Author: pwang
Date: 2012-03-26 16:25:33 -0700 (Mon, 26 Mar 2012)
New Revision: 28656
Modified:
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/data_mapper/PSIMI25EntryMapper.java
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabParser.java
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchIndex.java
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CyNetworkNamingImpl.java
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CySessionManagerImpl.java
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/actions/dummies/DummyNetwork.java
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/actions/dummies/DummyNetworkView.java
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkPanel.java
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/TreeCellRenderer.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/BrowserTable.java
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/BrowserTableModel.java
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/CustomHeaderRenderer.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/util/TableBrowserUtil.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ImportAttributeTableReaderTask.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/GeneAssociationReader.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBOReader.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/MapGeneAssociationTask.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/RegisterOntologyTask.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/ImportTablePanel.java
Log:
Fixed bug#810
Modified:
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/data_mapper/PSIMI25EntryMapper.java
===================================================================
---
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/data_mapper/PSIMI25EntryMapper.java
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/data_mapper/PSIMI25EntryMapper.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -12,7 +12,7 @@
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 psidev.psi.mi.xml.model.Alias;
import psidev.psi.mi.xml.model.Attribute;
@@ -156,7 +156,7 @@
final CyNode node = network.addNode();
final String nameColumn =
interactor.getNames().getShortLabel();
- nodeTable.getRow(node.getSUID()).set(CyTableEntry.NAME,
nameColumn);
+ nodeTable.getRow(node.getSUID()).set(CyNetwork.NAME,
nameColumn);
final InteractorType itrType =
interactor.getInteractorType();
final Names typeNames = itrType.getNames();
@@ -230,9 +230,9 @@
// TODO: what's the best value for interaction?
edgeTable.getRow(edge.getSUID()).set(CyEdge.INTERACTION, "pp");
- final String sourceName =
nodeTable.getRow(sourceCyNode.getSUID()).get(CyTableEntry.NAME, String.class);
- final String targetName =
nodeTable.getRow(targetCyNode.getSUID()).get(CyTableEntry.NAME, String.class);
- edgeTable.getRow(edge.getSUID()).set(CyTableEntry.NAME,
sourceName + " (pp) " + targetName);
+ final String sourceName =
nodeTable.getRow(sourceCyNode.getSUID()).get(CyNetwork.NAME, String.class);
+ final String targetName =
nodeTable.getRow(targetCyNode.getSUID()).get(CyNetwork.NAME, String.class);
+ edgeTable.getRow(edge.getSUID()).set(CyNetwork.NAME, sourceName
+ " (pp) " + targetName);
mapNames(edgeTable, edge.getSUID(), interaction.getNames(),
null);
mapAttributes(interaction.getAttributes(), edgeTable,
edge.getSUID());
Modified:
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabParser.java
===================================================================
---
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabParser.java
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabParser.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -18,7 +18,7 @@
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.work.TaskMonitor;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -143,8 +143,8 @@
CyRow targetRow = network.getRow(target);
// set various node attrs
- sourceRow.set(CyTableEntry.NAME, sourceRawID);
- targetRow.set(CyTableEntry.NAME, targetRawID);
+ sourceRow.set(CyNetwork.NAME, sourceRawID);
+ targetRow.set(CyNetwork.NAME, targetRawID);
setInteractorType(sourceRow,mline.srcAliases);
setInteractorType(targetRow,mline.tgtAliases);
@@ -165,7 +165,7 @@
interactionId =
mline.interactionIDs.get(0);
edgeRow.set(INTERACTION, interactionId);
- edgeRow.set(CyTableEntry.NAME, sourceRawID + "
(" + interactionId + ") " + targetRawID);
+ edgeRow.set(CyNetwork.NAME, sourceRawID + " ("
