Author: mes
Date: 2010-09-05 16:44:35 -0700 (Sun, 05 Sep 2010)
New Revision: 21706
Modified:
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyDataTableFactoryImpl.java
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyDataTableImpl.java
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyNetworkFactoryImpl.java
core3/model-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
core3/model-impl/trunk/src/test/java/org/cytoscape/model/CyDataTableTest.java
core3/model-impl/trunk/src/test/java/org/cytoscape/model/TestCyNetworkFactory.java
Log:
added the concept of primary key to CyDataTable
Modified:
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
===================================================================
---
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
2010-09-05 23:44:18 UTC (rev 21705)
+++
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
2010-09-05 23:44:35 UTC (rev 21706)
@@ -46,6 +46,7 @@
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.model.CyDataTable;
import org.cytoscape.model.CyTableManager;
+import org.cytoscape.model.CyDataTableFactory;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
@@ -107,7 +108,7 @@
* Creates a new ArrayGraph object.
* @param eh The CyEventHelper used for firing events.
*/
- public ArrayGraph(final CyEventHelper eh, final CyTableManager
tableMgr) {
+ public ArrayGraph(final CyEventHelper eh, final CyTableManager
tableMgr, final CyDataTableFactory tableFactory) {
this.tableMgr = tableMgr;
suid = SUIDFactory.getNextSUID();
numSubNetworks = 0;
@@ -118,23 +119,23 @@
edgePointers = new ArrayList<EdgePointer>();
netAttrMgr = new HashMap<String, CyDataTable>();
- netAttrMgr.put(CyNetwork.DEFAULT_ATTRS, new
CyDataTableImpl(null, suid + " network", true,eh));
- netAttrMgr.put(CyNetwork.HIDDEN_ATTRS, new
CyDataTableImpl(null, suid + " network", false,eh));
+ netAttrMgr.put(CyNetwork.DEFAULT_ATTRS,
tableFactory.createTable( suid + " network", "SUID", Long.class, true));
+ netAttrMgr.put(CyNetwork.HIDDEN_ATTRS,
tableFactory.createTable( suid + " network", "SUID", Long.class, false));
netAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn("name",String.class,false);
attrs().set("name","");
// potential leak since "this" isn't yet fully constructed
nodeAttrMgr = new HashMap<String, CyDataTable>();
- nodeAttrMgr.put(CyNetwork.DEFAULT_ATTRS, new
CyDataTableImpl(null, suid + " node", true,eh));
- nodeAttrMgr.put(CyNetwork.HIDDEN_ATTRS, new
CyDataTableImpl(null, suid + " node", false,eh));
+ nodeAttrMgr.put(CyNetwork.DEFAULT_ATTRS,
tableFactory.createTable( suid + " node", "SUID", Long.class, true));
+ nodeAttrMgr.put(CyNetwork.HIDDEN_ATTRS,
tableFactory.createTable( suid + " node", "SUID", Long.class, false));
nodeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn("name",String.class,false);
nodeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn("selected",Boolean.class,false);
edgeAttrMgr = new HashMap<String, CyDataTable>();
- edgeAttrMgr.put(CyNetwork.DEFAULT_ATTRS, new
CyDataTableImpl(null, suid + " edge", true,eh));
- edgeAttrMgr.put(CyNetwork.HIDDEN_ATTRS, new
CyDataTableImpl(null, suid + " edge", false,eh));
+ edgeAttrMgr.put(CyNetwork.DEFAULT_ATTRS,
tableFactory.createTable( suid + " edge", "SUID", Long.class, true));
+ edgeAttrMgr.put(CyNetwork.HIDDEN_ATTRS,
tableFactory.createTable( suid + " edge", "SUID", Long.class, false));
edgeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn("name",String.class,false);
edgeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn("selected",Boolean.class,false);
Modified:
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyDataTableFactoryImpl.java
===================================================================
---
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyDataTableFactoryImpl.java
2010-09-05 23:44:18 UTC (rev 21705)
+++
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyDataTableFactoryImpl.java
2010-09-05 23:44:35 UTC (rev 21706)
@@ -60,15 +60,8 @@
tables = new HashMap<Long,CyDataTable>();
}
- /**
- * @param name The name of the CyDataTable.
- * @param pub Whether or not the CyDataTable should be public.
- *
- * @return A new {...@link CyDataTable} with the specified name that is
either public or not (see
- * {...@link CyDataTable#isPublic}.
