Author: mes
Date: 2011-12-12 14:03:31 -0800 (Mon, 12 Dec 2011)
New Revision: 27771
Added:
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyTableEntryTest.java
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableEntryTest.java
Removed:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/Identifiable.java
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractIdentifiableTest.java
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/IdentifiableTest.java
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTable.java
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTableEntry.java
core3/api/trunk/viewmodel-api/src/main/java/org/cytoscape/view/model/View.java
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DGraphView.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/UnrecognizedVisualPropertyManager.java
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderTest.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArraySubGraph.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableEntryImpl.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/NameSetListener.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/VirtualColumnAdder.java
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyNetworkTableManagerTest.java
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableManagerTest.java
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableTest.java
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/TableTestSupportTest.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/VizMapPropertyBuilder.java
Log:
removed the Identifiable interface and merged it with CyTableEntry
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTable.java
===================================================================
--- core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTable.java
2011-12-12 21:49:39 UTC (rev 27770)
+++ core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTable.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -41,7 +41,7 @@
* types.
* @CyAPI.Api.Interface
*/
-public interface CyTable extends Identifiable {
+public interface CyTable extends CyTableEntry {
/**
* Mutability of the table specifies whether or not it is able to be
deleted..
*
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTableEntry.java
===================================================================
---
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTableEntry.java
2011-12-12 21:49:39 UTC (rev 27770)
+++
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTableEntry.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -34,11 +34,21 @@
* entries will be things like nodes, edges, and networks..
* @CyAPI.Api.Interface
*/
-public interface CyTableEntry extends Identifiable {
+public interface CyTableEntry {
/**
* A String column created by default for every CyTableEntry that
* holds the name of the entry.
*/
String NAME = "name";
+
+ /**
+ * This will be used as column name of SUID.
+ */
+ String SUID = "SUID";
+ /**
+ * Returns the SUID of the implementing object.
+ * @return the SUID of the implementing object.
+ */
+ long getSUID();
}
Deleted:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/Identifiable.java
===================================================================
---
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/Identifiable.java
2011-12-12 21:49:39 UTC (rev 27770)
+++
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/Identifiable.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -1,57 +0,0 @@
-
-/*
- Copyright (c) 2008, The Cytoscape Consortium (www.cytoscape.org)
-
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
- This library is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License as published
- by the Free Software Foundation; either version 2.1 of the License, or
- any later version.
-
- This library is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- documentation provided hereunder is on an "as is" basis, and the
- Institute for Systems Biology and the Whitehead Institute
- have no obligations to provide maintenance, support,
- updates, enhancements or modifications. In no event shall the
- Institute for Systems Biology and the Whitehead Institute
- be liable to any party for direct, indirect, special,
- incidental or consequential damages, including lost profits, arising
- out of the use of this software and its documentation, even if the
- Institute for Systems Biology and the Whitehead Institute
- have been advised of the possibility of such damage. See
- the GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with this library; if not, write to the Free Software Foundation,
- Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
-*/
-
-package org.cytoscape.model;
-
-/**
- * Any object that implements this interface shall return a session unique
- * identifier that shall be unique among all instances of objects that
- * implement this interface. The identifier shall be greater than 0.
- * @CyAPI.Api.Interface
- */
-public interface Identifiable {
-
- /**
- * This will be used as column name of SUID.
- */
- static final String SUID = "SUID";
-
- /**
- * Returns the SUID of the implementing object.
- * @return the SUID of the implementing object.
