Author: mes
Date: 2010-10-25 16:02:06 -0700 (Mon, 25 Oct 2010)
New Revision: 22405
Modified:
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DGraphView.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/TextDataTableReader.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/expression/ExpressionData.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleComplexAttribute.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutTask.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayoutTask.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTable.java
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyTableTest.java
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
core3/psi-mi-impl/trunk/
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/cyto_mapper/MapToCytoscape.java
Log:
changed createColumn syntax for CyTable
Modified:
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DGraphView.java
===================================================================
---
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DGraphView.java
2010-10-25 22:56:28 UTC (rev 22404)
+++
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DGraphView.java
2010-10-25 23:02:06 UTC (rev 22405)
@@ -395,11 +395,11 @@
this.manager = manager;
final CyTable nodeCAM = dataFactory.createTable("node view",
"SUID", Long.class, false);
- nodeCAM.createColumn("hidden", Boolean.class, false);
+ nodeCAM.createColumn("hidden", Boolean.class);
tableMgr.getTableMap("NODE", networkModel).put("VIEW", nodeCAM);
final CyTable edgeCAM = dataFactory.createTable("edge view",
"SUID", Long.class, false);
- edgeCAM.createColumn("hidden", Boolean.class, false);
+ edgeCAM.createColumn("hidden", Boolean.class);
tableMgr.getTableMap("EDGE", networkModel).put("VIEW", edgeCAM);
// creating empty subnetworks
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/TextDataTableReader.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/TextDataTableReader.java
2010-10-25 22:56:28 UTC (rev 22404)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/TextDataTableReader.java
2010-10-25 23:02:06 UTC (rev 22405)
@@ -78,7 +78,7 @@
String.class, true);
for ( String col : columnNames )
- table.createColumn(col, String.class, false);
+ table.createColumn(col, String.class);
return table;
}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/expression/ExpressionData.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/expression/ExpressionData.java
2010-10-25 22:56:28 UTC (rev 22404)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/expression/ExpressionData.java
2010-10-25 23:02:06 UTC (rev 22405)
@@ -1055,14 +1055,14 @@
String[] condNames = getConditionNames();
// first set up the columns
- table.createColumn("geneName",String.class,true);
+ table.createColumn("geneName",String.class);
for (int condNum = 0; condNum < condNames.length; condNum++) {
String condName = condNames[condNum];
String eStr = condName + "exp";
String sStr = condName + "sig";
- table.createColumn(eStr,Double.class,false);
- table.createColumn(sStr,Double.class,false);
+ table.createColumn(eStr,Double.class);
+ table.createColumn(sStr,Double.class);
}
// now create the rows and populate
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleComplexAttribute.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleComplexAttribute.java
2010-10-25 22:56:28 UTC (rev 22404)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleComplexAttribute.java
2010-10-25 23:02:06 UTC (rev 22405)
@@ -60,7 +60,7 @@
if (Map.class == manager.currentAttributes
.getType(manager.currentAttributeID)) {
manager.currentAttributes.getDataTable().createColumn(
- manager.currentAttributeID,
Map.class, false);
+ manager.currentAttributeID,
Map.class);
}
// Now define set the attribute
if (manager.objectTarget != null)
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutTask.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutTask.java
2010-10-25 22:56:28 UTC (rev 22404)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutTask.java
2010-10-25 23:02:06 UTC (rev 22405)
@@ -62,7 +62,7 @@
// update the __layoutAlgorithm attribute
final CyRow networkAttributes =
network.getCyRow(CyNetwork.HIDDEN_ATTRS);
- networkAttributes.getDataTable().createColumn(LAYOUT_ALGORITHM,
String.class, false);
+ networkAttributes.getDataTable().createColumn(LAYOUT_ALGORITHM,
String.class);
networkAttributes.set(LAYOUT_ALGORITHM, name);
logger.debug("Layout finished: " +
(System.currentTimeMillis()-start) + " msec.");
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayoutTask.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayoutTask.java
2010-10-25 22:56:28 UTC (rev 22404)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayoutTask.java
2010-10-25 23:02:06 UTC (rev 22405)
@@ -48,7 +48,7 @@
// Create attribute
CyTable table = tableMgr.getTableMap(CyTableEntry.NODE,
network).get(CyNetwork.DEFAULT_ATTRS);
if(table.getColumnTypeMap().keySet().contains(DEGREE_ATTR_NAME)
== false) {
- table.createColumn(DEGREE_ATTR_NAME, Double.class,
false);
+ table.createColumn(DEGREE_ATTR_NAME, Double.class);
}
// just add the unlocked nodes
Modified: core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTable.java
===================================================================
--- core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTable.java
2010-10-25 22:56:28 UTC (rev 22404)
+++ core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTable.java
2010-10-25 23:02:06 UTC (rev 22405)
@@ -97,13 +97,11 @@
void deleteColumn(String columnName);
/**
- * Create a column of the specified name with the specified type
- * and uniqueness.
