Author: mes
Date: 2012-08-05 17:01:01 -0700 (Sun, 05 Aug 2012)
New Revision: 30103
Added:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/AbstractTableFacade.java
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/LocalTableFacade.java.with_abstract
Modified:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/api/model-api/src/main/java/org/cytoscape/model/CyNetwork.java
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/api/model-api/src/main/java/org/cytoscape/model/subnetwork/CyRootNetwork.java
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyRootNetworkImpl.java
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/CySubNetworkImpl.java
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/DefaultTablesNetwork.java
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/SharedTableFacade.java
Log:
first step in add row facade support
Modified:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/api/model-api/src/main/java/org/cytoscape/model/CyNetwork.java
===================================================================
---
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/api/model-api/src/main/java/org/cytoscape/model/CyNetwork.java
2012-08-04 08:40:48 UTC (rev 30102)
+++
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/api/model-api/src/main/java/org/cytoscape/model/CyNetwork.java
2012-08-06 00:01:01 UTC (rev 30103)
@@ -57,6 +57,17 @@
String DEFAULT_ATTRS = "USER";
/**
+ * The name of the local <b>public</b>
+ * CyTable that is created by default for CyNetworks,
+ * CyNodes, and CyEdges. This table contains attributes
+ * which are specific to only this network.
+ * -- see {@link CyTableManager} for more information.
+ * The table should be referenced using this constant:
+ * <code>CyNetwork.DEFAULT_ATTRS</code>.
+ */
+ String LOCAL_ATTRS = "LOCAL_ATTRS";
+
+ /**
* The name of the default <b>hidden</b> CyTable that is created
* by default for CyNetworks, CyNodes, and
* CyEdges. Other CyTables may also be associated with networks --
Modified:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/api/model-api/src/main/java/org/cytoscape/model/subnetwork/CyRootNetwork.java
===================================================================
---
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/api/model-api/src/main/java/org/cytoscape/model/subnetwork/CyRootNetwork.java
2012-08-04 08:40:48 UTC (rev 30102)
+++
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/api/model-api/src/main/java/org/cytoscape/model/subnetwork/CyRootNetwork.java
2012-08-06 00:01:01 UTC (rev 30103)
@@ -69,11 +69,20 @@
public interface CyRootNetwork extends CyNetwork {
/**
- * The name of the table shared by all subnetworks.
+ * The name of the table containing the attributes shared
+ * by all subnetworks of this root network.
+ * Direct use of this table is discouraged!
*/
String SHARED_ATTRS = "SHARED_ATTRS";
/**
+ * The name of the table that enables sharing default attributes
+ * with all subnetworks.
+ * Direct use of this table is discouraged!
+ */
+ String SHARED_DEFAULT_ATTRS = "SHARED_DEFAULT_ATTRS";
+
+ /**
* The name of the shared name column found in the SHARED_ATTRS table.
This
* column value will be updated any time the value of the
CyNetwork.NAME
* column in a default table is set. The purpose of this column is to
serve
Added:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/AbstractTableFacade.java
===================================================================
---
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/AbstractTableFacade.java
(rev 0)
+++
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/AbstractTableFacade.java
2012-08-06 00:01:01 UTC (rev 30103)
@@ -0,0 +1,252 @@
+
+/*
+ Copyright (c) 2008, 2010-2012, 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.internal;
+
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.cytoscape.equations.Equation;
+import org.cytoscape.equations.Interpreter;
+import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.model.CyIdentifiable;
+import org.cytoscape.model.CyColumn;
+import org.cytoscape.model.CyRow;
+import org.cytoscape.model.CyTable;
+import org.cytoscape.model.SavePolicy;
+import org.cytoscape.model.SUIDFactory;
+import org.cytoscape.model.VirtualColumnInfo;
+import org.cytoscape.model.events.ColumnCreatedEvent;
+import org.cytoscape.model.events.ColumnDeletedEvent;
+import org.cytoscape.model.events.ColumnNameChangedEvent;
+import org.cytoscape.model.events.RowSetRecord;
+import org.cytoscape.model.events.RowsCreatedEvent;
+import org.cytoscape.model.events.RowsSetEvent;
+import org.cytoscape.model.events.TableAddedEvent;
+import org.cytoscape.model.events.TableAddedListener;
+import org.cytoscape.model.events.TablePrivacyChangedEvent;
+import org.cytoscape.model.events.TableTitleChangedEvent;
+
+import com.google.common.collect.SetMultimap;
+import com.google.common.collect.HashMultimap;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+
+/**
+ * An abstract table facade class.