- */
- public CyDataTable createTable(String name, boolean pub) {
- CyDataTable cdt = new CyDataTableImpl(null,name,pub,help);
+ public CyDataTable createTable(String name, String primaryKey, Class<?>
primaryKeyType, boolean pub) {
+ CyDataTable cdt = new
CyDataTableImpl(name,primaryKey,primaryKeyType,pub,help);
tables.put( cdt.getSUID(), cdt );
return cdt;
}
Modified:
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyDataTableImpl.java
===================================================================
---
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyDataTableImpl.java
2010-09-05 23:44:18 UTC (rev 21705)
+++
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyDataTableImpl.java
2010-09-05 23:44:35 UTC (rev 21706)
@@ -39,6 +39,7 @@
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import java.util.Collections;
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.model.CyDataTable;
@@ -53,8 +54,8 @@
*/
public class CyDataTableImpl implements CyDataTable {
- private final Map<String, Map<Long, Object>> attributes;
- private final Map<Long, CyRow> rows;
+ private final Map<String, Map<Object, Object>> attributes;
+ private final Map<Object, CyRow> rows;
private final Map<String, Class<?>> types;
private final Map<String, Boolean> unique;
@@ -68,9 +69,10 @@
// Unique ID.
private final long suid;
- private CyEventHelper eventHelper;
+ private final String primaryKey;
+ private final Class<?> primaryKeyType;
- private long rowSUID = -1;
+ private final CyEventHelper eventHelper;
/**
* Creates a new CyDataTableImpl object.
@@ -82,24 +84,19 @@
* @param pub
* DOCUMENT ME!
*/
- public CyDataTableImpl(Map<String, Class<?>> typeMap, String name,
+ public CyDataTableImpl(String title, String primaryKey, Class<?>
primaryKeyType,
boolean pub, final CyEventHelper eventHelper) {
- this.title = name;
+ this.title = title;
+ this.primaryKey = primaryKey;
+ this.primaryKeyType = primaryKeyType;
this.pub = pub;
this.suid = SUIDFactory.getNextSUID();
this.eventHelper = eventHelper;
- attributes = new HashMap<String, Map<Long, Object>>();
- rows = new HashMap<Long, CyRow>();
-
- if (typeMap == null) {
- types = new HashMap<String, Class<?>>();
- unique = new HashMap<String, Boolean>();
- } else {
- types = new HashMap<String, Class<?>>(typeMap);
- // TODO!
- unique = new HashMap<String, Boolean>();
- }
-
+ attributes = new HashMap<String, Map<Object, Object>>();
+ rows = new HashMap<Object, CyRow>();
+ types = new HashMap<String, Class<?>>();
+ types.put(primaryKey,primaryKeyType);
+ unique = new HashMap<String, Boolean>();
}
/**
@@ -145,9 +142,17 @@
* @return DOCUMENT ME!
*/
public Map<String, Class<?>> getColumnTypeMap() {
- return new HashMap<String, Class<?>>(types);
+ return Collections.unmodifiableMap(types);
}
+ public String getPrimaryKey() {
+ return primaryKey;
+ }
+
+ public Class<?> getPrimaryKeyType() {
+ return primaryKeyType;
+ }
+
/**
* DOCUMENT ME!
*
@@ -189,7 +194,7 @@
if (curr == null) {
types.put(attributeName, cls);
- attributes.put(attributeName, new HashMap<Long,
Object>());
+ attributes.put(attributeName, new HashMap<Object,
Object>());
unique.put(attributeName, u);
// Fire event
@@ -235,7 +240,7 @@
if (columnName == null)
throw new NullPointerException("column name is null");
- Map<Long, Object> vals = attributes.get(columnName);
+ Map<Object, Object> vals = attributes.get(columnName);
if (vals == null)
throw new NullPointerException("attribute does not
exist");
@@ -256,7 +261,8 @@
*
* @return DOCUMENT ME!