+ * Create a column of the specified name and the specified type.
* @param columnName The name identifying the attribute.
* @param type The type of the column.
- * @param unique Whether the values contained in the column must be
unique
*/
- <T> void createColumn(String columnName, Class<?extends T> type,
boolean unique);
+ <T> void createColumn(String columnName, Class<?extends T> type);
/**
* Returns the list of all values contained in the specified column.
Modified:
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyTableTest.java
===================================================================
---
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyTableTest.java
2010-10-25 22:56:28 UTC (rev 22404)
+++
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyTableTest.java
2010-10-25 23:02:06 UTC (rev 22405)
@@ -70,8 +70,8 @@
* DOCUMENT ME!
*/
public void testAddStringAttr() {
- mgr.createColumn("someString", String.class, false);
- mgr.createColumn("someStringElse", String.class, false);
+ mgr.createColumn("someString", String.class);
+ mgr.createColumn("someStringElse", String.class);
attrs.set("someString", "apple");
attrs.set("someStringElse", "orange");
@@ -88,8 +88,8 @@
* DOCUMENT ME!
*/
public void testAddIntAttr() {
- mgr.createColumn("someInt", Integer.class, false);
- mgr.createColumn("someOtherInt", Integer.class, false);
+ mgr.createColumn("someInt", Integer.class);
+ mgr.createColumn("someOtherInt", Integer.class);
attrs.set("someInt", 50);
attrs.set("someOtherInt", 100);
@@ -106,8 +106,8 @@
* DOCUMENT ME!
*/
public void testAddDoubleAttr() {
- mgr.createColumn("someDouble", Double.class, false);
- mgr.createColumn("someOtherDouble", Double.class, false);
+ mgr.createColumn("someDouble", Double.class);
+ mgr.createColumn("someOtherDouble", Double.class);
attrs.set("someDouble", 3.14);
attrs.set("someOtherDouble", 2.76);
@@ -124,8 +124,8 @@
* DOCUMENT ME!
*/
public void testAddBooleanAttr() {
- mgr.createColumn("someBoolean", Boolean.class, false);
- mgr.createColumn("someOtherBoolean", Boolean.class, false);
+ mgr.createColumn("someBoolean", Boolean.class);
+ mgr.createColumn("someOtherBoolean", Boolean.class);
attrs.set("someBoolean", true);
attrs.set("someOtherBoolean", false);
@@ -142,7 +142,7 @@
* DOCUMENT ME!
*/
public void testAddListAttr() {
- mgr.createColumn("someList", List.class, false);
+ mgr.createColumn("someList", List.class);
List<String> l = new LinkedList<String>();
l.add("orange");
@@ -159,7 +159,7 @@
* DOCUMENT ME!
*/
public void testAddMapAttr() {
- mgr.createColumn("someMap", Map.class, false);
+ mgr.createColumn("someMap", Map.class);
Map<String, Integer> m = new HashMap<String, Integer>();
m.put("orange", 1);
@@ -209,9 +209,9 @@
// You can't have an attribute with the same name, but
// a different type.