+ interactionId + ") " + targetRawID);
setTypedEdgeListAttribute(edgeRow,
mline.interactionTypes, INTERACTION_TYPE_ID, INTERACTION_TYPE);
setTypedEdgeListAttribute(edgeRow,
mline.detectionMethods, DETECTION_METHOD_ID, DETECTION_METHOD);
Modified:
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchIndex.java
===================================================================
---
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchIndex.java
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchIndex.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -44,7 +44,7 @@
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.CyTableUtil;
import org.cytoscape.search.internal.util.EnhancedSearchUtils;
import org.cytoscape.work.TaskMonitor;
@@ -99,7 +99,7 @@
* Make a Document object with an un-indexed identifier field and
indexed
* attribute fields
*/
- private static Document createDocument(CyNetwork network, CyTableEntry
graphObject, String graphObjectType, int index) {
+ private static Document createDocument(CyNetwork network,
CyIdentifiable graphObject, String graphObjectType, int index) {
Document doc = new Document();
String identifier = Integer.toString(index);
Modified:
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CyNetworkNamingImpl.java
===================================================================
---
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CyNetworkNamingImpl.java
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CyNetworkNamingImpl.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -32,7 +32,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.session.CyNetworkNaming;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -55,7 +55,7 @@
@Override
public String getSuggestedSubnetworkTitle(final CyNetwork
parentNetwork) {
for (int i = 0; true; i++) {
- final String parentName =
parentNetwork.getRow(parentNetwork).get(CyTableEntry.NAME, String.class);
+ final String parentName =
parentNetwork.getRow(parentNetwork).get(CyNetwork.NAME, String.class);
final String nameCandidate = parentName + " <" +
SUBNETWORK_SUFFIX + " " + (i+1) + ">";
if (!isNetworkTitleTaken(nameCandidate))
Modified:
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CySessionManagerImpl.java
===================================================================
---
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CySessionManagerImpl.java
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CySessionManagerImpl.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -51,7 +51,7 @@
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.CyTableManager;
import org.cytoscape.model.CyTableMetadata;
import org.cytoscape.model.subnetwork.CyRootNetwork;
@@ -157,7 +157,7 @@
}
@SuppressWarnings("unchecked")
- private static Class<? extends CyTableEntry>[] TYPES = new Class[] {
CyNetwork.class, CyNode.class, CyEdge.class };
+ private static Class<? extends CyIdentifiable>[] TYPES = new Class[] {
CyNetwork.class, CyNode.class, CyEdge.class };
private Set<CyTableMetadata> buildMetadata(Set<CyTable> tables,
Set<CyNetwork> networks) {
Set<CyTableMetadata> result = new HashSet<CyTableMetadata>();
@@ -175,7 +175,7 @@
allNetworks.add(rootNet);
// TODO: remove it once manager is
fixed to return all tables
- for (Class<? extends CyTableEntry> type
: TYPES) {
+ for (Class<? extends CyIdentifiable>
type : TYPES) {
Map<String, CyTable> tableMap =
netTblMgr.getTables(rootNet, type);
allTables.addAll(tableMap.values());
}
@@ -206,7 +206,7 @@
Map<CyTable, Set<CyTableMetadata>> result = new
HashMap<CyTable, Set<CyTableMetadata>>();
for (CyNetwork network : networks) {
- for (Class<? extends CyTableEntry> type : TYPES) {
+ for (Class<? extends CyIdentifiable> type : TYPES) {
Map<String, CyTable> tableMap =
netTblMgr.getTables(network, type);
for (Entry<String, CyTable> entry :
tableMap.entrySet()) {
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/actions/dummies/DummyNetwork.java
===================================================================
---
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/actions/dummies/DummyNetwork.java
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/actions/dummies/DummyNetwork.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -27,6 +27,6 @@
public CyTable getDefaultNetworkTable() {return null;}
public CyTable getDefaultNodeTable() {return null;}
public CyTable getDefaultEdgeTable() {return null;}
- public CyRow getRow(CyTableEntry entry, String tableName) {return null;}
