Author: pwang
Date: 2012-03-26 16:22:19 -0700 (Mon, 26 Mar 2012)
New Revision: 28654
Added:
core3/impl/trunk/group-data-impl/.settings/
core3/impl/trunk/gui-cmdline-parser-impl/.settings/
Modified:
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/util/SelectUtil.java
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/FilterMainPanel.java
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/FilterSettingPanel.java
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/quickfind/util/CyAttributesUtil.java
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/quickfind/util/QuickFindImpl.java
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/quickfind/view/QuickFindConfigDialog.java
core3/impl/trunk/graphml-impl/src/main/java/org/cytoscape/io/internal/read/graphml/GraphMLParser.java
core3/impl/trunk/graphml-impl/src/test/java/org/cytoscape/data/reader/graphml/GraphMLReaderTest.java
core3/impl/trunk/group-impl/src/main/java/org/cytoscape/group/internal/CyGroupImpl.java
Log:
Fixed bug#810
Modified:
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/util/SelectUtil.java
===================================================================
---
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/util/SelectUtil.java
2012-03-26 23:20:35 UTC (rev 28653)
+++
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/util/SelectUtil.java
2012-03-26 23:22:19 UTC (rev 28654)
@@ -8,7 +8,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
public class SelectUtil {
public static void unselectAllNodes(CyNetwork network) {
@@ -27,8 +27,8 @@
setSelectedState(network, list, selected);
}
- static void setSelectedState(CyNetwork network, Collection<? extends
CyTableEntry> list, Boolean selected) {
- for (CyTableEntry edge : list) {
+ static void setSelectedState(CyNetwork network, Collection<? extends
CyIdentifiable> list, Boolean selected) {
+ for (CyIdentifiable edge : list) {
CyRow row = network.getRow(edge);
row.set(CyNetwork.SELECTED, selected);
}
@@ -43,7 +43,7 @@
return getSelected(cyNetwork, cyNetwork.getEdgeList());
}
- static <T extends CyTableEntry> Set<T> getSelected(CyNetwork network,
Collection<T> items) {
+ static <T extends CyIdentifiable> Set<T> getSelected(CyNetwork network,
Collection<T> items) {
Set<T> entries = new HashSet<T>();
for (T item : items) {
CyRow row = network.getRow(item);
@@ -62,7 +62,7 @@
selectAll(cyNetwork,cyNetwork.getEdgeList());
}
- static <T extends CyTableEntry> void selectAll(CyNetwork network,
Collection<T> items) {
+ static <T extends CyIdentifiable> void selectAll(CyNetwork network,
Collection<T> items) {
for (T item : items) {
CyRow row = network.getRow(item);
if (!row.get(CyNetwork.SELECTED, Boolean.class)) {
@@ -79,7 +79,7 @@
return countSelected(cyNetwork, cyNetwork.getNodeList());
}
- static <T extends CyTableEntry> int countSelected(CyNetwork network,
Collection<T> items) {
+ static <T extends CyIdentifiable> int countSelected(CyNetwork network,
Collection<T> items) {
int count = 0;
for (T item : items) {
CyRow row = network.getRow(item);
Modified:
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/FilterMainPanel.java
===================================================================
---
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/FilterMainPanel.java
2012-03-26 23:20:35 UTC (rev 28653)
+++
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/FilterMainPanel.java
2012-03-26 23:22:19 UTC (rev 28654)
@@ -87,7 +87,7 @@
import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.events.NetworkAboutToBeDestroyedEvent;
import org.cytoscape.model.events.NetworkAboutToBeDestroyedListener;
import org.cytoscape.model.events.NetworkAddedEvent;
@@ -381,7 +381,7 @@
*/
private List<Object> getCyAttributesList(CyNetwork network, String
pType) {
Vector<String> attributeList = new Vector<String>();
- Collection<? extends CyTableEntry> entries = null;
+ Collection<? extends CyIdentifiable> entries = null;
if (pType.equalsIgnoreCase("node")) {
entries = network.getNodeList();
@@ -395,7 +395,7 @@
return Collections.emptyList();
}
- CyTableEntry tableEntry = entries.iterator().next();
+ CyIdentifiable tableEntry = entries.iterator().next();
final Collection<CyColumn> columns =
network.getRow(tableEntry).getTable().getColumns();
for (final CyColumn column : columns) {
Modified:
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/FilterSettingPanel.java
===================================================================