- */
- long getSUID();
-}
Copied:
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyTableEntryTest.java
(from rev 27769,
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractIdentifiableTest.java)
===================================================================
---
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyTableEntryTest.java
(rev 0)
+++
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyTableEntryTest.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -0,0 +1,64 @@
+/*
+ Copyright (c) 2008, 2011, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.model;
+
+
+import static org.junit.Assert.*;
+import org.junit.Test;
+
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+
+import java.lang.RuntimeException;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+
+public abstract class AbstractCyTableEntryTest {
+ protected CyNetwork net;
+
+ @Test
+ public void testGetSUID() {
+ CyNode n1 = net.addNode();
+ assertTrue("suid >= 0", n1.getSUID() >= 0);
+
+ CyNode n2 = net.addNode();
+ assertTrue("suid >= 0", n2.getSUID() >= 0);
+
+ CyEdge e1 = net.addEdge(n1, n2, true);
+ assertTrue("suid >= 0", e1.getSUID() >= 0);
+
+ CyEdge e2 = net.addEdge(n1, n2, false);
+ assertTrue("suid >= 0", e2.getSUID() >= 0);
+
+ assertTrue("suid >= 0", net.getSUID() >= 0);
+ }
+}
Deleted:
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractIdentifiableTest.java
===================================================================
---
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractIdentifiableTest.java
2011-12-12 21:49:39 UTC (rev 27770)
+++
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractIdentifiableTest.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -1,64 +0,0 @@
-/*
- Copyright (c) 2008, 2011, The Cytoscape Consortium (www.cytoscape.org)
-
- This library is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License as published
- by the Free Software Foundation; either version 2.1 of the License, or
- any later version.
-
- This library is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- documentation provided hereunder is on an "as is" basis, and the
- Institute for Systems Biology and the Whitehead Institute
- have no obligations to provide maintenance, support,
- updates, enhancements or modifications. In no event shall the
- Institute for Systems Biology and the Whitehead Institute
- be liable to any party for direct, indirect, special,
- incidental or consequential damages, including lost profits, arising
- out of the use of this software and its documentation, even if the
- Institute for Systems Biology and the Whitehead Institute
- have been advised of the possibility of such damage. See
- the GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with this library; if not, write to the Free Software Foundation,
- Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
-*/
-package org.cytoscape.model;
-
-
-import static org.junit.Assert.*;
-import org.junit.Test;
-
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-
-import java.lang.RuntimeException;
-
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-
-public abstract class AbstractIdentifiableTest {
- protected CyNetwork net;
-
- @Test
- public void testGetSUID() {
- CyNode n1 = net.addNode();
- assertTrue("suid >= 0", n1.getSUID() >= 0);
-
- CyNode n2 = net.addNode();
- assertTrue("suid >= 0", n2.getSUID() >= 0);
-
- CyEdge e1 = net.addEdge(n1, n2, true);
- assertTrue("suid >= 0", e1.getSUID() >= 0);
-
- CyEdge e2 = net.addEdge(n1, n2, false);
- assertTrue("suid >= 0", e2.getSUID() >= 0);
-
- assertTrue("suid >= 0", net.getSUID() >= 0);
- }
-}
Modified:
core3/api/trunk/viewmodel-api/src/main/java/org/cytoscape/view/model/View.java
===================================================================
---
core3/api/trunk/viewmodel-api/src/main/java/org/cytoscape/view/model/View.java
2011-12-12 21:49:39 UTC (rev 27770)
+++
core3/api/trunk/viewmodel-api/src/main/java/org/cytoscape/view/model/View.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -34,7 +34,7 @@
*/
package org.cytoscape.view.model;
-import org.cytoscape.model.Identifiable;
+import org.cytoscape.model.CyTableEntry;
/**
@@ -47,7 +47,7 @@
* In the future versions, Attributes can be this parameter.
* @CyAPI.Api.Interface
*/
-public interface View<S> extends Identifiable {
+public interface View<S> extends CyTableEntry {
/**
* Assign a value to the given Visual Property of this view.
