(targetName);
CyEdge mergedEdge = mergedNetwork.addEdge(source, target, true);
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/AttributeUtil.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/AttributeUtil.java
2012-03-26 22:26:13 UTC (rev 28652)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/AttributeUtil.java
2012-03-26 23:20:35 UTC (rev 28653)
@@ -6,16 +6,16 @@
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.model.CyNetwork;
public class AttributeUtil {
- public static void set(CyNetwork network, CyTableEntry entry, String
name, Object value, Class<?> type) {
+ public static void set(CyNetwork network, CyIdentifiable entry, String
name, Object value, Class<?> type) {
set(network, entry, null, name, value, type);
}
- public static void copyAttributes(CyNetwork network, CyTableEntry
source, CyTableEntry target) {
+ public static void copyAttributes(CyNetwork network, CyIdentifiable
source, CyIdentifiable target) {
CyRow sourceRow = network.getRow(source);
for (Entry<String, Object> entry :
sourceRow.getAllValues().entrySet()) {
String key = entry.getKey();
@@ -32,7 +32,7 @@
}
- public static void set(CyNetwork network, CyTableEntry entry, String
tableName, String name, Object value, Class<?> type) {
+ public static void set(CyNetwork network, CyIdentifiable entry, String
tableName, String name, Object value, Class<?> type) {
CyRow row = (tableName==null) ? network.getRow(entry) :
network.getRow(entry,tableName);
CyTable table = row.getTable();
CyColumn column = table.getColumn(name);
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/BioPaxUtil.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/BioPaxUtil.java
2012-03-26 22:26:13 UTC (rev 28652)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/BioPaxUtil.java
2012-03-26 23:20:35 UTC (rev 28653)
@@ -724,7 +724,7 @@
setChemicalModificationAttributes(network, node,
chemicalModificationsWrapper);
}
// update the name (also used for node's label and quick find)
- AttributeUtil.set(network, node, CyNode.NAME, name,
String.class);
+ AttributeUtil.set(network, node, CyNetwork.NAME, name,
String.class);
// traverse to create the rest of attr.
bpeAutoMapper.traverse(element, null);
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/SelectUtil.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/SelectUtil.java
2012-03-26 22:26:13 UTC (rev 28652)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/SelectUtil.java
2012-03-26 23:20:35 UTC (rev 28653)
@@ -8,7 +8,7 @@
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;
public class SelectUtil {
public static void unselectAllNodes(CyNetwork network) {
@@ -27,8 +27,8 @@
setSelectedState(network, list, selected);
}
- static void setSelectedState(CyNetwork network, Collection<? extends
CyTableEntry> list, Boolean selected) {
- for (CyTableEntry edge : list) {
+ static void setSelectedState(CyNetwork network, Collection<? extends
CyIdentifiable> list, Boolean selected) {
+ for (CyIdentifiable edge : list) {
CyRow row = network.getRow(edge);
row.set(CyNetwork.SELECTED, selected);
}
@@ -43,7 +43,7 @@
return getSelected(cyNetwork, cyNetwork.getEdgeList());
}
- static <T extends CyTableEntry> Set<T> getSelected(CyNetwork network,
Collection<T> items) {
+ static <T extends CyIdentifiable> Set<T> getSelected(CyNetwork network,
Collection<T> items) {
Set<T> entries = new HashSet<T>();
for (T item : items) {
CyRow row = network.getRow(item);
@@ -62,7 +62,7 @@
selectAll(cyNetwork, cyNetwork.getEdgeList());
}
- static <T extends CyTableEntry> void selectAll(CyNetwork network,
Collection<T> items) {
+ static <T extends CyIdentifiable> void selectAll(CyNetwork network,
Collection<T> items) {
for (T item : items) {
CyRow row = network.getRow(item);
if (!row.get(CyNetwork.SELECTED, Boolean.class)) {
@@ -79,7 +79,7 @@
return countSelected(cyNetwork,cyNetwork.getNodeList());
}
- static <T extends CyTableEntry> int countSelected(CyNetwork
network,Collection<T> items) {
+ static <T extends CyIdentifiable> int countSelected(CyNetwork
