Author: mes
Date: 2012-01-24 17:27:58 -0800 (Tue, 24 Jan 2012)
New Revision: 28098
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTableFactory.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/CyTableFactoryImpl.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableImpl.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
Log:
fixes #591 we are now a bit smarter about the size of tables that we create by
default, which was the root of the time and memory consumption problems here.
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTableFactory.java
===================================================================
---
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTableFactory.java
2012-01-25 00:53:06 UTC (rev 28097)
+++
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTableFactory.java
2012-01-25 01:27:58 UTC (rev 28098)
@@ -35,6 +35,35 @@
* @CyAPI.Api.Interface
*/
public interface CyTableFactory {
+ /**
+ * A description of the initial size of the table.
+ * Used only for the initial construction of the table
+ * and does not in any way limit the eventual size
+ * of the table!
+ */
+ enum InitialTableSize {
+ /** Small - about 100 entries. */
+ SMALL(100),
+ /** Medium - about 1000 entries. */
+ MEDIUM(1000),
+ /** Large - about 10,000 entries. */
+ LARGE(10000),
+ ;
+
+ private final int size;
+ private InitialTableSize(int size) {
+ this.size = size;
+ }
+
+ /**
+ * Returns the actual size value for the given enum.
+ * @return the actual size value for the given enum.
+ */
+ public int getSize() {
+ return size;
+ }
+ }
+
/**
* Creates a CyTable object with the specified name, primary key,
visibility, and mutability.
* @param title The name of the CyTable.
@@ -42,9 +71,22 @@
* @param primaryKeyType The type of the primaryKey column for this
table.
* @param pub Whether or not the CyTable should be public.
* @param isMutable if true, the table can be deleted later on,
otherwise it can't
+ * @param initialSize a rough guess as to the expected size of the
table
* @return A new {@link CyTable} with the specified name that is either
public or not (see
* {@link CyTable#isPublic}.
*/
CyTable createTable(String title, String primaryKey, Class<?>
primaryKeyType, boolean pub,
+ boolean isMutable, InitialTableSize initialSize);
+ /**
+ * Creates a CyTable object with the specified name, primary key,
visibility, and mutability.
+ * @param title The name of the CyTable.
+ * @param primaryKey The name primaryKey column for this table.
+ * @param primaryKeyType The type of the primaryKey column for this
table.
+ * @param pub Whether or not the CyTable should be public.
+ * @param isMutable if true, the table can be deleted later on,
otherwise it can't
+ * @return A new {@link CyTable} with the specified name that is either
public or not (see
+ * {@link CyTable#isPublic}.
+ */
+ CyTable createTable(String title, String primaryKey, Class<?>
primaryKeyType, boolean pub,
boolean isMutable);
}
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
2012-01-25 00:53:06 UTC (rev 28097)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
2012-01-25 01:27:58 UTC (rev 28098)
@@ -52,6 +52,7 @@
import org.cytoscape.model.events.NetworkAddedEvent;
import org.cytoscape.model.subnetwork.CyRootNetwork;
import org.cytoscape.model.subnetwork.CySubNetwork;
+import org.cytoscape.model.CyTableFactory.InitialTableSize;
import org.cytoscape.service.util.CyServiceRegistrar;
@@ -153,13 +154,13 @@
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", CyTableEntry.SUID, Long.class, publicTables, false));
- netAttrMgr.put(CyNetwork.HIDDEN_ATTRS, tableFactory.createTable(suidx
+ " hidden network", CyTableEntry.SUID, Long.class, false, false));
+ netAttrMgr.put(CyNetwork.DEFAULT_ATTRS, tableFactory.createTable(suidx
