Author: rodche
Date: 2011-12-09 11:55:41 -0800 (Fri, 09 Dec 2011)
New Revision: 27753
Removed:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/util/SelectUtil.java
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecuteGetRecordByCPathId.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/GetParentInteractionsTask.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ViewNetworkNeighborhoodTask.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/util/AttributeUtil.java
Log:
Updated to sync with the recent core API changes... Removed unused utility
class.
Modified: csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml
===================================================================
--- csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml 2011-12-09
19:15:04 UTC (rev 27752)
+++ csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml 2011-12-09
19:55:41 UTC (rev 27753)
@@ -46,7 +46,6 @@
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>layout-api</artifactId>
- <version>${cytoscape.api.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
@@ -67,7 +66,6 @@
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>biopax-api</artifactId>
- <version>${parent.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecuteGetRecordByCPathId.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecuteGetRecordByCPathId.java
2011-12-09 19:15:04 UTC (rev 27752)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecuteGetRecordByCPathId.java
2011-12-09 19:55:41 UTC (rev 27753)
@@ -212,13 +212,13 @@
private void addLinksToCPathInstance(CyNetwork cyNetwork) {
String serverName = CPathProperties.serverName;
String serverURL = CPathProperties.cPathUrl;
- CyRow row = cyNetwork.getCyRow();
+ CyRow row = cyNetwork.getCyRow(cyNetwork);
String cPathServerDetailsUrl =
row.get(ExecuteGetRecordByCPathId.CPATH_SERVER_DETAILS_URL, String.class);
if (cPathServerDetailsUrl == null) {
- AttributeUtil.set(cyNetwork,
ExecuteGetRecordByCPathId.CPATH_SERVER_NAME_ATTRIBUTE, serverName,
- String.class);
+ AttributeUtil.set(cyNetwork, cyNetwork,
ExecuteGetRecordByCPathId.CPATH_SERVER_NAME_ATTRIBUTE,
+ serverName, String.class);
String url = serverURL.replaceFirst("webservice.do",
"record2.do?id=");
- AttributeUtil.set(cyNetwork,
ExecuteGetRecordByCPathId.CPATH_SERVER_DETAILS_URL, url, String.class);
+ AttributeUtil.set(cyNetwork, cyNetwork,
ExecuteGetRecordByCPathId.CPATH_SERVER_DETAILS_URL, url, String.class);
}
}
@@ -236,10 +236,10 @@
final CyNetwork cyNetwork = view.getModel();
// Set the Quick Find Default Index
- AttributeUtil.set(cyNetwork, "quickfind.default_index",
"biopax.node_label", String.class);
+ AttributeUtil.set(cyNetwork, cyNetwork,
"quickfind.default_index", "biopax.node_label", String.class);
// Specify that this is a BINARY_NETWORK
- AttributeUtil.set(cyNetwork,
BinarySifVisualStyleFactory.BINARY_NETWORK, Boolean.TRUE, Boolean.class);
+ AttributeUtil.set(null, cyNetwork,
BinarySifVisualStyleFactory.BINARY_NETWORK, Boolean.TRUE, Boolean.class);
// Get all node details.
getNodeDetails(cyNetwork, taskMonitor);
@@ -262,7 +262,7 @@
networkTitleWithUnderscores =
networkTitleWithUnderscores.replaceAll(" ", "_");
CyNetworkNaming naming =
cPathFactory.getCyNetworkNaming();
networkTitleWithUnderscores =
naming.getSuggestedNetworkTitle(networkTitleWithUnderscores);
- AttributeUtil.set(cyNetwork,
CyNetwork.NAME, networkTitleWithUnderscores, String.class);
+ AttributeUtil.set(cyNetwork, cyNetwork,
CyNetwork.NAME, networkTitleWithUnderscores, String.class);
}
});
} else {
@@ -276,7 +276,6 @@
//TODO may be remove this method
private void postProcessingBioPAX(final CyNetworkView view, TaskMonitor
taskMonitor) {
- final CyNetwork cyNetwork = view.getModel();
if (haltFlag == false) {
if (taskMonitor != null) {
taskMonitor.setStatusMessage("Creating Network
View...");
@@ -309,7 +308,7 @@
Map<String, CyNode> nodes = new HashMap<String,
CyNode>();
for (int j = 0; j < currentList.size(); j++) {
CyNode node = currentList.get(j);
- String name = node.getCyRow().get(CyNode.NAME,
String.class);
+ String name =
cyNetwork.getCyRow(node).get(CyNode.NAME, String.class);
nodes.put(name, node);
ids[j] = name;
}
@@ -350,7 +349,7 @@
List<CyNode> currentList = new ArrayList<CyNode>();
int counter = 0;
for (CyNode node : cyNetwork.getNodeList()) {
- CyRow row = node.getCyRow();
+ CyRow row = cyNetwork.getCyRow(node);
String label = row.get(CyNode.NAME, String.class);
// If we already have details on this node, skip it.