- public CyRow getRow(CyTableEntry entry) {return null;}
+ public CyRow getRow(CyIdentifiable entry, String tableName) {return
null;}
+ public CyRow getRow(CyIdentifiable entry) {return null;}
}
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/actions/dummies/DummyNetworkView.java
===================================================================
---
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/actions/dummies/DummyNetworkView.java
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/actions/dummies/DummyNetworkView.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -13,7 +13,7 @@
public Collection<View<CyNode>> getNodeViews() {return null;}
public View<CyEdge> getEdgeView(final CyEdge edge) {return null;}
public Collection<View<CyEdge>> getEdgeViews() {return null;}
- public Collection<View<? extends CyTableEntry>> getAllViews() {return
null;}
+ public Collection<View<? extends CyIdentifiable>> getAllViews() {return
null;}
public void fitContent() {}
public void fitSelected() {}
public void updateView() {}
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkPanel.java
===================================================================
---
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkPanel.java
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkPanel.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -69,7 +69,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.events.NetworkAboutToBeDestroyedEvent;
import org.cytoscape.model.events.NetworkAboutToBeDestroyedListener;
import org.cytoscape.model.events.NetworkAddedEvent;
@@ -407,7 +407,7 @@
// if it's the network name, then update the
title
CyNetwork n = nameTables.get(e.getSource());
if (n != null) {
- final String title =
n.getRow(n).get(CyTableEntry.NAME, String.class);
+ final String title =
n.getRow(n).get(CyNetwork.NAME, String.class);
updateTitle(n, title);
return;
}
@@ -515,7 +515,7 @@
parentTreeNode = new NetworkTreeNode("", null);
// Actual tree node for this network
- String netName =
network.getRow(network).get(CyTableEntry.NAME, String.class);
+ String netName =
network.getRow(network).get(CyNetwork.NAME, String.class);
if (netName == null) {
logger.error("Network name is null--SUID=" +
network.getSUID());
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
===================================================================
---
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -58,7 +58,7 @@
import org.cytoscape.application.events.SetCurrentNetworkViewListener;
import org.cytoscape.application.swing.CyHelpBroker;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.property.CyProperty;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewManager;
@@ -458,7 +458,7 @@
String title =
view.getVisualProperty(BasicVisualLexicon.NETWORK_TITLE);
if (title == null || title.isEmpty())
- title =
view.getModel().getRow(view.getModel()).get(CyTableEntry.NAME, String.class);
+ title =
view.getModel().getRow(view.getModel()).get(CyNetwork.NAME, String.class);
return title;
}
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/TreeCellRenderer.java
===================================================================
---
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/TreeCellRenderer.java
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/view/TreeCellRenderer.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -16,7 +16,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.util.swing.JTreeTable;
import org.cytoscape.view.model.CyNetworkViewManager;
@@ -77,7 +77,7 @@
setForeground(treeNode.getNodeColor());
setForeground(treeNode.getNodeColor());
-
setToolTipText(treeNode.getNetwork().getRow(treeNode.getNetwork()).get(CyTableEntry.NAME,
String.class));
+
setToolTipText(treeNode.getNetwork().getRow(treeNode.getNetwork()).get(CyNetwork.NAME,
String.class));
return this;
}
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
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/AttributeBrowserToolBar.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -69,7 +69,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.subnetwork.CyRootNetwork;
import org.cytoscape.model.subnetwork.CySubNetwork;
import org.cytoscape.service.util.CyServiceRegistrar;
@@ -117,20 +117,20 @@
private final JToggleButton selectionModeButton;
- private final Class<? extends CyTableEntry> objType;
+ private final Class<? extends CyIdentifiable> objType;