---
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/FilterSettingPanel.java
2012-03-26 23:20:35 UTC (rev 28653)
+++
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/FilterSettingPanel.java
2012-03-26 23:22:19 UTC (rev 28654)
@@ -88,7 +88,7 @@
import org.cytoscape.filter.internal.widgets.slider.JRangeSliderExtended;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyRow;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.model.CyNetworkView;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -203,7 +203,7 @@
private Class<?> getAttributeDataType(CyNetwork network, String
pAttribute, int pType) {
- Collection<? extends CyTableEntry> entries;
+ Collection<? extends CyIdentifiable> entries;
if (pType == QuickFind.INDEX_NODES) {
entries = network.getNodeList();
@@ -217,7 +217,7 @@
return null;
}
- CyTableEntry entry = entries.iterator().next();
+ CyIdentifiable entry = entries.iterator().next();
CyRow row = network.getRow(entry);
return row.getTable().getColumn(pAttribute).getType();
}
Modified:
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/quickfind/util/CyAttributesUtil.java
===================================================================
---
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/quickfind/util/CyAttributesUtil.java
2012-03-26 23:20:35 UTC (rev 28653)
+++
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/quickfind/util/CyAttributesUtil.java
2012-03-26 23:22:19 UTC (rev 28654)
@@ -45,7 +45,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyRow;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
/**
@@ -67,7 +67,7 @@
* @param attributeKey Attribute Key.
* @return array of String Objects or null.
*/
- public static String[] getAttributeValues(CyNetwork network,
CyTableEntry graphObject, String attributeKey) {
+ public static String[] getAttributeValues(CyNetwork network,
CyIdentifiable graphObject, String attributeKey) {
String[] terms = null;
if (attributeKey.equals(QuickFind.UNIQUE_IDENTIFIER)) {
@@ -136,13 +136,13 @@
* @param numDistinctValues Number of Distinct Values.
* @return Array of Distinct Value Strings.
*/
- public static String[] getDistinctAttributeValues(CyNetwork network,
Iterator<? extends CyTableEntry> iterator,
+ public static String[] getDistinctAttributeValues(CyNetwork network,
Iterator<? extends CyIdentifiable> iterator,
String attributeKey,
int numDistinctValues) {
Set<String> set = new HashSet<String>();
int counter = 0;
while (iterator.hasNext() && (counter < numDistinctValues)) {
- CyTableEntry graphObject = iterator.next();
+ CyIdentifiable graphObject = iterator.next();
String[] values =
CyAttributesUtil.getAttributeValues(network,graphObject, attributeKey);
if ((values != null) && (values.length > 0)) {
@@ -183,7 +183,7 @@
}
public static boolean isNullAttribute(CyNetwork cyNetwork, String
indexType, String attributeName) {
- Collection<? extends CyTableEntry> entries;
+ Collection<? extends CyIdentifiable> entries;
if (indexType.equals("node")) {
entries = cyNetwork.getNodeList();
} else if (indexType.equals("edge")) {
@@ -194,7 +194,7 @@
if (entries.size() == 0) {
return true;
}
- for (CyTableEntry entry : entries) {
+ for (CyIdentifiable entry : entries) {
CyRow row = cyNetwork.getRow(entry);
Class<?> type =
row.getTable().getColumn(attributeName).getType();
if (row.get(attributeName, type) != null) {
Modified:
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/quickfind/util/QuickFindImpl.java
===================================================================
---
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/quickfind/util/QuickFindImpl.java
2012-03-26 23:20:35 UTC (rev 28653)
+++
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/quickfind/util/QuickFindImpl.java
2012-03-26 23:22:19 UTC (rev 28654)
@@ -44,7 +44,7 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.work.TaskMonitor;
@@ -334,7 +334,7 @@
//
Date start = new Date();
- Iterator<? extends CyTableEntry> iterator;
+ Iterator<? extends CyIdentifiable> iterator;
if (indexType == QuickFind.INDEX_NODES) {
taskMonitor.setStatusMessage("Indexing node
attributes");
@@ -351,7 +351,7 @@
while (iterator.hasNext()) {
currentProgress++;
- CyTableEntry graphObject = iterator.next();
+ CyIdentifiable graphObject = iterator.next();
addToIndex(network,attributeType, graphObject,
controllingAttribute, index);
// Determine percent complete
@@ -403,7 +403,7 @@
* @param controllingAttribute Controlling attribute.