+ */
+public abstract class AbstractTableFacade implements CyTable {
+
+ private static final Logger logger =
LoggerFactory.getLogger(AbstractTableFacade.class);
+ private final CyTable actual;
+ private final Long suid;
+ private final Map<CyRow,CyRow> facadeRows;
+
+ public AbstractTableFacade(CyTable actual) {
+ this.actual = actual;
+ this.suid = Long.valueOf(SUIDFactory.getNextSUID());
+ this.facadeRows = new HashMap<CyRow,CyRow>();
+ }
+
+ public Long getSUID() {
+ return suid;
+ }
+
+ public boolean isPublic() {
+ return actual.isPublic();
+ }
+
+ public void setPublic (boolean isPublic) {
+ actual.setPublic(isPublic);
+ }
+
+ public CyTable.Mutability getMutability() {
+ return actual.getMutability();
+ }
+
+ public String getTitle() {
+ return actual.getTitle();
+ }
+
+ public void setTitle(String title) {
+ actual.setTitle(title);
+ }
+
+ public CyColumn getPrimaryKey() {
+ return actual.getPrimaryKey();
+ }
+
+ public CyColumn getColumn(String columnName) {
+ return actual.getColumn(columnName);
+ }
+
+ public Collection<CyColumn> getColumns() {
+ return actual.getColumns();
+ }
+
+ public void deleteColumn(String columnName) {
+ actual.deleteColumn(columnName);
+
+ }
+
+ public CyRow getRow(Object primaryKey) {
+ CyRow actualRow = actual.getRow(primaryKey);
+ if ( actualRow == null )
+ return null;
+
+ return getFacadeRow(actualRow);
+ }
+
+ private CyRow getFacadeRow(CyRow actualRow) {
+ CyRow ret = facadeRows.get(actualRow);
+ if ( ret == null ) {
+ ret = new RowFacade(actualRow,this);
+ facadeRows.put(actualRow,ret);
+ }
+
+ return ret;
+ }
+
+ public boolean rowExists(Object primaryKey) {
+ return actual.rowExists(primaryKey);
+ }
+
+ public boolean deleteRows(Collection<?> primaryKeys) {
+ return actual.deleteRows(primaryKeys);
+ }
+
+ public List<CyRow> getAllRows() {
+ return getFacadeRows(actual.getAllRows());
+ }
+
+ public String getLastInternalError() {
+ return actual.getLastInternalError();
+ }
+
+ public Collection<CyRow> getMatchingRows(String columnName, Object
value) {
+ return getFacadeRows(actual.getMatchingRows(columnName,value));
+ }
+
+ private List<CyRow> getFacadeRows(Collection<CyRow> rows) {
+ List<CyRow> frows = new ArrayList<CyRow>( rows.size() );
+ for ( CyRow r : rows )
+ frows.add( getFacadeRow(r) );
+
+ return frows;
+ }
+
+ public int countMatchingRows(String columnName, Object value) {
+ return actual.countMatchingRows(columnName, value);
+
+ }
+
+ public int getRowCount() {
+ return actual.getRowCount();
+ }
+
+ public SavePolicy getSavePolicy() {
+ return actual.getSavePolicy();
+ }
+
+ public void setSavePolicy(SavePolicy policy) {
+ actual.setSavePolicy(policy);
+ }
+
+ public void swap(CyTable otherTable) {
+ // TODO do we need to do something here?