private final CyApplicationManager appManager;
public AttributeBrowserToolBar(final CyServiceRegistrar
serviceRegistrar, final EquationCompiler compiler,
final TableTaskFactory deleteTableTaskFactoryService,
DialogTaskManager guiTaskManagerServiceRef,
- final JComboBox tableChooser, final Class<? extends
CyTableEntry> objType, final CyApplicationManager appManager) {
+ final JComboBox tableChooser, final Class<? extends
CyIdentifiable> objType, final CyApplicationManager appManager) {
this(serviceRegistrar, compiler, deleteTableTaskFactoryService,
guiTaskManagerServiceRef, tableChooser,
new JToggleButton(), objType, appManager);
}
public AttributeBrowserToolBar(final CyServiceRegistrar
serviceRegistrar, final EquationCompiler compiler,
final TableTaskFactory deleteTableTaskFactoryService,
DialogTaskManager guiTaskManagerServiceRef,
- final JComboBox tableChooser, final JToggleButton
selectionModeButton, Class<? extends CyTableEntry> objType, final
CyApplicationManager appManager) {
+ final JComboBox tableChooser, final JToggleButton
selectionModeButton, Class<? extends CyIdentifiable> objType, final
CyApplicationManager appManager) {
this.compiler = compiler;
this.selectionModeButton = selectionModeButton;
this.appManager = appManager;
Modified:
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/BrowserTable.java
===================================================================
---
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/BrowserTable.java
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/BrowserTable.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -59,7 +59,7 @@
import org.cytoscape.model.CyNetworkTableManager;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.util.swing.OpenBrowser;
import org.cytoscape.view.model.CyNetworkView;
import org.slf4j.Logger;
Modified:
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/BrowserTableModel.java
===================================================================
---
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/BrowserTableModel.java
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/BrowserTableModel.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -22,7 +22,7 @@
import org.cytoscape.model.CyNetworkTableManager;
import org.cytoscape.model.CyRow;
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;
@@ -375,7 +375,7 @@
// Find Primary key index.
for (int i = 0; i < columnCount; i++) {
final String colName = table.getColumnName(i);
- if (colName.equals(CyTableEntry.SUID)) {
+ if (colName.equals(CyIdentifiable.SUID)) {
tablePKeyIndex = i;
break;
}
@@ -387,10 +387,10 @@
for(RowSetRecord rowSetRecord : rows) {
if(rowSetRecord.getColumn().equals(CyNetwork.SELECTED)){
if(((Boolean)rowSetRecord.getValue()) == true){
-
suidMapSelected.put(rowSetRecord.getRow().get(CyTableEntry.SUID, Long.class),
(Boolean) rowSetRecord.getValue());
+
suidMapSelected.put(rowSetRecord.getRow().get(CyIdentifiable.SUID, Long.class),
(Boolean) rowSetRecord.getValue());
}
else{
-
suidMapUnselected.put(rowSetRecord.getRow().get(CyTableEntry.SUID, Long.class),
(Boolean) rowSetRecord.getValue());
+
suidMapUnselected.put(rowSetRecord.getRow().get(CyIdentifiable.SUID,
Long.class), (Boolean) rowSetRecord.getValue());
}
}
}
Modified:
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/CustomHeaderRenderer.java
===================================================================
---
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/CustomHeaderRenderer.java
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/CustomHeaderRenderer.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -44,7 +44,7 @@
import javax.swing.table.TableCellRenderer;
import org.cytoscape.model.CyColumn;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
final class CustomHeaderRenderer extends JLabel implements TableCellRenderer {
@@ -117,7 +117,7 @@
if(col.getType() == List.class) {
toolTip = "<html>This is a List column<br />" +
"The lists contain " +
col.getListElementType() + "</html>";
- } else if(text.equals(CyTableEntry.SUID))
+ } else if(text.equals(CyIdentifiable.SUID))
toolTip = "Session-Unique ID (Primary Key). This is
column is immutable.";
else
toolTip = "Data type of this column is " +
col.getType().getName();
@@ -131,7 +131,7 @@
setBackground(COLUMN_COLOR);
}
- if (text.equals(CyTableEntry.SUID))
+ if (text.equals(CyIdentifiable.SUID))
this.setFont(COLUMN_SUID_FONT);
else
this.setFont(COLUMN_FONT);
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