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
2011-12-12 21:49:39 UTC (rev 27770)
+++
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DGraphView.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -99,7 +99,7 @@
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.CyTableFactory;
-import org.cytoscape.model.Identifiable;
+import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.events.AboutToRemoveEdgesEvent;
import org.cytoscape.model.events.AboutToRemoveEdgesListener;
import org.cytoscape.model.events.AboutToRemoveNodesEvent;
@@ -460,11 +460,11 @@
this.menuTaskManager = menuTaskManager;
this.cyEventHelper = cyEventHelper;
- final CyTable nodeCAM = dataFactory.createTable("node view",
Identifiable.SUID, Long.class, false, false);
+ final CyTable nodeCAM = dataFactory.createTable("node view",
CyTableEntry.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",
Identifiable.SUID, Long.class, false, false);
+ final CyTable edgeCAM = dataFactory.createTable("edge view",
CyTableEntry.SUID, Long.class, false, false);
edgeCAM.createColumn("hidden", Boolean.class, false);
tableMgr.setTable(model, CyEdge.class, "VIEW", edgeCAM);
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/UnrecognizedVisualPropertyManager.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/UnrecognizedVisualPropertyManager.java
2011-12-12 21:49:39 UTC (rev 27770)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/UnrecognizedVisualPropertyManager.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -12,7 +12,7 @@
import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.model.CyTableManager;
-import org.cytoscape.model.Identifiable;
+import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.SUIDFactory;
import org.cytoscape.model.CyTable.SavePolicy;
import org.cytoscape.view.model.CyNetworkView;
@@ -25,8 +25,8 @@
public static final String RENDERER_TABLE_TITLE =
"UnrecognizedRenderer";
public static final String VISUAL_PROPERTY_TABLE_TITLE =
"UnrecognizedVisualProperties";
- private static final String RENDERER_TABLE_PK = Identifiable.SUID;
- private static final String VISUAL_PROPERTY_TABLE_PK =
Identifiable.SUID;
+ private static final String RENDERER_TABLE_PK = CyTableEntry.SUID;
+ private static final String VISUAL_PROPERTY_TABLE_PK =
CyTableEntry.SUID;
private final CyTableFactory tableFactory;
private final CyTableManager tableMgr;
Modified:
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderTest.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderTest.java
2011-12-12 21:49:39 UTC (rev 27770)
+++
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderTest.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -13,7 +13,7 @@
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableManager;
-import org.cytoscape.model.Identifiable;
+import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.CyTable.Mutability;
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.model.TableTestSupport;
@@ -56,7 +56,7 @@
assertEquals(2, table.getRowCount());
CyRow row = table.getRow(5L);
assertNotNull(row);
- Long value = row.get(Identifiable.SUID, Long.class);
+ Long value = row.get(CyTableEntry.SUID, Long.class);
assertEquals((Long) 5L, value);
assertTrue(table.isPublic());
assertEquals(Mutability.MUTABLE, table.getMutability());
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
2011-12-12 21:49:39 UTC (rev 27770)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -46,7 +46,7 @@
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.CyTableFactory;
-import org.cytoscape.model.Identifiable;
+import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.SUIDFactory;
import org.cytoscape.model.events.ColumnCreatedListener;
import org.cytoscape.model.events.RowsSetListener;
@@ -135,13 +135,13 @@
private Map<String,CyTable> createNetworkTables(long suidx) {
Map<String,CyTable> netAttrMgr = new HashMap<String, CyTable>();
- netAttrMgr.put(CyNetwork.DEFAULT_ATTRS, tableFactory.createTable(suidx
+ " default network", Identifiable.SUID, Long.class, publicTables, false));
- netAttrMgr.put(CyNetwork.HIDDEN_ATTRS, tableFactory.createTable(suidx