public void testAddDuplicateNameAttr() {
- mgr.createColumn("something", String.class, false);
+ mgr.createColumn("something", String.class);
try {
- mgr.createColumn("something", Integer.class, false);
+ mgr.createColumn("something", Integer.class);
} catch (Exception e) {
return;
}
@@ -219,7 +219,7 @@
}
public void testRowSetMicroListener() {
- mgr.createColumn("someString", String.class, false);
+ mgr.createColumn("someString", String.class);
attrs.set("someString", "apple");
Object last = eventHelper.getLastMicroListener();
@@ -228,7 +228,7 @@
}
public void testColumnCreatedEvent() {
- mgr.createColumn("someInt", Integer.class, false);
+ mgr.createColumn("someInt", Integer.class);
Object last = eventHelper.getLastAsynchronousEvent();
assertNotNull( last );
@@ -236,7 +236,7 @@
}
public void testColumnDeletedEvent() {
- mgr.createColumn("someInt", Integer.class, false);
+ mgr.createColumn("someInt", Integer.class);
mgr.deleteColumn("someInt");
Object last = eventHelper.getLastSynchronousEvent();
@@ -245,13 +245,13 @@
}
public void testColumnCreate() {
- mgr.createColumn("someInt", Integer.class, false);
+ mgr.createColumn("someInt", Integer.class);
assertTrue( mgr.getColumnTypeMap().containsKey("someInt") );
assertEquals( mgr.getColumnTypeMap().get("someInt"),
Integer.class );
}
public void testColumnDelete() {
- mgr.createColumn("someInt", Integer.class, false);
+ mgr.createColumn("someInt", Integer.class);
assertTrue( mgr.getColumnTypeMap().containsKey("someInt") );
mgr.deleteColumn("someInt");
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
2010-10-25 22:56:28 UTC (rev 22404)
+++
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
2010-10-25 23:02:06 UTC (rev 22405)
@@ -123,8 +123,8 @@
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(CyTableEntry.NAME,String.class,false);
-
netAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyTableEntry.SELECTED,Boolean.class,false);
+
netAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyTableEntry.NAME,String.class);
+
netAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyTableEntry.SELECTED,Boolean.class);
getCyRow().set(CyTableEntry.NAME,"");
// potential leak since "this" isn't yet fully constructed
@@ -132,16 +132,16 @@
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(CyTableEntry.NAME,String.class,false);
-
nodeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyTableEntry.SELECTED,Boolean.class,false);
+
nodeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyTableEntry.NAME,String.class);
+
nodeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyTableEntry.SELECTED,Boolean.class);
edgeAttrMgr = new HashMap<String, CyTable>();
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(CyTableEntry.NAME,String.class,false);
-
edgeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyTableEntry.SELECTED,Boolean.class,false);
-
edgeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyEdge.INTERACTION,String.class,false);
+
edgeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyTableEntry.NAME,String.class);
+
edgeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyTableEntry.SELECTED,Boolean.class);
+
edgeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyEdge.INTERACTION,String.class);
eventHelper = eh;
Modified:
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
===================================================================
---
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
2010-10-25 22:56:28 UTC (rev 22404)
+++
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
2010-10-25 23:02:06 UTC (rev 22405)
@@ -176,18 +176,17 @@
/**
* DOCUMENT ME!
- *
- * @param <T>
+ * @param type
* DOCUMENT ME!
* @param attributeName
* DOCUMENT ME!
- * @param type
- * DOCUMENT ME!
* @param u
* DOCUMENT ME!
+ *
+ * @param <T>
+ * DOCUMENT ME!
*/
- public <T> void createColumn(String attributeName, Class<? extends T>
type,
- boolean u) {
+ public <T> void createColumn(String attributeName, Class<? extends T>
type) {
if (attributeName == null)
throw new NullPointerException("attribute name is
null");
Property changes on: core3/psi-mi-impl/trunk
___________________________________________________________________
Name: svn:ignore
+ target
Modified:
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/cyto_mapper/MapToCytoscape.java
===================================================================
---
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/cyto_mapper/MapToCytoscape.java
2010-10-25 22:56:28 UTC (rev 22404)
+++
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/cyto_mapper/MapToCytoscape.java
2010-10-25 23:02:06 UTC (rev 22405)
@@ -566,7 +566,7 @@
if (attrObject instanceof String) {
String object;
if (!attributes.contains(key, String.class)) {
-
attributes.getDataTable().createColumn(key, String.class, true);
+
attributes.getDataTable().createColumn(key, String.class);
object = null;
} else {
object = attributes.get(key,
String.class);
@@ -612,7 +612,7 @@
private <T> void addAttribute(CyRow attributes, String name, T value) {
if (!attributes.contains(name, value.getClass())) {
- attributes.getDataTable().createColumn(name,
value.getClass(), true);
+ attributes.getDataTable().createColumn(name,
value.getClass());
}
attributes.set(name, value);
}
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