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/DefaultTableBrowser.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -27,7 +27,7 @@
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.CyTableManager;
import org.cytoscape.model.events.NetworkAboutToBeDestroyedEvent;
import org.cytoscape.model.events.NetworkAboutToBeDestroyedListener;
@@ -49,13 +49,13 @@
private final JToggleButton selectionModeButton;
private final JComboBox networkChooser;
- private final Class<? extends CyTableEntry> objType;
+ private final Class<? extends CyIdentifiable> objType;
private boolean rowSelectionMode;
private boolean ignoreSetCurrentNetwork = true;
- public DefaultTableBrowser(String tabTitle, Class<? extends
CyTableEntry> objType, CyTableManager tableManager,
+ public DefaultTableBrowser(String tabTitle, Class<? extends
CyIdentifiable> objType, CyTableManager tableManager,
CyNetworkTableManager networkTableManager,
CyServiceRegistrar serviceRegistrar, EquationCompiler compiler,
OpenBrowser openBrowser, CyNetworkManager
networkManager, TableTaskFactory deleteTableTaskFactoryService,
DialogTaskManager guiTaskManagerServiceRef,
PopupMenuHelper popupMenuHelper,
@@ -214,7 +214,7 @@
}
setOpaque(true);
-
this.setText(network.getRow(network).get(CyTableEntry.NAME, String.class));
+
this.setText(network.getRow(network).get(CyNetwork.NAME, String.class));
return this;
}
}
Modified:
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/util/TableBrowserUtil.java
===================================================================
---
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/util/TableBrowserUtil.java
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/util/TableBrowserUtil.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -14,7 +14,7 @@
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;
public final class TableBrowserUtil {
@@ -402,7 +402,7 @@
for (CyNetwork network : networks) {
for (Class<?> type : OBJECT_TYPES) {
final Map<String, CyTable> objTables =
networkTableManager.getTables(network,
- (Class<? extends CyTableEntry>)
type);
+ (Class<? extends
CyIdentifiable>) type);
nonGlobalTables.addAll(objTables.values());
}
}
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ImportAttributeTableReaderTask.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ImportAttributeTableReaderTask.java
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ImportAttributeTableReaderTask.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -17,7 +17,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.CyTableManager;
import org.cytoscape.tableimport.internal.reader.AttributeMappingParameters;
import org.cytoscape.tableimport.internal.reader.DefaultAttributeTableReader;
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/GeneAssociationReader.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/GeneAssociationReader.java
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/GeneAssociationReader.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -24,7 +24,7 @@
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.CyTableFactory;
import org.cytoscape.model.CyTableManager;
import org.cytoscape.tableimport.internal.util.OntologyDAGManager;
@@ -220,8 +220,8 @@
logger.warn("Could not find associated Ontology DAG.");
else {
this.dagTable = ontologyDAG.getDefaultNodeTable();
- termIDList =
ontologyDAG.getDefaultNodeTable().getColumn(CyTableEntry.NAME).getValues(String.class);
- logger.debug("DAG Name = " +
ontologyDAG.getRow(ontologyDAG).get(CyTableEntry.NAME, String.class));
+ termIDList =
ontologyDAG.getDefaultNodeTable().getColumn(CyNetwork.NAME).getValues(String.class);
+ logger.debug("DAG Name = " +
ontologyDAG.getRow(ontologyDAG).get(CyNetwork.NAME, String.class));
}
BufferedReader bufRd = new BufferedReader(new
InputStreamReader(is));
@@ -238,7 +238,7 @@
}
// Create result table
- table = tableFactory.createTable(tableName, CyTableEntry.NAME,
String.class, true, true);
+ table = tableFactory.createTable(tableName, CyNetwork.NAME,
String.class, true, true);
createColumns();
@@ -403,7 +403,7 @@
// Set primary key for the table, which is DB Object ID
final String primaryKeyValue = entries[DB_OBJ_ID];
final CyRow row = table.getRow(primaryKeyValue);
- row.set(CyTableEntry.NAME, primaryKeyValue);
+ row.set(CyNetwork.NAME, primaryKeyValue);
// Check namespace
final String namespace = NAMESPACE_MAP.get(entries[ASPECT]);
@@ -501,7 +501,7 @@
}