+ " hidden network", Identifiable.SUID, Long.class, false, false));
+ netAttrMgr.put(CyNetwork.DEFAULT_ATTRS, tableFactory.createTable(suidx
+ " default network", CyTableEntry.SUID, Long.class, publicTables, false));
+ netAttrMgr.put(CyNetwork.HIDDEN_ATTRS, tableFactory.createTable(suidx
+ " hidden network", CyTableEntry.SUID, Long.class, false, false));
netAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyTableEntry.NAME,
String.class, true);
if ( suidx == suid ) {
- netAttrMgr.put(CyRootNetwork.SHARED_ATTRS,
tableFactory.createTable(suidx + " shared network", Identifiable.SUID,
Long.class, publicTables, false));
+ netAttrMgr.put(CyRootNetwork.SHARED_ATTRS,
tableFactory.createTable(suidx + " shared network", CyTableEntry.SUID,
Long.class, publicTables, false));
netAttrMgr.get(CyRootNetwork.SHARED_ATTRS).createColumn(CyRootNetwork.SHARED_NAME,
String.class, true);
} else
linkDefaultTables(
netTables.get(CyRootNetwork.SHARED_ATTRS),
@@ -152,14 +152,14 @@
private Map<String,CyTable> createNodeTables(long suidx) {
Map<String,CyTable> nodeAttrMgr = new HashMap<String, CyTable>();
- nodeAttrMgr.put(CyNetwork.DEFAULT_ATTRS,
tableFactory.createTable(suidx + " default node", Identifiable.SUID,
Long.class, publicTables, false));
- nodeAttrMgr.put(CyNetwork.HIDDEN_ATTRS, tableFactory.createTable(suidx
+ " hidden node", Identifiable.SUID, Long.class, false, false));
+ nodeAttrMgr.put(CyNetwork.DEFAULT_ATTRS,
tableFactory.createTable(suidx + " default node", CyTableEntry.SUID,
Long.class, publicTables, false));
+ nodeAttrMgr.put(CyNetwork.HIDDEN_ATTRS, tableFactory.createTable(suidx
+ " hidden node", CyTableEntry.SUID, Long.class, false, false));
nodeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyTableEntry.NAME,
String.class, true);
nodeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyNetwork.SELECTED,
Boolean.class, true, Boolean.FALSE);
if ( suidx == suid ) {
- nodeAttrMgr.put(CyRootNetwork.SHARED_ATTRS,
tableFactory.createTable(suidx + " shared node", Identifiable.SUID, Long.class,
publicTables, false));
+ nodeAttrMgr.put(CyRootNetwork.SHARED_ATTRS,
tableFactory.createTable(suidx + " shared node", CyTableEntry.SUID, Long.class,
publicTables, false));
nodeAttrMgr.get(CyRootNetwork.SHARED_ATTRS).createColumn(CyRootNetwork.SHARED_NAME,
String.class, true);
} else
linkDefaultTables(
nodeTables.get(CyRootNetwork.SHARED_ATTRS),
@@ -170,15 +170,15 @@
private Map<String,CyTable> createEdgeTables(long suidx) {
Map<String,CyTable> edgeAttrMgr = new HashMap<String, CyTable>();
- edgeAttrMgr.put(CyNetwork.DEFAULT_ATTRS,
tableFactory.createTable(suidx + " default edge", Identifiable.SUID,
Long.class, publicTables, false));
- edgeAttrMgr.put(CyNetwork.HIDDEN_ATTRS, tableFactory.createTable(suidx
+ " hidden edge", Identifiable.SUID, Long.class, false, false));
+ edgeAttrMgr.put(CyNetwork.DEFAULT_ATTRS,
tableFactory.createTable(suidx + " default edge", CyTableEntry.SUID,
Long.class, publicTables, false));
+ edgeAttrMgr.put(CyNetwork.HIDDEN_ATTRS, tableFactory.createTable(suidx
+ " hidden edge", CyTableEntry.SUID, Long.class, false, false));
edgeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyTableEntry.NAME,
String.class, true);
edgeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyNetwork.SELECTED,
Boolean.class, true, Boolean.FALSE);
edgeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyEdge.INTERACTION,
String.class, true);
if ( suidx == suid ) {
- edgeAttrMgr.put(CyRootNetwork.SHARED_ATTRS,
tableFactory.createTable(suidx + " shared edge", Identifiable.SUID, Long.class,
publicTables, false));
+ edgeAttrMgr.put(CyRootNetwork.SHARED_ATTRS,
tableFactory.createTable(suidx + " shared edge", CyTableEntry.SUID, Long.class,
publicTables, false));
edgeAttrMgr.get(CyRootNetwork.SHARED_ATTRS).createColumn(CyRootNetwork.SHARED_NAME,
String.class, true);
} else
linkDefaultTables(
edgeTables.get(CyRootNetwork.SHARED_ATTRS),
@@ -189,7 +189,7 @@
private void linkDefaultTables(CyTable srcTable, CyTable tgtTable) {
// Add all columns from source table as virtual columns in
target table.