+ actual.swap(otherTable);
+ }
+
+ private class RowFacade implements CyRow {
+ private final CyRow actualRow;
+ private final CyTable table;
+
+ RowFacade(CyRow actualRow, CyTable table) {
+ this.actualRow = actualRow;
+ this.table = table;
+ }
+
+ @Override
+ public void set(String attributeName, Object value) {
+ actualRow.set(attributeName,value);
+ }
+
+ @Override
+ public <T> T get(String attributeName, Class<? extends T> c) {
+ return actualRow.get(attributeName, c);
+ }
+
+ @Override
+ public <T> T get(String attributeName, Class<? extends T> c, T
defValue) {
+ return actualRow.get(attributeName, c, defValue);
+ }
+
+ @Override
+ public <T> List<T> getList(String attributeName, Class<T> c) {
+ return actualRow.getList(attributeName, c);
+ }
+
+ @Override
+ public <T> List<T> getList(String attributeName, Class<T> c,
List<T> defValue) {
+ return actualRow.getList( attributeName, c, defValue);
+ }
+
+ @Override
+ public Object getRaw(String attributeName) {
+ return actualRow.getRaw(attributeName);
+ }
+
+ @Override
+ public boolean isSet(String attributeName) {
+ return actualRow.isSet(attributeName);
+ }
+
+ @Override
+ public Map<String, Object> getAllValues() {
+ return actualRow.getAllValues();
+ }
+
+ @Override
+ public CyTable getTable() {
+ return table;
+ }
+
+ @Override
+ public String toString() {
+ return "FACADE of: " + actualRow.toString();
+ }
+ }
+}
Modified:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyRootNetworkImpl.java
===================================================================
---
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyRootNetworkImpl.java
2012-08-04 08:40:48 UTC (rev 30102)
+++
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyRootNetworkImpl.java
2012-08-06 00:01:01 UTC (rev 30103)
@@ -108,9 +108,9 @@
createRootNetworkTables();
initTables(this,
- (SharedTableFacade)(networkTableMgr.getTable(this,
CyNetwork.class, "SHARED_ATTRS_FACADE")),
- (SharedTableFacade)(networkTableMgr.getTable(this,
CyNode.class, "SHARED_ATTRS_FACADE")),
-
(SharedTableFacade)(networkTableMgr.getTable(this, CyEdge.class,
"SHARED_ATTRS_FACADE")) );
+ (SharedTableFacade)(networkTableMgr.getTable(this,
CyNetwork.class, CyRootNetwork.SHARED_DEFAULT_ATTRS)),
+ (SharedTableFacade)(networkTableMgr.getTable(this,
CyNode.class, CyRootNetwork.SHARED_DEFAULT_ATTRS)),
+
(SharedTableFacade)(networkTableMgr.getTable(this, CyEdge.class,
CyRootNetwork.SHARED_DEFAULT_ATTRS)) );
getRow(this).set(CyNetwork.NAME, "");
@@ -160,7 +160,7 @@
final CyTable edgeSharedTable = new
SharedTableFacade(rawEdgeSharedTable,this,CyEdge.class,networkTableMgr);
networkTableMgr.setTable(this, CyEdge.class,
CyRootNetwork.SHARED_ATTRS, rawEdgeSharedTable);
- networkTableMgr.setTable(this, CyEdge.class,
"SHARED_ATTRS_FACADE", edgeSharedTable);
+ networkTableMgr.setTable(this, CyEdge.class,
CyRootNetwork.SHARED_DEFAULT_ATTRS, edgeSharedTable);
edgeSharedTable.createColumn(CyRootNetwork.SHARED_NAME,
String.class, true);
edgeSharedTable.createColumn(CyRootNetwork.SHARED_INTERACTION,
String.class, true);
@@ -171,7 +171,7 @@
final CyTable networkSharedTable = new
SharedTableFacade(rawNetworkSharedTable,this,CyNetwork.class,networkTableMgr);
networkTableMgr.setTable(this, CyNetwork.class,
CyRootNetwork.SHARED_ATTRS, rawNetworkSharedTable);
- networkTableMgr.setTable(this, CyNetwork.class,
"SHARED_ATTRS_FACADE", networkSharedTable);
+ networkTableMgr.setTable(this, CyNetwork.class,
CyRootNetwork.SHARED_DEFAULT_ATTRS, networkSharedTable);
networkSharedTable.createColumn(CyRootNetwork.SHARED_NAME,
String.class, true);
@@ -179,7 +179,7 @@
final CyTable nodeSharedTable = new
SharedTableFacade(rawNodeSharedTable,this,CyNode.class,networkTableMgr);