private String convertToName(final String id) {
- final Collection<CyRow> rows =
ontologyDAG.getDefaultNodeTable().getMatchingRows(CyTableEntry.NAME, id);
+ final Collection<CyRow> rows =
ontologyDAG.getDefaultNodeTable().getMatchingRows(CyNetwork.NAME, id);
if (rows != null) {
final CyRow row = rows.iterator().next();
final String termName = row.get(OBOReader.TERM_NAME,
String.class);
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBOReader.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBOReader.java
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBOReader.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -33,7 +33,7 @@
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.tableimport.internal.util.OntologyDAGManager;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
@@ -151,7 +151,7 @@
networkTable.createColumn(DAG_ATTR, Boolean.class,
true);
networkTable.getRow(ontologyDAG.getSUID()).set(DAG_ATTR, true);
- ontologyDAG.getRow(ontologyDAG).set(CyTableEntry.NAME, dagName);
+ ontologyDAG.getRow(ontologyDAG).set(CyNetwork.NAME, dagName);
}
@@ -203,7 +203,7 @@
termNode = termID2nodeMap.get(val);
if (termNode == null) {
termNode = this.ontologyDAG.addNode();
-
ontologyDAG.getRow(termNode).set(CyTableEntry.NAME, val);
+
ontologyDAG.getRow(termNode).set(CyNetwork.NAME, val);
termID2nodeMap.put(val, termNode);
id = val;
}
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/MapGeneAssociationTask.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/MapGeneAssociationTask.java
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/MapGeneAssociationTask.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -8,7 +8,7 @@
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import
org.cytoscape.tableimport.internal.reader.ontology.GeneAssociationReader;
import org.cytoscape.tableimport.internal.reader.ontology.OBOReader;
import org.cytoscape.work.AbstractTask;
@@ -63,8 +63,8 @@
// TODO: parallelize this
private void buildMapping(TaskMonitor taskMonitor, final String
networkName, CyTable nodeTable, CyTable globalTable) {
- final List<String> nodeNames =
nodeTable.getColumn(CyTableEntry.NAME).getValues(String.class);
- final List<String> globalKeys =
globalTable.getColumn(CyTableEntry.NAME).getValues(String.class);
+ final List<String> nodeNames =
nodeTable.getColumn(CyNetwork.NAME).getValues(String.class);
+ final List<String> globalKeys =
globalTable.getColumn(CyNetwork.NAME).getValues(String.class);
// Create immutable key column for this mapping
final String colName = "Mapping Key for " + networkName;
@@ -87,6 +87,6 @@
taskMonitor.setProgress(progress);
}
- nodeTable.addVirtualColumns(globalTable, CyTableEntry.NAME,
false);
+ nodeTable.addVirtualColumns(globalTable, CyNetwork.NAME, false);
}
}
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/RegisterOntologyTask.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/RegisterOntologyTask.java
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/RegisterOntologyTask.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -3,7 +3,7 @@
import org.cytoscape.io.read.CyNetworkReader;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
import org.slf4j.Logger;
@@ -33,7 +33,7 @@
if(network == null)
throw new NullPointerException("No Ontology DAG
loaded");
- network.getRow(network).set(CyTableEntry.NAME, name);
+ network.getRow(network).set(CyNetwork.NAME, name);
manager.addNetwork(network);
logger.debug("Registered: model ID = " + network.getSUID());
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/ImportTablePanel.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/ImportTablePanel.java
2012-03-26 23:24:10 UTC (rev 28655)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/ImportTablePanel.java
2012-03-26 23:25:33 UTC (rev 28656)
@@ -109,7 +109,7 @@
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.model.CyTableManager;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.property.CyProperty;
import org.cytoscape.property.bookmark.Bookmarks;
import org.cytoscape.property.bookmark.BookmarksUtil;
@@ -176,7 +176,7 @@
public static final String NETWORK_IMPORT_TEMPLATE_CHANGED =
"networkImportTemplateChanged";
private static final String[] keyTable = { "Alias?", "Column (Attribute
Name)", "Data Type" };
- private static final String ID = CyTableEntry.NAME;
+ private static final String ID = CyNetwork.NAME;
// Key column index
protected int keyInFile;
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