*/
- public CyRow getRow(final long suid) {
+ public CyRow getRow(final Object suid) {
+ checkKey(suid);
CyRow row = rows.get(suid);
if (row != null)
return row;
@@ -266,39 +272,31 @@
return row;
}
- public List<CyRow> getAllRows()
- {
- return new ArrayList<CyRow>(rows.values());
- }
+ private void checkKey(final Object suid) {
+ if ( suid == null )
+ throw new NullPointerException("key is null");
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public CyRow addRow() {
- long r;
- synchronized (this) {
- r = rowSUID--;
- }
+ if ( !primaryKeyType.isAssignableFrom( suid.getClass() ) )
+ throw new IllegalArgumentException("key of type " +
suid.getClass() + " and not the expected: " + primaryKeyType);
- CyRow row = new InternalRow(r, this);
- rows.put(r, row);
+ }
- return row;
+ public List<CyRow> getAllRows() {
+ return new ArrayList<CyRow>(rows.values());
}
+
// internal methods
- private void removeX(long suid, String attributeName) {
+ private void removeX(Object suid, String attributeName) {
if (attributes.containsKey(attributeName)) {
- Map<Long, Object> map = attributes.get(attributeName);
+ Map<Object, Object> map = attributes.get(attributeName);
if (map.containsKey(suid))
map.remove(suid);
}
}
- private void setX(long suid, String attrName, Object value) {
+ private void setX(Object suid, String attrName, Object value) {
if (value == null)
throw new NullPointerException("value is null");
@@ -308,19 +306,19 @@
checkType(value);
- Map<Long, Object> vls = attributes.get(attrName);
+ Map<Object, Object> vls = attributes.get(attrName);
if (types.get(attrName).isAssignableFrom(value.getClass())) {
// TODO this is an implicit addRow - not sure if we
want to refactor this or not
vls.put(suid, value);
- eventHelper.getMicroListener(RowSetMicroListener.class,
getRow(suid)).handleRowSet(attrName, value);
+ eventHelper.getMicroListener(RowSetMicroListener.class,
getRow(suid)).handleRowSet(attrName,value);
} else
throw new IllegalArgumentException("value is not of
type: "
+ types.get(attrName));
}
- private Object getRawX(long suid, String attrName) {
- Map<Long, Object> vls = attributes.get(attrName);
+ private Object getRawX(Object suid, String attrName) {
+ Map<Object, Object> vls = attributes.get(attrName);
if (vls == null)
return null;
@@ -328,7 +326,7 @@
return vls.get(suid);
}
- private <T> T getX(long suid, String attrName, Class<? extends T> type)
{
+ private <T> T getX(Object suid, String attrName, Class<? extends T>
type) {
Object vl = getRawX(suid, attrName);
if (vl == null)
@@ -337,9 +335,9 @@
return type.cast(vl);
}
- private <T> boolean containsX(long suid, String attrName,
+ private <T> boolean containsX(Object suid, String attrName,
Class<? extends T> type) {
- Map<Long, Object> vls = attributes.get(attrName);
+ Map<Object, Object> vls = attributes.get(attrName);
if (vls == null)
return false;
@@ -356,8 +354,8 @@
return false;
}
- private Class<?> containsX(long suid, String attrName) {
- Map<Long, Object> vls = attributes.get(attrName);
+ private Class<?> containsX(Object suid, String attrName) {
+ Map<Object, Object> vls = attributes.get(attrName);
if (vls == null)
return null;
@@ -420,10 +418,10 @@
}
private class InternalRow implements CyRow {
- private final long suid;
+ private final Object suid;
private final CyDataTable table;
- InternalRow(long suid, CyDataTable table) {
+ InternalRow(Object suid, CyDataTable table) {
this.suid = suid;
this.table = table;
}
@@ -469,16 +467,17 @@
InternalRow ir = (InternalRow) o;
+ // TODO is this sufficent since we're not using long
any more?
if (ir.suid == this.suid)
return true;
else
-
return false;
}
public @Override
int hashCode() {
- return (int) (suid ^ (suid >>> 32));
+ // TODO is this right?
+ return suid.hashCode();
}
public CyDataTable getDataTable() {
Modified:
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyNetworkFactoryImpl.java
===================================================================
---
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyNetworkFactoryImpl.java
2010-09-05 23:44:18 UTC (rev 21705)
+++
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyNetworkFactoryImpl.java
2010-09-05 23:44:35 UTC (rev 21706)
@@ -38,6 +38,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyTableManager;
+import org.cytoscape.model.CyDataTableFactory;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -51,31 +52,35 @@
private final CyEventHelper help;
private final CyTableManager mgr;
+ private final CyDataTableFactory tableFactory;
/**
* Creates a new CyNetworkFactoryImpl object.
*
* @param help An instance of CyEventHelper.