+ " default network", CyTableEntry.SUID, Long.class, publicTables,
false,InitialTableSize.SMALL));
+ netAttrMgr.put(CyNetwork.HIDDEN_ATTRS, tableFactory.createTable(suidx
+ " hidden network", CyTableEntry.SUID, Long.class, false,
false,InitialTableSize.SMALL));
netAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyTableEntry.NAME,
String.class, true);
if ( suidx == suid ) {
- netAttrMgr.put(CyRootNetwork.SHARED_ATTRS,
tableFactory.createTable(suidx + " shared network", CyTableEntry.SUID,
Long.class, publicTables, false));
+ netAttrMgr.put(CyRootNetwork.SHARED_ATTRS,
tableFactory.createTable(suidx + " shared network", CyTableEntry.SUID,
Long.class, publicTables, false,InitialTableSize.SMALL));
netAttrMgr.get(CyRootNetwork.SHARED_ATTRS).createColumn(CyRootNetwork.SHARED_NAME,
String.class, true);
} else
linkDefaultTables(
netTables.get(CyRootNetwork.SHARED_ATTRS),
@@ -170,14 +171,14 @@
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", CyTableEntry.SUID,
Long.class, publicTables, false));
- nodeAttrMgr.put(CyNetwork.HIDDEN_ATTRS, tableFactory.createTable(suidx
+ " hidden node", CyTableEntry.SUID, Long.class, false, false));
+ nodeAttrMgr.put(CyNetwork.DEFAULT_ATTRS,
tableFactory.createTable(suidx + " default node", CyTableEntry.SUID,
Long.class, publicTables, false,getTableSize()));
+ nodeAttrMgr.put(CyNetwork.HIDDEN_ATTRS, tableFactory.createTable(suidx
+ " hidden node", CyTableEntry.SUID, Long.class, false, false,getTableSize()));
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", CyTableEntry.SUID, Long.class,
publicTables, false));
+ nodeAttrMgr.put(CyRootNetwork.SHARED_ATTRS,
tableFactory.createTable(suidx + " shared node", CyTableEntry.SUID, Long.class,
publicTables, false,getTableSize()));
nodeAttrMgr.get(CyRootNetwork.SHARED_ATTRS).createColumn(CyRootNetwork.SHARED_NAME,
String.class, true);
} else
linkDefaultTables(
nodeTables.get(CyRootNetwork.SHARED_ATTRS),
@@ -188,15 +189,15 @@
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", CyTableEntry.SUID,
Long.class, publicTables, false));
- edgeAttrMgr.put(CyNetwork.HIDDEN_ATTRS, tableFactory.createTable(suidx
+ " hidden edge", CyTableEntry.SUID, Long.class, false, false));
+ edgeAttrMgr.put(CyNetwork.DEFAULT_ATTRS,
tableFactory.createTable(suidx + " default edge", CyTableEntry.SUID,
Long.class, publicTables, false,getTableSize()));
+ edgeAttrMgr.put(CyNetwork.HIDDEN_ATTRS, tableFactory.createTable(suidx
+ " hidden edge", CyTableEntry.SUID, Long.class, false, false,getTableSize()));
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", CyTableEntry.SUID, Long.class,
publicTables, false));
+ edgeAttrMgr.put(CyRootNetwork.SHARED_ATTRS,
tableFactory.createTable(suidx + " shared edge", CyTableEntry.SUID, Long.class,
publicTables, false,getTableSize()));
edgeAttrMgr.get(CyRootNetwork.SHARED_ATTRS).createColumn(CyRootNetwork.SHARED_NAME,
String.class, true);
} else
linkDefaultTables(
edgeTables.get(CyRootNetwork.SHARED_ATTRS),
@@ -961,7 +962,16 @@
return sub;
}
+ private InitialTableSize getTableSize() {
+ if ( numSubNetworks < 5 )
+ return InitialTableSize.LARGE;
+ else if ( numSubNetworks < 15 )
+ return InitialTableSize.MEDIUM;
+ else
+ return InitialTableSize.SMALL;
+ }
+
/**
* {@inheritDoc}
*/
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableFactoryImpl.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableFactoryImpl.java
2012-01-25 00:53:06 UTC (rev 28097)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableFactoryImpl.java
2012-01-25 01:27:58 UTC (rev 28098)
@@ -67,10 +67,15 @@
}
public CyTable createTable(final String name, final String primaryKey,
final Class<?> primaryKeyType,
- final boolean pub, final boolean isMutable)
+ final boolean pub, final boolean isMutable) {
+ return
createTable(name,primaryKey,primaryKeyType,pub,isMutable,CyTableFactory.InitialTableSize.MEDIUM);