networkTableMgr.setTable(this, CyNode.class,
CyRootNetwork.SHARED_ATTRS, rawNodeSharedTable);
- networkTableMgr.setTable(this, CyNode.class,
"SHARED_ATTRS_FACADE", nodeSharedTable);
+ networkTableMgr.setTable(this, CyNode.class,
CyRootNetwork.SHARED_DEFAULT_ATTRS, nodeSharedTable);
nodeSharedTable.createColumn(CyRootNetwork.SHARED_NAME,
String.class, true);
}
@@ -288,10 +288,10 @@
networkAddedListenerDelegator.addListener(sub);
subNetworks.add(sub);
-
nameSetListener.addInterestedTables(sub.getDefaultNetworkTable(),networkTableMgr.getTable(this,
CyNetwork.class, "SHARED_ATTRS_FACADE"));
-
nameSetListener.addInterestedTables(sub.getDefaultNodeTable(),networkTableMgr.getTable(this,
CyNode.class, "SHARED_ATTRS_FACADE"));
-
nameSetListener.addInterestedTables(sub.getDefaultEdgeTable(),networkTableMgr.getTable(this,
CyEdge.class, "SHARED_ATTRS_FACADE"));
-
interactionSetListener.addInterestedTables(sub.getDefaultEdgeTable(),
networkTableMgr.getTable(this, CyEdge.class, "SHARED_ATTRS_FACADE"));
+
nameSetListener.addInterestedTables(sub.getDefaultNetworkTable(),networkTableMgr.getTable(this,
CyNetwork.class, CyRootNetwork.SHARED_DEFAULT_ATTRS));
+
nameSetListener.addInterestedTables(sub.getDefaultNodeTable(),networkTableMgr.getTable(this,
CyNode.class, CyRootNetwork.SHARED_DEFAULT_ATTRS));
+
nameSetListener.addInterestedTables(sub.getDefaultEdgeTable(),networkTableMgr.getTable(this,
CyEdge.class, CyRootNetwork.SHARED_DEFAULT_ATTRS));
+
interactionSetListener.addInterestedTables(sub.getDefaultEdgeTable(),
networkTableMgr.getTable(this, CyEdge.class,
CyRootNetwork.SHARED_DEFAULT_ATTRS));
return sub;
@@ -327,17 +327,17 @@
@Override
public CyTable getSharedNetworkTable() {
- return networkTableMgr.getTable(this, CyNetwork.class,
"SHARED_ATTRS_FACADE");
+ return networkTableMgr.getTable(this, CyNetwork.class,
CyRootNetwork.SHARED_DEFAULT_ATTRS);
}
@Override
public CyTable getSharedNodeTable() {
- return networkTableMgr.getTable(this, CyNode.class,
"SHARED_ATTRS_FACADE");
+ return networkTableMgr.getTable(this, CyNode.class,
CyRootNetwork.SHARED_DEFAULT_ATTRS);
}
@Override
public CyTable getSharedEdgeTable() {
- return networkTableMgr.getTable(this, CyEdge.class,
"SHARED_ATTRS_FACADE");
+ return networkTableMgr.getTable(this, CyEdge.class,
CyRootNetwork.SHARED_DEFAULT_ATTRS);
}
@Override
Modified:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/CySubNetworkImpl.java
===================================================================
---
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/CySubNetworkImpl.java
2012-08-04 08:40:48 UTC (rev 30102)
+++
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/CySubNetworkImpl.java
2012-08-06 00:01:01 UTC (rev 30103)
@@ -90,9 +90,9 @@
this.savePolicy = savePolicy;
initTables(this,
- (SharedTableFacade)(networkTableMgr.getTable(parent,
CyNetwork.class, "SHARED_ATTRS_FACADE")),
- (SharedTableFacade)(networkTableMgr.getTable(parent,
CyNode.class, "SHARED_ATTRS_FACADE")),
-
(SharedTableFacade)(networkTableMgr.getTable(parent, CyEdge.class,
"SHARED_ATTRS_FACADE")) );
+ (SharedTableFacade)(networkTableMgr.getTable(parent,
CyNetwork.class, CyRootNetwork.SHARED_DEFAULT_ATTRS)),
+ (SharedTableFacade)(networkTableMgr.getTable(parent,
CyNode.class, CyRootNetwork.SHARED_DEFAULT_ATTRS)),
+
(SharedTableFacade)(networkTableMgr.getTable(parent, CyEdge.class,
CyRootNetwork.SHARED_DEFAULT_ATTRS)) );
fireAddedNodesAndEdgesEvents = false;
}
Modified:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/DefaultTablesNetwork.java
===================================================================
---
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/DefaultTablesNetwork.java