*/
- public CyNetworkFactoryImpl(final CyEventHelper help, final
CyTableManager mgr) {
+ public CyNetworkFactoryImpl(final CyEventHelper help, final
CyTableManager mgr, final CyDataTableFactory tableFactory) {
if (help == null)
throw new NullPointerException("CyEventHelper is null");
if (mgr == null)
throw new NullPointerException("CyTableManager is
null");
+ if (tableFactory == null)
+ throw new NullPointerException("CyDataTableFactory is
null");
+
this.help = help;
this.mgr = mgr;
+ this.tableFactory = tableFactory;
}
/**
* {...@inheritdoc}
*/
public CyNetwork getInstance() {
- //return new MGraph(help);
- ArrayGraph net = new ArrayGraph(help,mgr);
- logger.info("ArrayGraph created: ID = " + net.getSUID());
- logger.info("ArrayGraph created: Base Graph ID = " +
net.getBaseNetwork().getSUID());
+ ArrayGraph net = new ArrayGraph(help,mgr,tableFactory);
+ logger.info("CyNetwork created: ID = " + net.getSUID());
+ logger.info("CyNetwork created: Base Graph ID = " +
net.getBaseNetwork().getSUID());
return net.getBaseNetwork();
}
}
Modified:
core3/model-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/model-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2010-09-05 23:44:18 UTC (rev 21705)
+++
core3/model-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2010-09-05 23:44:35 UTC (rev 21706)
@@ -18,13 +18,14 @@
<bean id="cyTableManager"
class="org.cytoscape.model.internal.CyTableManagerImpl">
</bean>
- <bean id="cyNetworkFactory"
class="org.cytoscape.model.internal.CyNetworkFactoryImpl">
+ <bean id="cyDataTableFactory"
class="org.cytoscape.model.internal.CyDataTableFactoryImpl">
<constructor-arg ref="cyEventHelperServiceRef" />
- <constructor-arg ref="cyTableManager" />
</bean>
- <bean id="cyDataTableFactory"
class="org.cytoscape.model.internal.CyDataTableFactoryImpl">
+ <bean id="cyNetworkFactory"
class="org.cytoscape.model.internal.CyNetworkFactoryImpl">
<constructor-arg ref="cyEventHelperServiceRef" />
+ <constructor-arg ref="cyTableManager" />
+ <constructor-arg ref="cyDataTableFactory" />
</bean>
<bean id="cyRootNetworkFactory"
class="org.cytoscape.model.internal.CyRootNetworkFactoryImpl"/>
Modified:
core3/model-impl/trunk/src/test/java/org/cytoscape/model/CyDataTableTest.java
===================================================================
---
core3/model-impl/trunk/src/test/java/org/cytoscape/model/CyDataTableTest.java
2010-09-05 23:44:18 UTC (rev 21705)
+++
core3/model-impl/trunk/src/test/java/org/cytoscape/model/CyDataTableTest.java
2010-09-05 23:44:35 UTC (rev 21706)
@@ -51,8 +51,8 @@
public void setUp() {
eventHelper = new DummyCyEventHelper();
- mgr = new CyDataTableImpl(null, "homer", true, eventHelper);
- attrs = mgr.getRow(1);
+ mgr = new CyDataTableImpl("homer", "SUID", Long.class, true,
eventHelper);
+ attrs = mgr.getRow(1l);
}
/**
Modified:
core3/model-impl/trunk/src/test/java/org/cytoscape/model/TestCyNetworkFactory.java
===================================================================
---
core3/model-impl/trunk/src/test/java/org/cytoscape/model/TestCyNetworkFactory.java
2010-09-05 23:44:18 UTC (rev 21705)
+++
core3/model-impl/trunk/src/test/java/org/cytoscape/model/TestCyNetworkFactory.java
2010-09-05 23:44:35 UTC (rev 21706)
@@ -37,32 +37,34 @@
package org.cytoscape.model;
-//import org.cytoscape.model.internal.CyNetworkImpl;
-//import org.cytoscape.model.internal.MGraph;
import org.cytoscape.model.internal.ArrayGraph;
import org.cytoscape.model.internal.CyTableManagerImpl;
+import org.cytoscape.model.internal.CyDataTableFactoryImpl;
import org.cytoscape.event.DummyCyEventHelper;
import org.cytoscape.model.subnetwork.CyRootNetwork;
import org.junit.Test;
+import static org.junit.Assert.*;
public class TestCyNetworkFactory {
public TestCyNetworkFactory() {};
public static CyNetwork getInstance() {
- //return new CyNetworkImpl(new DummyCyEventHelper());
- //return new MGraph(new DummyCyEventHelper());
- return new ArrayGraph(new DummyCyEventHelper(), new
CyTableManagerImpl());
+ DummyCyEventHelper deh = new DummyCyEventHelper();
+ return new ArrayGraph(deh, new CyTableManagerImpl(),new
CyDataTableFactoryImpl(deh));
}
- public static CyRootNetwork getRootInstance() {
- return new ArrayGraph(new DummyCyEventHelper(), new
CyTableManagerImpl());
+ public static CyRootNetwork getRootInstance() {
+ // This only works because we know that ArrayGraph (returned
from
+ // getInstance) is also a root network!
+ return (CyRootNetwork)getInstance();
}
@Test
public void testFactory() throws Exception {
-
+ CyNetwork n = getInstance();
+ assertNotNull(n);
}
}
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