- tgtTable.addVirtualColumns(srcTable,Identifiable.SUID,true);
+ tgtTable.addVirtualColumns(srcTable,CyTableEntry.SUID,true);
// Now add a listener for column created events to add
// virtual columns to any subsequent source columns added.
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArraySubGraph.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArraySubGraph.java
2011-12-12 21:49:39 UTC (rev 27770)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArraySubGraph.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -34,7 +34,7 @@
//import org.cytoscape.model.builder.CyNodeBuilder;
//import org.cytoscape.model.builder.CyEdgeBuilder;
-import org.cytoscape.model.Identifiable;
+import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyTable;
@@ -480,7 +480,7 @@
private void updateSharedNames(CyTable src, CyTable tgt) {
for ( CyRow sr : src.getAllRows() ) {
- CyRow tr = tgt.getRow(
sr.get(Identifiable.SUID,Long.class) );
+ CyRow tr = tgt.getRow(
sr.get(CyTableEntry.SUID,Long.class) );
tr.set( CyRootNetwork.SHARED_NAME,
sr.get(CyNetwork.NAME,String.class) );
}
}
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableEntryImpl.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableEntryImpl.java
2011-12-12 21:49:39 UTC (rev 27770)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableEntryImpl.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -34,11 +34,10 @@
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableEntry;
-import org.cytoscape.model.Identifiable;
import org.cytoscape.model.SUIDFactory;
-class CyTableEntryImpl implements CyTableEntry, Identifiable {
+class CyTableEntryImpl implements CyTableEntry {
private final long suid;
CyTableEntryImpl(long suid) {
@@ -50,7 +49,7 @@
}
/**
- * @see org.cytoscape.model.Identifiable#getSUID()
+ * @see org.cytoscape.model.CyTableEntry#getSUID()
*/
@Override
final public long getSUID() {
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/NameSetListener.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/NameSetListener.java
2011-12-12 21:49:39 UTC (rev 27770)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/NameSetListener.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -33,7 +33,7 @@
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.CyRow;
-import org.cytoscape.model.Identifiable;
+import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.events.RowsSetListener;
import org.cytoscape.model.events.RowsSetEvent;
import org.cytoscape.model.events.RowSetRecord;
@@ -67,7 +67,7 @@
if ( !record.getColumn().equals(CyTableEntry.NAME) )
return;
- CyRow r = shared.getRow( record.getRow().get(
Identifiable.SUID, Long.class ) );
+ CyRow r = shared.getRow( record.getRow().get(
CyTableEntry.SUID, Long.class ) );
if ( r != null )
r.set(CyRootNetwork.SHARED_NAME,
record.getValue());
}
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/VirtualColumnAdder.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/VirtualColumnAdder.java
2011-12-12 21:49:39 UTC (rev 27770)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/VirtualColumnAdder.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -31,7 +31,7 @@
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyColumn;
-import org.cytoscape.model.Identifiable;
+import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.events.ColumnCreatedEvent;
import org.cytoscape.model.events.ColumnCreatedListener;
@@ -62,7 +62,7 @@
if ( tgt.getColumn(srcName) != null )
return;
CyColumn srcCol = src.getColumn(srcName);
-
tgt.addVirtualColumn(srcName,srcName,src,Identifiable.SUID,srcCol.isImmutable());
+
tgt.addVirtualColumn(srcName,srcName,src,CyTableEntry.SUID,srcCol.isImmutable());
}
}
Modified:
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyNetworkTableManagerTest.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyNetworkTableManagerTest.java
2011-12-12 21:49:39 UTC (rev 27770)
+++
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyNetworkTableManagerTest.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -37,7 +37,7 @@
import org.cytoscape.equations.internal.interpreter.InterpreterImpl;
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.event.DummyCyEventHelper;
-import org.cytoscape.model.Identifiable;
+import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.CyTable.SavePolicy;
import org.cytoscape.model.internal.ArrayGraph;