2012-08-04 08:40:48 UTC (rev 30102)
+++
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/DefaultTablesNetwork.java
2012-08-06 00:01:01 UTC (rev 30103)
@@ -132,7 +132,7 @@
private void createNetworkTables(long suidx, CyTableFactory
tableFactory, boolean pubTables, SharedTableFacade sharedNetworkTable) {
final CyTable defTable = tableFactory.createTable(suidx
+ " default network", CyIdentifiable.SUID,
Long.class, pubTables, false, InitialTableSize.SMALL);
- networkTableManager.setTable(networkRef.get(), CyNetwork.class,
"LOCAL_ATTRS", defTable);
+ networkTableManager.setTable(networkRef.get(), CyNetwork.class,
CyNetwork.LOCAL_ATTRS, defTable);
LocalTableFacade localTable = new
LocalTableFacade(defTable,sharedNetworkTable);
networkTableManager.setTable(networkRef.get(), CyNetwork.class,
CyNetwork.DEFAULT_ATTRS, localTable);
if ( eventHelper instanceof TableEventHelperFacade )
@@ -149,7 +149,7 @@
private void createNodeTables(long suidx, CyTableFactory tableFactory,
boolean pubTables, int num, SharedTableFacade sharedNodeTable) {
final CyTable defTable = tableFactory.createTable(suidx
+ " default node", CyIdentifiable.SUID,
Long.class, pubTables, false, InitialTableSize.SMALL);
- networkTableManager.setTable(networkRef.get(), CyNode.class,
"LOCAL_ATTRS", defTable);
+ networkTableManager.setTable(networkRef.get(), CyNode.class,
CyNetwork.LOCAL_ATTRS, defTable);
LocalTableFacade localTable = new
LocalTableFacade(defTable,sharedNodeTable);
networkTableManager.setTable(networkRef.get(), CyNode.class,
CyNetwork.DEFAULT_ATTRS, localTable);
if ( eventHelper instanceof TableEventHelperFacade )
@@ -166,7 +166,7 @@
private void createEdgeTables(long suidx, CyTableFactory tableFactory,
boolean pubTables, int num, SharedTableFacade sharedEdgeTable) {
final CyTable defTable = tableFactory.createTable(suidx + "
default edge", CyIdentifiable.SUID, Long.class,
pubTables, false, InitialTableSize.SMALL);
- networkTableManager.setTable(networkRef.get(), CyEdge.class,
"LOCAL_ATTRS", defTable);
+ networkTableManager.setTable(networkRef.get(), CyEdge.class,
CyNetwork.LOCAL_ATTRS, defTable);
LocalTableFacade localTable = new
LocalTableFacade(defTable,sharedEdgeTable);
networkTableManager.setTable(networkRef.get(), CyEdge.class,
CyNetwork.DEFAULT_ATTRS, localTable);
Added:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/LocalTableFacade.java.with_abstract
===================================================================
---
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/LocalTableFacade.java.with_abstract
(rev 0)
+++
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/LocalTableFacade.java.with_abstract
2012-08-06 00:01:01 UTC (rev 30103)
@@ -0,0 +1,122 @@
+
+/*
+ Copyright (c) 2008, 2010-2012, 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.internal;
+
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.cytoscape.equations.Equation;
+import org.cytoscape.equations.Interpreter;
+import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.model.CyIdentifiable;
+import org.cytoscape.model.CyColumn;
+import org.cytoscape.model.CyRow;
+import org.cytoscape.model.CyTable;
+import org.cytoscape.model.SavePolicy;
+import org.cytoscape.model.SUIDFactory;
+import org.cytoscape.model.VirtualColumnInfo;
+import org.cytoscape.model.events.ColumnCreatedEvent;
+import org.cytoscape.model.events.ColumnDeletedEvent;
+import org.cytoscape.model.events.ColumnNameChangedEvent;
+import org.cytoscape.model.events.RowSetRecord;
+import org.cytoscape.model.events.RowsCreatedEvent;
+import org.cytoscape.model.events.RowsSetEvent;
+import org.cytoscape.model.events.TableAddedEvent;
