Author: kono
Date: 2012-07-26 15:15:36 -0700 (Thu, 26 Jul 2012)
New Revision: 30011
Removed:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/mapper/CyNetworkBuilder.java
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/mapper/Mitab25Mapper.java
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/ontology/
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/ui/ResultDialog.java
Modified:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/CyActivator.java
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICRestClient.java
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/mapper/InteractionClusterMapper.java
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/simpleclient/PSICQUICSimpleClient.java
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/task/ImportNetworkFromPSICQUICTask.java
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/ui/SourceStatusPanel.java
Log:
Network Builder code is consolidated to PSI-MI library ones. Also, URL
encoding bug fixed.
Modified:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/CyActivator.java
===================================================================
---
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/CyActivator.java
2012-07-26 21:45:23 UTC (rev 30010)
+++
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/CyActivator.java
2012-07-26 22:15:36 UTC (rev 30011)
@@ -1,8 +1,12 @@
package org.cytoscape.webservice.psicquic;
+import static org.cytoscape.work.ServiceProperties.MENU_GRAVITY;
+import static org.cytoscape.work.ServiceProperties.NODE_APPS_MENU;
+import static org.cytoscape.work.ServiceProperties.PREFERRED_MENU;
+import static org.cytoscape.work.ServiceProperties.TITLE;
+
import java.util.Properties;
-import org.cytoscape.application.swing.CyNodeViewContextMenuFactory;
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyNetworkManager;
@@ -14,7 +18,6 @@
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.webservice.psicquic.mapper.MergedNetworkBuilder;
import org.cytoscape.webservice.psicquic.task.ExpandNodeContextMenuFactory;
-import static org.cytoscape.work.ServiceProperties.*;
import org.cytoscape.work.swing.DialogTaskManager;
import org.osgi.framework.BundleContext;
@@ -35,8 +38,6 @@
VisualMappingManager vmm = getService(bc,
VisualMappingManager.class);
CyEventHelper eh = getService(bc, CyEventHelper.class);
- DialogTaskManager taskManager = getService(bc,
DialogTaskManager.class);
-
CreateNetworkViewTaskFactory createViewTaskFactoryServiceRef =
getService(bc,
CreateNetworkViewTaskFactory.class);
Modified:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICRestClient.java
===================================================================
---
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICRestClient.java
2012-07-26 21:45:23 UTC (rev 30010)
+++
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICRestClient.java
2012-07-26 22:15:36 UTC (rev 30011)
@@ -1,10 +1,11 @@
package org.cytoscape.webservice.psicquic;
import java.io.IOException;
-import java.io.InputStream;
import java.net.URL;
+import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.Collection;
+import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
@@ -12,7 +13,6 @@
import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
-import java.util.WeakHashMap;
import java.util.concurrent.Callable;
import java.util.concurrent.CancellationException;
import java.util.concurrent.CompletionService;
@@ -27,7 +27,6 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
-import org.cytoscape.webservice.psicquic.mapper.CyNetworkBuilder;
import org.cytoscape.webservice.psicquic.mapper.MergedNetworkBuilder;
import org.cytoscape.webservice.psicquic.simpleclient.PSICQUICSimpleClient;
import org.cytoscape.work.TaskMonitor;
@@ -68,10 +67,10 @@
public static final Long ERROR_TIMEOUT = -2l;
public static final Long ERROR_CANCEL = -3l;
- // Timeout for search. TODO: Make public as property.
+ // Timeout for search. TODO: Make public as property.
private static final long SEARCH_TIMEOUT_MSEC = 7000;
-
- // Timeout for import. TODO: Make public as property.
+
+ // Timeout for import. TODO: Make public as property.