* @param index Index to add to.
*/
- private void addToIndex(CyNetwork network, Class<?> attributeType,
CyTableEntry graphObject,
+ private void addToIndex(CyNetwork network, Class<?> attributeType,
CyIdentifiable graphObject,
String controllingAttribute, GenericIndex
index) {
CyRow row = network.getRow(graphObject);
// Get attribute values, and index
@@ -431,7 +431,7 @@
* @param graphObject Graph Object.
* @param index Index to add to.
*/
- private void addStringsToIndex(String[] value, CyTableEntry
graphObject, GenericIndex index) {
+ private void addStringsToIndex(String[] value, CyIdentifiable
graphObject, GenericIndex index) {
// Add to index
for (int i = 0; i < value.length; i++) {
index.addToIndex(value[i], graphObject);
Modified:
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/quickfind/view/QuickFindConfigDialog.java
===================================================================
---
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/quickfind/view/QuickFindConfigDialog.java
2012-03-26 23:20:35 UTC (rev 28653)
+++
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/quickfind/view/QuickFindConfigDialog.java
2012-03-26 23:22:19 UTC (rev 28654)
@@ -69,7 +69,7 @@
import org.cytoscape.filter.internal.quickfind.util.QuickFind;
import org.cytoscape.filter.internal.widgets.autocomplete.index.GenericIndex;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.VisualLexicon;
import org.cytoscape.view.presentation.RenderingEngine;
@@ -672,7 +672,7 @@
// Obtain distinct attribute values
CyNetwork network = applicationManager.getCurrentNetwork();
- Iterator<? extends CyTableEntry> iterator;
+ Iterator<? extends CyIdentifiable> iterator;
if (parentDialog.getIndexType() == QuickFind.INDEX_NODES) {
iterator = network.getNodeList().iterator();
Modified:
core3/impl/trunk/graphml-impl/src/main/java/org/cytoscape/io/internal/read/graphml/GraphMLParser.java
===================================================================
---
core3/impl/trunk/graphml-impl/src/main/java/org/cytoscape/io/internal/read/graphml/GraphMLParser.java
2012-03-26 23:20:35 UTC (rev 28653)
+++
core3/impl/trunk/graphml-impl/src/main/java/org/cytoscape/io/internal/read/graphml/GraphMLParser.java
2012-03-26 23:22:19 UTC (rev 28654)
@@ -20,7 +20,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.model.subnetwork.CySubNetwork;
import org.cytoscape.session.CyNetworkNaming;
@@ -39,7 +39,7 @@
private Map<String, String> datatypeMap;
private Map<String, String> datanameMap;
- private CyTableEntry currentObject = null;
+ private CyIdentifiable currentObject = null;
// Attribute values
private String currentAttributeID = null;
@@ -61,7 +61,7 @@
// Current CyNetwork. GraphML can have multiple networks in a file.
private CyNetwork currentNetwork;
- private final Map<String, CyTableEntry> nodeid2CyNodeMap;
+ private final Map<String, CyIdentifiable> nodeid2CyNodeMap;
private String lastTag;
private CyNode lastNode;
@@ -82,7 +82,7 @@
datatypeMap = new HashMap<String, String>();
datanameMap = new HashMap<String, String>();
- this.nodeid2CyNodeMap = new HashMap<String, CyTableEntry>();
+ this.nodeid2CyNodeMap = new HashMap<String, CyIdentifiable>();
}
CyNetwork[] getCyNetworks() {
@@ -154,7 +154,7 @@
network.removeNodes(toBeRemoved);
}
}
- currentNetwork.getRow(currentNetwork).set(CyTableEntry.NAME,
networkID);
+ currentNetwork.getRow(currentNetwork).set(CyNetwork.NAME,
networkID);
networkStack.push(currentNetwork);
cyNetworks.add(currentNetwork);
@@ -174,7 +174,7 @@
currentObject =
nodeid2CyNodeMap.get(currentAttributeID);
if (currentObject == null) {
currentObject = rootNetwork.addNode();
-
rootNetwork.getRow(currentObject).set(CyTableEntry.NAME, currentAttributeID);
+
rootNetwork.getRow(currentObject).set(CyNetwork.NAME, currentAttributeID);
nodeid2CyNodeMap.put(currentAttributeID,