+ }
+
+ public CyTable createTable(final String name, final String primaryKey,
final Class<?> primaryKeyType,
+ final boolean pub, final boolean isMutable,
final CyTableFactory.InitialTableSize size)
{
final CyTableImpl table = new CyTableImpl(name, primaryKey,
primaryKeyType, pub, isMutable,
- SavePolicy.SESSION_FILE,
help, interpreter);
+ SavePolicy.SESSION_FILE,
help, interpreter, size.getSize());
eventDelegator.addListener(table);
return table;
}
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
2012-01-25 00:53:06 UTC (rev 28097)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
2012-01-25 01:27:58 UTC (rev 28098)
@@ -87,6 +87,7 @@
private final CyEventHelper eventHelper;
private final Interpreter interpreter;
+ private final int defaultInitSize;
String lastInternalError = null;
@@ -101,7 +102,8 @@
*/
public CyTableImpl(final String title, final String primaryKey,
Class<?> primaryKeyType,
final boolean pub, final boolean isMutable,
SavePolicy savePolicy,
- final CyEventHelper eventHelper, final Interpreter
interpreter)
+ final CyEventHelper eventHelper, final Interpreter
interpreter,
+ final int defaultInitSize)
{
this.title = title;
this.primaryKey = primaryKey;
@@ -112,11 +114,12 @@
this.interpreter = interpreter;
this.savePolicy = savePolicy;
this.fireEvents = !pub;
+ this.defaultInitSize = defaultInitSize;
currentlyActiveAttributes = new HashSet<String>();
attributes = new HashMap<String, Map<Object, Object>>();
reverse = new HashMap<String, SetMultimap<Object,Object>>();
- rows = new HashMap<Object, CyRow>(10000, 0.5f);
+ rows = new HashMap<Object, CyRow>(defaultInitSize, 0.5f);
types = new HashMap<String, CyColumn>();
VirtualColumnInfo virtualInfo = new
VirtualColumnInfoImpl(false, null, null, null, null, true);
@@ -370,7 +373,7 @@
/* isPrimaryKey
= */ false,
isImmutable,
defaultValue));
- attributes.put(columnName, new HashMap<Object,
Object>(10000));
+ attributes.put(columnName, new HashMap<Object,
Object>(defaultInitSize));
reverse.put(columnName, HashMultimap.create());
}
@@ -410,7 +413,7 @@
/* isPrimaryKey
= */ false,
isImmutable,
defaultValue));
- attributes.put(columnName, new HashMap<Object,
Object>(10000));
+ attributes.put(columnName, new HashMap<Object,
Object>(defaultInitSize));
reverse.put(columnName, HashMultimap.create());
}
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
2012-01-25 00:53:06 UTC (rev 28097)
+++
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableManagerTest.java
2012-01-25 01:27:58 UTC (rev 28098)
@@ -91,9 +91,9 @@
CyEventHelper eventHelper = new DummyCyEventHelper();
final Interpreter interpreter = new InterpreterImpl();
CyTable table = new CyTableImpl("homer", CyTableEntry.SUID,
Long.class, true, true, SavePolicy.SESSION_FILE,
- eventHelper, interpreter);
+ eventHelper, interpreter,1000);
CyTable table2 = new CyTableImpl("marge", CyTableEntry.SUID,
Long.class, true, true, SavePolicy.SESSION_FILE,
- eventHelper, interpreter);
+ eventHelper, interpreter,1000);
table.createColumn("x", Long.class, false);
CyColumn column = table.getColumn("x");
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
2012-01-25 00:53:06 UTC (rev 28097)
+++
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableTest.java
2012-01-25 01:27:58 UTC (rev 28098)
@@ -59,10 +59,10 @@
eventHelper = new DummyCyEventHelper();
final Interpreter interpreter = new InterpreterImpl();
table = new CyTableImpl("homer", CyTableEntry.SUID, Long.class,
false, true, SavePolicy.SESSION_FILE,
- eventHelper, interpreter);
+ eventHelper, interpreter, 1000);
attrs = table.getRow(1L);
table2 = new CyTableImpl("marge", CyTableEntry.SUID,
Long.class, false, true, SavePolicy.SESSION_FILE,
- eventHelper, interpreter);
+ eventHelper, interpreter, 1000);
}
@After
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