private static final long IMPORT_TIMEOUT = 1000;
private final CyNetworkFactory factory;
@@ -80,121 +79,73 @@
private boolean canceled = false;
- public PSICQUICRestClient(final CyNetworkFactory factory, final
RegistryManager regManager, final MergedNetworkBuilder builder) {
+ public PSICQUICRestClient(final CyNetworkFactory factory, final
RegistryManager regManager,
+ final MergedNetworkBuilder builder) {
this.factory = factory;
this.regManager = regManager;
this.builder = builder;
}
- public Map<String, CyNetwork> importNetwork(final String query, final
Collection<String> targetServices,
- final SearchMode mode, final TaskMonitor tm) {
+ public CyNetwork importMergedNetwork(final String query, final
Collection<String> targetServices,
+ final SearchMode mode, final TaskMonitor tm) throws
IOException {
- canceled = false;
+ final InteractionCluster importedCluster = importMerged(query,
targetServices, mode, tm);
+ final CyNetwork network = builder.buildNetwork(importedCluster);
- tm.setTitle("Loading network data from PSICQUIC Remote
Services");
+ tm.setProgress(1.0d);
+ return network;
+ }
- Map<String, CyNetwork> resultMap = new
ConcurrentHashMap<String, CyNetwork>();
- final ExecutorService exe = Executors.newCachedThreadPool();
- final CompletionService<Map<CyNetwork, String>>
completionService = new ExecutorCompletionService<Map<CyNetwork, String>>(
- exe);
+ public Collection<CyNetwork> importNetworks(final String query, final
Collection<String> targetServices,
+ final SearchMode mode, final TaskMonitor tm) throws
IOException {
- final long startTime = System.currentTimeMillis();
+ final Set<CyNetwork> networks = new HashSet<CyNetwork>();
+ final Map<String, Collection<BinaryInteraction>> result =
importNetwork(query, targetServices, mode, tm);
- // Submit the query for each active service
- double completed = 0.0d;
- final double increment = 1.0d / (double) targetServices.size();
+ for (String source : result.keySet()) {
+ tm.setStatusMessage("Merging results...");
+ final InteractionCluster iC = new InteractionCluster();
+
iC.setBinaryInteractionIterator(result.get(source).iterator());
+ iC.setMappingIdDbNames(MAPPING_NAMES);
+ iC.runService();
- final SortedSet<String> sourceSet = new TreeSet<String>();
- final Set<ImportNetworkTask> taskSet = new
HashSet<ImportNetworkTask>();
- for (final String serviceURL : targetServices) {
- ImportNetworkTask task = new
ImportNetworkTask(serviceURL, query, mode);
- completionService.submit(task);
- taskSet.add(task);
- sourceSet.add(serviceURL);
+ final CyNetwork network = builder.buildNetwork(iC);
+ final String networkName =
regManager.getSource2NameMap().get(source);
+ network.getRow(network).set(CyNetwork.NAME,
networkName);
+ networks.add(network);
}
- for (int i = 0; i < targetServices.size(); i++) {
- if (canceled) {
- logger.warn("Interrupted by user: network
import task");
- exe.shutdownNow();
- resultMap.clear();
- resultMap = null;
+ tm.setProgress(1.0d);
+ return networks;
+ }
- return new ConcurrentHashMap<String,
CyNetwork>();
- }
+ public InteractionCluster importNeighbours(final String query, final
Collection<String> targetServices,
+ final SearchMode mode, final TaskMonitor tm) throws
IOException {
+ return importMerged(query, targetServices, mode, tm);
+ }
- Future<Map<CyNetwork, String>> future = null;
- try {
- future = completionService.take();
- final Map<CyNetwork, String> ret = future.get();
- final CyNetwork network =
ret.keySet().iterator().next();
- final String source = ret.get(network);
- resultMap.put(source, network);
- sourceSet.remove(source);
+ private final InteractionCluster importMerged(final String query, final
Collection<String> targetServices,
+ final SearchMode mode, final TaskMonitor tm) {
- completed = completed + increment;
- tm.setProgress(completed);
+ final Map<String, Collection<BinaryInteraction>> result =
importNetwork(query, targetServices, mode, tm);
+ final Collection<Collection<BinaryInteraction>>
binaryInteractions = result.values();
+ final List<BinaryInteraction> allInteractions = new
ArrayList<BinaryInteraction>();
+ for (Collection<BinaryInteraction> interactions :
binaryInteractions)
+ allInteractions.addAll(interactions);
- final StringBuilder sBuilder = new
StringBuilder();
- for (String sourceStr : sourceSet) {
-
sBuilder.append(regManager.getSource2NameMap().get(sourceStr) + " ");
- }
+ tm.setStatusMessage("Merging results...");
+ InteractionCluster iC = new InteractionCluster();
+ iC.setBinaryInteractionIterator(allInteractions.iterator());
+ iC.setMappingIdDbNames(MAPPING_NAMES);
+ iC.runService();
- tm.setStatusMessage((i + 1) + " / " +
targetServices.size() + " tasks finished.\n"
- + "Still waiting responses from
the following databases:\n\n" + sBuilder.toString());
-
- } catch (InterruptedException ie) {
- for (ImportNetworkTask t : taskSet)
- t.cancel();
- taskSet.clear();
-
- List<Runnable> tasks = exe.shutdownNow();
- logger.warn("Interrupted: network import.