import org.cytoscape.model.internal.CyNetworkTableManagerImpl;
Copied:
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableEntryTest.java
(from rev 27769,
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/IdentifiableTest.java)
===================================================================
---
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableEntryTest.java
(rev 0)
+++
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableEntryTest.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -0,0 +1,47 @@
+/*
+ Copyright (c) 2008, 2011, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.model;
+
+
+import org.cytoscape.model.CyNetwork;
+
+import org.junit.Before;
+import org.junit.After;
+
+
+public class CyTableEntryTest extends AbstractCyTableEntryTest {
+ @Before
+ public void setUp() {
+ net = TestCyNetworkFactory.getInstance();
+ }
+
+ @After
+ public void tearDown() {
+ net = null;
+ }
+}
Modified:
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableManagerTest.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableManagerTest.java
2011-12-12 21:49:39 UTC (rev 27770)
+++
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableManagerTest.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -37,7 +37,7 @@
import org.cytoscape.equations.internal.interpreter.InterpreterImpl;
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.event.DummyCyEventHelper;
-import org.cytoscape.model.Identifiable;
+import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.CyTable.SavePolicy;
import org.cytoscape.model.internal.ArrayGraph;
import org.cytoscape.model.internal.CyNetworkTableManagerImpl;
@@ -90,9 +90,9 @@
public void tableWithVirtColumnDeletionTest() {
CyEventHelper eventHelper = new DummyCyEventHelper();
final Interpreter interpreter = new InterpreterImpl();
- CyTable table = new CyTableImpl("homer", Identifiable.SUID,
Long.class, true, true, SavePolicy.SESSION_FILE,
+ CyTable table = new CyTableImpl("homer", CyTableEntry.SUID,
Long.class, true, true, SavePolicy.SESSION_FILE,
eventHelper, interpreter);
- CyTable table2 = new CyTableImpl("marge", Identifiable.SUID,
Long.class, true, true, SavePolicy.SESSION_FILE,
+ CyTable table2 = new CyTableImpl("marge", CyTableEntry.SUID,
Long.class, true, true, SavePolicy.SESSION_FILE,
eventHelper, interpreter);
table.createColumn("x", Long.class, false);
Modified:
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableTest.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableTest.java
2011-12-12 21:49:39 UTC (rev 27770)
+++
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableTest.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -40,7 +40,7 @@
import org.cytoscape.equations.internal.EquationParserImpl;
import org.cytoscape.equations.internal.interpreter.InterpreterImpl;
import org.cytoscape.event.DummyCyEventHelper;
-import org.cytoscape.model.Identifiable;
+import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.CyTable.SavePolicy;
import org.cytoscape.model.internal.CyTableImpl;
import org.cytoscape.model.events.RowSetRecord;
@@ -58,10 +58,10 @@
public void setUp() {
eventHelper = new DummyCyEventHelper();
final Interpreter interpreter = new InterpreterImpl();
- table = new CyTableImpl("homer", Identifiable.SUID, Long.class,
false, true, SavePolicy.SESSION_FILE,
+ table = new CyTableImpl("homer", CyTableEntry.SUID, Long.class,
false, true, SavePolicy.SESSION_FILE,
eventHelper, interpreter);
attrs = table.getRow(1L);
- table2 = new CyTableImpl("marge", Identifiable.SUID,
Long.class, false, true, SavePolicy.SESSION_FILE,
+ table2 = new CyTableImpl("marge", CyTableEntry.SUID,
Long.class, false, true, SavePolicy.SESSION_FILE,
eventHelper, interpreter);
}
Deleted:
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/IdentifiableTest.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/IdentifiableTest.java
2011-12-12 21:49:39 UTC (rev 27770)
+++
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/IdentifiableTest.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -1,47 +0,0 @@
-/*
- Copyright (c) 2008, 2011, The Cytoscape Consortium (www.cytoscape.org)
-
- This library is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License as published
- by the Free Software Foundation; either version 2.1 of the License, or
- any later version.