currentObject);
}
@@ -188,7 +188,7 @@
currentObject =
nodeid2CyNodeMap.get(currentAttributeID);
if (currentObject == null) {
currentObject = currentNetwork.addNode();
-
currentNetwork.getRow(currentObject).set(CyTableEntry.NAME, currentAttributeID);
+
currentNetwork.getRow(currentObject).set(CyNetwork.NAME, currentAttributeID);
nodeid2CyNodeMap.put(currentAttributeID,
currentObject);
}
}
@@ -207,7 +207,7 @@
if (networkStack.size() > 1) {
final CyNetwork rootNetwork = networkStack.get(0);
currentObject = rootNetwork.addEdge(sourceNode,
targetNode, directed);
-
rootNetwork.getRow(currentObject).set(CyTableEntry.NAME, currentEdgeSourceName
+ " (-) " + currentEdgeTargetName);
+ rootNetwork.getRow(currentObject).set(CyNetwork.NAME,
currentEdgeSourceName + " (-) " + currentEdgeTargetName);
rootNetwork.getRow(currentObject).set(CyEdge.INTERACTION, "-");
for (CyNetwork network : networkStack) {
@@ -218,7 +218,7 @@
} else {
try {
currentObject =
currentNetwork.addEdge(sourceNode, targetNode, directed);
-
currentNetwork.getRow(currentObject).set(CyTableEntry.NAME,
currentEdgeSourceName + " (-) " + currentEdgeTargetName);
+
currentNetwork.getRow(currentObject).set(CyNetwork.NAME, currentEdgeSourceName
+ " (-) " + currentEdgeTargetName);
currentNetwork.getRow(currentObject).set(CyEdge.INTERACTION, "-");
} catch (Exception e) {
logger.warn("Edge entry ignored: " +
currentEdgeSourceName + " (-) " + currentEdgeTargetName, e);
Modified:
core3/impl/trunk/graphml-impl/src/test/java/org/cytoscape/data/reader/graphml/GraphMLReaderTest.java
===================================================================
---
core3/impl/trunk/graphml-impl/src/test/java/org/cytoscape/data/reader/graphml/GraphMLReaderTest.java
2012-03-26 23:20:35 UTC (rev 28653)
+++
core3/impl/trunk/graphml-impl/src/test/java/org/cytoscape/data/reader/graphml/GraphMLReaderTest.java
2012-03-26 23:22:19 UTC (rev 28654)
@@ -13,7 +13,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.NetworkTestSupport;
import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
@@ -141,7 +141,7 @@
final CyNetwork rootNetwork = networks[0];
for(CyNode node: rootNetwork.getNodeList())
- System.out.println("In root network: " +
rootNetwork.getRow(node).get(CyTableEntry.NAME, String.class));
+ System.out.println("In root network: " +
rootNetwork.getRow(node).get(CyNetwork.NAME, String.class));
assertEquals(11, rootNetwork.getNodeCount());
assertEquals(12, rootNetwork.getEdgeCount());
@@ -172,7 +172,7 @@
final CyNetwork rootNetwork = networks[0];
for(CyNode node: rootNetwork.getNodeList())
- System.out.println("In root network: " +
rootNetwork.getRow(node).get(CyTableEntry.NAME, String.class));
+ System.out.println("In root network: " +
rootNetwork.getRow(node).get(CyNetwork.NAME, String.class));
assertEquals(8, rootNetwork.getNodeCount());
assertEquals(10, rootNetwork.getEdgeCount());
Modified:
core3/impl/trunk/group-impl/src/main/java/org/cytoscape/group/internal/CyGroupImpl.java
===================================================================
---
core3/impl/trunk/group-impl/src/main/java/org/cytoscape/group/internal/CyGroupImpl.java
2012-03-26 23:20:35 UTC (rev 28653)
+++
core3/impl/trunk/group-impl/src/main/java/org/cytoscape/group/internal/CyGroupImpl.java
2012-03-26 23:22:19 UTC (rev 28654)
@@ -50,7 +50,7 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.subnetwork.CyRootNetwork;
import org.cytoscape.model.subnetwork.CySubNetwork;
@@ -705,7 +705,7 @@
return source;
}
- private void createIfNecessary(CyTableEntry entry, String tableName,
+ private void createIfNecessary(CyIdentifiable entry, String tableName,
String attribute, Class type) {
CyTable table = rootNetwork.getRow(entry, tableName).getTable();
if (table.getColumn(attribute) == null)
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