Remaining = " + tasks.size(), ie);
- resultMap.clear();
- resultMap = null;
- return new ConcurrentHashMap<String,
CyNetwork>();
- } catch (ExecutionException e) {
- logger.warn("Error occured in network import",
e);
- continue;
- }
- }
-
- try {
- exe.shutdown();
- exe.awaitTermination(IMPORT_TIMEOUT, TimeUnit.SECONDS);
-
- long endTime = System.currentTimeMillis();
- double sec = (endTime - startTime) / (1000.0);
- logger.info("PSICUQIC Import Finished in " + sec + "
sec.");
- } catch (Exception ex) {
- logger.warn("Import operation timeout", ex);
- return resultMap;
- } finally {
- taskSet.clear();
- sourceSet.clear();
- }
-
- return resultMap;
+ return iC;
}
- public CyNetwork importClusteredNetwork(final String query, final
Collection<String> targetServices,
- final SearchMode mode, final TaskMonitor tm) throws
IOException {
-
- InteractionCluster importedCluster = importClustered(query,
targetServices, mode, tm);
+ private Map<String, Collection<BinaryInteraction>> importNetwork(final
String query,
+ final Collection<String> targetServices, final
SearchMode mode, final TaskMonitor tm) {
+ final Map<String, Collection<BinaryInteraction>> result = new
HashMap<String, Collection<BinaryInteraction>>();
- final CyNetwork network = builder.buildNetwork(importedCluster);
-
- tm.setProgress(1.0d);
- return network;
- }
-
- public InteractionCluster importNeighbours(final String query, final
Collection<String> targetServices,
- final SearchMode mode, final TaskMonitor tm) throws
IOException {
- return importClustered(query, targetServices, mode, tm);
- }
-
- private final InteractionCluster importClustered(final String query,
final Collection<String> targetServices,
- final SearchMode mode, final TaskMonitor tm) {
canceled = false;
tm.setTitle("Loading network data from Remote PSICQUIC
Services");
@@ -211,16 +162,16 @@
final double increment = 1.0d / (double) targetServices.size();
final SortedSet<String> sourceSet = new TreeSet<String>();
- final Set<ImportNetworkAsStreamsTask> taskSet = new
HashSet<ImportNetworkAsStreamsTask>();
+ final Set<ImportNetworkAsMitabTask> taskSet = new
HashSet<ImportNetworkAsMitabTask>();
for (final String serviceURL : targetServices) {
- ImportNetworkAsStreamsTask task = new
ImportNetworkAsStreamsTask(serviceURL, query, mode);
+ final ImportNetworkAsMitabTask task = new
ImportNetworkAsMitabTask(serviceURL, query, mode);
completionService.submit(task);
taskSet.add(task);
sourceSet.add(serviceURL);
}
- final List<BinaryInteraction> binaryInteractions = new
ArrayList<BinaryInteraction>();
- for (int i = 0; i < targetServices.size(); i++) {
+ int i = 0;
+ for (final String service : targetServices) {
if (canceled) {
logger.warn("Interrupted by user: network
import task");
exe.shutdownNow();
@@ -234,8 +185,10 @@
try {
future = completionService.take();
final Collection<BinaryInteraction> ret =
future.get();
- if (ret != null)
- binaryInteractions.addAll(ret);
+ if (ret != null) {
+ result.put(service, ret);
+ // binaryInteractions.addAll(ret);
+ }
completed = completed + increment;
tm.setProgress(completed);
@@ -249,7 +202,7 @@
+ "Still waiting responses from
the following databases:\n\n" + sBuilder.toString());
} catch (InterruptedException ie) {
- for (ImportNetworkAsStreamsTask t : taskSet) {
+ for (ImportNetworkAsMitabTask t : taskSet) {
// t.cancel();
}
@@ -264,6 +217,8 @@
logger.warn("Error occured in network import",
e);
continue;
}
+
+ i++;
}
try {
@@ -281,13 +236,7 @@
sourceSet.clear();
}
- tm.setStatusMessage("Merging results...");
- InteractionCluster iC = new InteractionCluster();
- iC.setBinaryInteractionIterator(binaryInteractions.iterator());
- iC.setMappingIdDbNames(MAPPING_NAMES);
- iC.runService();
-
- return iC;
+ return result;
}
public Map<String, Long> search(final String query, final
Collection<String> targetServices, final SearchMode mode,
@@ -359,7 +308,7 @@
* Search each data source and return aggregated result.