-
- This library is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- documentation provided hereunder is on an "as is" basis, and the
- Institute for Systems Biology and the Whitehead Institute
- have no obligations to provide maintenance, support,
- updates, enhancements or modifications. In no event shall the
- Institute for Systems Biology and the Whitehead Institute
- be liable to any party for direct, indirect, special,
- incidental or consequential damages, including lost profits, arising
- out of the use of this software and its documentation, even if the
- Institute for Systems Biology and the Whitehead Institute
- have been advised of the possibility of such damage. See
- the GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with this library; if not, write to the Free Software Foundation,
- Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
-*/
-package org.cytoscape.model;
-
-
-import org.cytoscape.model.CyNetwork;
-
-import org.junit.Before;
-import org.junit.After;
-
-
-public class IdentifiableTest extends AbstractIdentifiableTest {
- @Before
- public void setUp() {
- net = TestCyNetworkFactory.getInstance();
- }
-
- @After
- public void tearDown() {
- net = null;
- }
-}
Modified:
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/TableTestSupportTest.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/TableTestSupportTest.java
2011-12-12 21:49:39 UTC (rev 27770)
+++
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/TableTestSupportTest.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -1,7 +1,7 @@
package org.cytoscape.model;
-import org.cytoscape.model.Identifiable;
+import org.cytoscape.model.CyTableEntry;
import org.junit.Before;
import org.junit.After;
@@ -26,8 +26,8 @@
@Before
public void setUp() {
eventHelper = support.getDummyCyEventHelper();
- table = factory.createTable(Integer.toString(
rand.nextInt(10000) ), Identifiable.SUID, Long.class, false, true);
- table2 = factory.createTable(Integer.toString(
rand.nextInt(10000) ), Identifiable.SUID, Long.class, false, true);
+ table = factory.createTable(Integer.toString(
rand.nextInt(10000) ), CyTableEntry.SUID, Long.class, false, true);
+ table2 = factory.createTable(Integer.toString(
rand.nextInt(10000) ), CyTableEntry.SUID, Long.class, false, true);
attrs = table.getRow(1l);
}
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
2011-12-12 21:49:39 UTC (rev 27770)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/VizMapPropertyBuilder.java
2011-12-12 22:03:31 UTC (rev 27771)
@@ -50,7 +50,7 @@
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.CyTableManager;
-import org.cytoscape.model.Identifiable;
+import org.cytoscape.model.CyTableEntry;
import org.cytoscape.view.model.VisualProperty;
import org.cytoscape.view.vizmap.VisualMappingFunction;
import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
@@ -247,7 +247,7 @@
id =
net.getRow(go).get(CyTableEntry.NAME, String.class);
- if (attrName.equals(Identifiable.SUID))
+ if (attrName.equals(CyTableEntry.SUID))
value = go.getSUID();
else if
(attrClass.isAssignableFrom(List.class))
value =
net.getRow(go).getList(attrName, column.getListElementType());
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