+import org.cytoscape.model.events.TableAddedListener;
+import org.cytoscape.model.events.TablePrivacyChangedEvent;
+import org.cytoscape.model.events.TableTitleChangedEvent;
+
+import com.google.common.collect.SetMultimap;
+import com.google.common.collect.HashMultimap;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+
+/**
+ * A facade class that provides a unified interface for a default table
+ * that has properties of both shared and local tables. All accessor methods
+ * query the local table. All table metadata (public, mutability, etc.) is
+ * stored and accessed in the local table. All column creation methods create
the columns
+ * on the shared table and then immediately create a virtual column of this
+ * new column in the local table. All virtual column methods create virtual
+ * columns in both the shared and local tables.
+ */
+public final class LocalTableFacade extends AbstractTableFacade implements
CyTable {
+
+
+ private static final Logger logger =
LoggerFactory.getLogger(LocalTableFacade.class);
+ private final CyTable shared;
+ private final CyTable local;
+
+ public LocalTableFacade(CyTable local, SharedTableFacade shared) {
+ super(local);
+ this.local = local;
+ this.shared = shared;
+
+ // this adds virtual columns for any existing columns already
in the shared table
+ local.addVirtualColumns(shared.getActualTable(),
CyIdentifiable.SUID, true);
+ }
+
+ CyTable getLocalTable() {
+ return local;
+ }
+
+ public <T> void createColumn(String columnName, Class<?extends T> type,
boolean isImmutable) {
+ createColumn(columnName,type,isImmutable,null);
+ }
+
+ public <T> void createColumn(String columnName, Class<?extends T> type,
boolean isImmutable, T defaultValue) {
+ logger.debug("delegating createColumn '" + columnName + "' from
local " + local.getTitle() + " to shared: " + shared.getTitle());
+ shared.createColumn(columnName,type,isImmutable,defaultValue);
+ }
+
+ public <T> void createListColumn(String columnName, Class<T>
listElementType, boolean isImmutable) {
+ createListColumn(columnName,listElementType,isImmutable,null);
+ }
+
+ public <T> void createListColumn(String columnName, Class<T>
listElementType, boolean isImmutable, List<T> defaultValue ) {
+
shared.createListColumn(columnName,listElementType,isImmutable,defaultValue);
+ }
+
+ public String addVirtualColumn(String virtualColumn, String
sourceColumn, CyTable sourceTable, String targetJoinKey, boolean isImmutable) {
+ String s = shared.addVirtualColumn(virtualColumn, sourceColumn,
sourceTable, targetJoinKey, isImmutable);
+ return s;
+ }
+
+ public void addVirtualColumns(CyTable sourceTable, String
targetJoinKey, boolean isImmutable) {
+ shared.addVirtualColumns(sourceTable, targetJoinKey,
isImmutable);
+ }
+}
Modified:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/SharedTableFacade.java
===================================================================
---
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/SharedTableFacade.java
2012-08-04 08:40:48 UTC (rev 30102)
+++
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/model-impl/impl/src/main/java/org/cytoscape/model/internal/SharedTableFacade.java
2012-08-06 00:01:01 UTC (rev 30103)
@@ -43,6 +43,7 @@
import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
+import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.SavePolicy;
import org.cytoscape.model.SUIDFactory;
import org.cytoscape.model.CyNetworkTableManager;
@@ -70,18 +71,17 @@
/**
*/
-public final class SharedTableFacade implements CyTable {
+public final class SharedTableFacade extends AbstractTableFacade implements
CyTable {
private static final Logger logger =