network,Collection<T> items) {
int count = 0;
for (T item : items) {
CyRow row = network.getRow(item);
Modified:
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DGraphView.java
===================================================================
---
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DGraphView.java
2012-03-26 22:26:13 UTC (rev 28652)
+++
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DGraphView.java
2012-03-26 23:20:35 UTC (rev 28653)
@@ -95,7 +95,7 @@
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.CyTableFactory;
import org.cytoscape.model.events.AboutToRemoveEdgesEvent;
import org.cytoscape.model.events.AboutToRemoveEdgesListener;
@@ -462,11 +462,11 @@
this.menuTaskManager = menuTaskManager;
this.cyEventHelper = cyEventHelper;
- final CyTable nodeCAM = dataFactory.createTable("node view",
CyTableEntry.SUID, Long.class, false, false);
+ final CyTable nodeCAM = dataFactory.createTable("node view",
CyIdentifiable.SUID, Long.class, false, false);
nodeCAM.createColumn("hidden", Boolean.class, false);
tableMgr.setTable(model, CyNode.class, "VIEW", nodeCAM);
- final CyTable edgeCAM = dataFactory.createTable("edge view",
CyTableEntry.SUID, Long.class, false, false);
+ final CyTable edgeCAM = dataFactory.createTable("edge view",
CyIdentifiable.SUID, Long.class, false, false);
edgeCAM.createColumn("hidden", Boolean.class, false);
tableMgr.setTable(model, CyEdge.class, "VIEW", edgeCAM);
@@ -498,7 +498,7 @@
logger.debug("Phase 2: Canvas created: time = "
+ (System.currentTimeMillis() - start));
- this.title = model.getRow(model).get(CyTableEntry.NAME,
String.class);
+ this.title = model.getRow(model).get(CyNetwork.NAME,
String.class);
// Create view model / presentations for the graph
for (final CyNode nn : model.getNodeList())
@@ -2836,8 +2836,8 @@
}
@Override
- public Collection<View<? extends CyTableEntry>> getAllViews() {
- final Set<View<? extends CyTableEntry>> views = new
HashSet<View<? extends CyTableEntry>>();
+ public Collection<View<? extends CyIdentifiable>> getAllViews() {
+ final Set<View<? extends CyIdentifiable>> views = new
HashSet<View<? extends CyIdentifiable>>();
views.addAll(getNodeViews());
views.addAll(getEdgeViews());
Modified:
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/FlagAndSelectionHandler.java
===================================================================
---
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/FlagAndSelectionHandler.java
2012-03-26 22:26:13 UTC (rev 28652)
+++
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/FlagAndSelectionHandler.java
2012-03-26 23:20:35 UTC (rev 28653)
@@ -43,7 +43,7 @@
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.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -138,11 +138,11 @@
select(selectedEdges, true);
}
- private void select(final Collection<? extends CyTableEntry>
nodesOrEdges, final boolean selected) {
+ private void select(final Collection<? extends CyIdentifiable>
nodesOrEdges, final boolean selected) {
if (nodesOrEdges.isEmpty())
return;
- for (final CyTableEntry nodeOrEdge : nodesOrEdges)
+ for (final CyIdentifiable nodeOrEdge : nodesOrEdges)
network.getRow(nodeOrEdge).set(CyNetwork.SELECTED,
selected);
}
Modified:
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/AddNodeTask.java
===================================================================
---
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/AddNodeTask.java
2012-03-26 22:26:13 UTC (rev 28652)
+++
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/AddNodeTask.java
2012-03-26 23:20:35 UTC (rev 28653)
@@ -59,8 +59,8 @@
nodeName = "Node_"+ new_node_index;
new_node_index++;
- net.getRow(n).set(CyNode.NAME, nodeName);
- rnm.getRootNetwork(net).getRow(n).set(CyNode.NAME, nodeName);
+ net.getRow(n).set(CyNetwork.NAME, nodeName);
+ rnm.getRootNetwork(net).getRow(n).set(CyNetwork.NAME, nodeName);
eh.flushPayloadEvents();
View<CyNode> nv = view.getNodeView(n);
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