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/GetParentInteractionsTask.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/GetParentInteractionsTask.java
2011-12-09 19:15:04 UTC (rev 27752)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/GetParentInteractionsTask.java
2011-12-09 19:55:41 UTC (rev 27753)
@@ -28,7 +28,7 @@
private final CPath2Factory factory;
public GetParentInteractionsTask (CyNetwork network, CyNode node,
CPath2Factory factory) {
- this.uri = node.getCyRow().get(MapBioPaxToCytoscape.BIOPAX_RDF_ID,
String.class);
+ this.uri =
network.getCyRow(node).get(MapBioPaxToCytoscape.BIOPAX_RDF_ID, String.class);
this.node = node;
this.network = network;
this.factory = factory;
@@ -52,7 +52,7 @@
CySwingApplication application = factory.getCySwingApplication();
JDialog dialog = new JDialog(application.getJFrame());
- String nodeLabel = node.getCyRow().get(CyNode.NAME, String.class);
+ String nodeLabel = network.getCyRow(node).get(CyNode.NAME,
String.class);
if (nodeLabel != null) {
dialog.setTitle(nodeLabel);
} else {
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ViewNetworkNeighborhoodTask.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ViewNetworkNeighborhoodTask.java
2011-12-09 19:15:04 UTC (rev 27752)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ViewNetworkNeighborhoodTask.java
2011-12-09 19:55:41 UTC (rev 27753)
@@ -27,7 +27,8 @@
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
- CyRow row = networkView.getModel().getCyRow();
+ CyNetwork cyNetwork = networkView.getModel();
+ CyRow row = cyNetwork.getCyRow(cyNetwork);
// grab web services url from network attributes
String webServicesURL = row.get("biopax.web_services_url",
String.class);
if (webServicesURL == null) {
@@ -42,7 +43,7 @@
// generate menu url
CyNode cyNode = nodeView.getModel();
- CyRow nodeRow = cyNode.getCyRow();
+ CyRow nodeRow = cyNetwork.getCyRow(cyNode);
String biopaxID = nodeRow.get(MapBioPaxToCytoscape.BIOPAX_RDF_ID,
String.class);
biopaxID = biopaxID.replace("CPATH-", "");
String neighborhoodParam = "Neighborhood: " + nodeRow.get(CyNode.NAME,
String.class);
@@ -79,7 +80,7 @@
return false;
}
- Boolean value =
cyNetwork.getCyRow().get(MapBioPaxToCytoscape.BIOPAX_NETWORK, Boolean.class);
+ Boolean value =
cyNetwork.getCyRow(cyNetwork).get(MapBioPaxToCytoscape.BIOPAX_NETWORK,
Boolean.class);
if (value == null || !value) {
return false;
}
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/util/AttributeUtil.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/util/AttributeUtil.java
2011-12-09 19:15:04 UTC (rev 27752)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/util/AttributeUtil.java
2011-12-09 19:55:41 UTC (rev 27753)
@@ -3,13 +3,14 @@
import java.util.List;
import org.cytoscape.model.CyColumn;
+import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableEntry;
public class AttributeUtil {
- public static void set(CyTableEntry entry, String name, Object value,
Class<?> type) {
- CyRow row = entry.getCyRow();
+ public static void set(CyNetwork network, CyTableEntry entry, String
name, Object value, Class<?> type) {
+ CyRow row = network.getCyRow(entry);
CyTable table = row.getTable();
CyColumn column = table.getColumn(name);
if (column == null) {
Deleted:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/util/SelectUtil.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/util/SelectUtil.java
2011-12-09 19:15:04 UTC (rev 27752)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/util/SelectUtil.java
2011-12-09 19:55:41 UTC (rev 27753)
@@ -1,92 +0,0 @@
-package org.cytoscape.cpathsquared.internal.util;
-
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.Set;
-
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyRow;
-import org.cytoscape.model.CyTableEntry;
-
-public class SelectUtil {
- public static void unselectAllNodes(CyNetwork network) {
- setSelectedState(network.getNodeList(), Boolean.FALSE);
- }
-
- public static void unselectAllEdges(CyNetwork network) {
- setSelectedState(network.getEdgeList(), Boolean.FALSE);
- }
-
- public static void setSelectedNodeState(Collection<CyNode> list,
boolean selected) {
- setSelectedState(list, selected);
- }
-
- public static void setSelectedEdgeState(Collection<CyEdge> list,
boolean selected) {
- setSelectedState(list, selected);
- }
-
- static void setSelectedState(Collection<? extends CyTableEntry> list,
Boolean selected) {
- for (CyTableEntry edge : list) {
- CyRow row = edge.getCyRow();
- row.set(CyNetwork.SELECTED, selected);
- }
-
- }
-
- public static Set<CyNode> getSelectedNodes(CyNetwork cyNetwork) {
- return getSelected(cyNetwork.getNodeList());
- }
-
- public static Set<CyEdge> getSelectedEdges(CyNetwork cyNetwork) {
- return getSelected(cyNetwork.getEdgeList());
- }
-
- static <T extends CyTableEntry> Set<T> getSelected(Collection<T> items)
{
- Set<T> entries = new HashSet<T>();
- for (T item : items) {
- CyRow row = item.getCyRow();
- if (row.get(CyNetwork.SELECTED, Boolean.class)) {
- entries.add(item);
- }
- }
- return entries;
- }
-
- public static void selectAllNodes(CyNetwork cyNetwork) {
- selectAll(cyNetwork.getNodeList());
- }
-
- public static void selectAllEdges(CyNetwork cyNetwork) {
- selectAll(cyNetwork.getEdgeList());
- }
-
- static <T extends CyTableEntry> void selectAll(Collection<T> items) {
- for (T item : items) {
- CyRow row = item.getCyRow();
- if (!row.get(CyNetwork.SELECTED, Boolean.class)) {
- row.set(CyNetwork.SELECTED, Boolean.TRUE);
- }
- }
- }
-
- public static int getSelectedNodeCount(CyNetwork cyNetwork) {
- return countSelected(cyNetwork.getNodeList());
- }
-
- public static int getSelectedEdgeCount(CyNetwork cyNetwork) {
- return countSelected(cyNetwork.getNodeList());
- }
-
- static <T extends CyTableEntry> int countSelected(Collection<T> items) {
- int count = 0;
- for (T item : items) {
- CyRow row = item.getCyRow();
- if (row.get(CyNetwork.SELECTED, Boolean.class)) {
- count++;
- }
- }
- return count;
- }
-}
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