LoggerFactory.getLogger(SharedTableFacade.class);
- private final CyTable shared;
- private final Long suid;
+ private final CyTable shared;
private final CyRootNetwork rootNetwork;
private final Class<? extends CyIdentifiable> type;
private final CyNetworkTableManager netTableMgr;
public SharedTableFacade(CyTable shared, CyRootNetwork rootNetwork,
Class<? extends CyIdentifiable> type, CyNetworkTableManager netTableMgr ) {
+ super(shared);
this.shared = shared;
- this.suid = Long.valueOf(SUIDFactory.getNextSUID());
this.rootNetwork = rootNetwork;
this.type = type;
this.netTableMgr = netTableMgr;
@@ -94,56 +94,15 @@
private List<CyTable> localTables() {
logger.debug(" - looking for local tables: ");
List<CyTable> tables = new ArrayList<CyTable>();
- tables.add( netTableMgr.getTable( rootNetwork, type,
"LOCAL_ATTRS" ) );
+ tables.add( netTableMgr.getTable( rootNetwork, type,
CyNetwork.LOCAL_ATTRS ) );
for (CyNetwork sub : rootNetwork.getSubNetworkList()) {
logger.debug(" -- found subnetwork with local tables:
" + sub.toString());
- tables.add( netTableMgr.getTable( sub, type,
"LOCAL_ATTRS" ) );
+ tables.add( netTableMgr.getTable( sub, type,
CyNetwork.LOCAL_ATTRS ) );
}
return tables;
}
- public Long getSUID() {
- return suid;
- }
-
- public boolean isPublic() {
- return shared.isPublic();
- }
-
- public void setPublic (boolean isPublic) {
- shared.setPublic(isPublic);
- }
-
- public CyTable.Mutability getMutability() {
- return shared.getMutability();
- }
-
- public String getTitle() {
- return shared.getTitle();
- }
-
- public void setTitle(String title) {
- shared.setTitle(title);
- }
-
- public CyColumn getPrimaryKey() {
- return shared.getPrimaryKey();
- }
-
- public CyColumn getColumn(String columnName) {
- return shared.getColumn(columnName);
- }
-
- public Collection<CyColumn> getColumns() {
- return shared.getColumns();
- }
-
- public void deleteColumn(String columnName) {
- shared.deleteColumn(columnName);
-
- }
-
public <T> void createColumn(String columnName, Class<?extends T> type,
boolean isImmutable) {
createColumn(columnName, type, isImmutable,null);
}
@@ -172,38 +131,6 @@
local.addVirtualColumn(columnName,columnName,shared,CyIdentifiable.SUID,isImmutable);
}
- public CyRow getRow(Object primaryKey) {
- return shared.getRow(primaryKey);
- }
-
- public boolean rowExists(Object primaryKey) {
- return shared.rowExists(primaryKey);
- }
-
- public boolean deleteRows(Collection<?> primaryKeys) {
- return shared.deleteRows(primaryKeys);
- }
-
- public List<CyRow> getAllRows() {
- return shared.getAllRows();
- }
-
- public String getLastInternalError() {
- return shared.getLastInternalError();
- }
-
- public Collection<CyRow> getMatchingRows(String columnName, Object
value) {
- return shared.getMatchingRows(columnName,value);
- }
-
- public int countMatchingRows(String columnName, Object value) {
- return shared.countMatchingRows(columnName, value);
- }
-
- public int getRowCount() {
- return shared.getRowCount();
- }
-
public String addVirtualColumn(String virtualColumn, String
sourceColumn, CyTable sourceTable, String targetJoinKey, boolean isImmutable) {
//String ret = shared.addVirtualColumn(virtualColumn,
sourceColumn, sourceTable, targetJoinKey, isImmutable);
for ( CyTable local : localTables() )
@@ -216,16 +143,4 @@
for ( CyTable local : localTables() )
local.addVirtualColumns(sourceTable, targetJoinKey,
isImmutable);
}
-
- public SavePolicy getSavePolicy() {
- return shared.getSavePolicy();
- }
-
- public void setSavePolicy(SavePolicy policy) {
- shared.setSavePolicy(policy);
- }
-
- public void swap(CyTable otherTable) {
- shared.swap(otherTable);
- }
}
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