*
*/
- private final class SearchTask implements Callable<Long> {
+ private static final class SearchTask implements Callable<Long> {
private final String serviceURL;
private final String query;
private final SearchMode mode;
@@ -383,69 +332,36 @@
}
}
- private final class ImportNetworkTask implements
Callable<Map<CyNetwork, String>> {
+ private static final class ImportNetworkAsMitabTask implements
Callable<Collection<BinaryInteraction>> {
private final String serviceURL;
private final String query;
private final SearchMode mode;
- private final Map<CyNetwork, String> returnThis;
-
- private final CyNetworkBuilder networkBuilder;
-
- private ImportNetworkTask(final String serviceURL, final String
query, final SearchMode mode) {
+ private ImportNetworkAsMitabTask(final String serviceURL, final
String query, final SearchMode mode) {
this.serviceURL = serviceURL;
this.query = query;
this.mode = mode;
- this.returnThis = new WeakHashMap<CyNetwork, String>();
- this.networkBuilder = new CyNetworkBuilder(factory);
}
@Override
- public Map<CyNetwork, String> call() throws Exception {
- final PSICQUICSimpleClient simpleClient = new
PSICQUICSimpleClient(serviceURL);
- InputStream is = null;
- if (mode == SearchMode.INTERACTOR)
- is = simpleClient.getByInteraction(query);
- else if (mode == SearchMode.MIQL)
- is = simpleClient.getByQuery(query);
+ public Collection<BinaryInteraction> call() throws Exception {
- // This can be null if interrupted.
- final CyNetwork network =
networkBuilder.buildNetwork(is);
- is.close();
- is = null;
+ String encodedStr = URLEncoder.encode(query, "UTF-8");
+ encodedStr = encodedStr.replaceAll("\\+", "%20");
- if (network != null)
- returnThis.put(network, serviceURL);
+ URL queryURL = null;
+ if (mode == SearchMode.INTERACTOR) {
+ // Query is list of interactors.
+ queryURL = new URL(serviceURL + "interactor/" +
encodedStr);
+ } else if (mode == SearchMode.MIQL) {
+ queryURL = new URL(serviceURL + "query/" +
encodedStr);
+ }
- return returnThis;
- }
+ if (queryURL == null)
+ throw new IllegalArgumentException("Could not
create query URL.");
- public void cancel() {
- networkBuilder.cancel();
- }
- }
+ logger.info("Query URL: " + queryURL);
- private final class ImportNetworkAsStreamsTask implements
Callable<Collection<BinaryInteraction>> {
- private final String serviceURL;
- private final String query;
- private final SearchMode mode;
-
- private ImportNetworkAsStreamsTask(final String serviceURL,
final String query, final SearchMode mode) {
- this.serviceURL = serviceURL;
- this.query = query;
- this.mode = mode;
- }
-
- @Override
- public Collection<BinaryInteraction> call() throws Exception {
- final PSICQUICSimpleClient simpleClient = new
PSICQUICSimpleClient(serviceURL);
- InputStream is = null;
- if (mode == SearchMode.INTERACTOR)
- is = simpleClient.getByInteraction(query);
- else if (mode == SearchMode.MIQL)
- is = simpleClient.getByQuery(query);
-
- URL queryURL = new URL(serviceURL + "query/" + query);
final PsimiTabReader mitabReader = new
PsimiTabReader(false);
return mitabReader.read(queryURL);
}
@@ -454,5 +370,4 @@
public void cancel() {
this.canceled = true;
}
-
-}
+}
\ No newline at end of file
Deleted:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/mapper/CyNetworkBuilder.java
===================================================================
---
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/mapper/CyNetworkBuilder.java
2012-07-26 21:45:23 UTC (rev 30010)
+++
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/mapper/CyNetworkBuilder.java
2012-07-26 22:15:36 UTC (rev 30011)
@@ -1,51 +0,0 @@
-package org.cytoscape.webservice.psicquic.mapper;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNetworkFactory;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class CyNetworkBuilder {
-
- private static final Logger logger =
LoggerFactory.getLogger(CyNetworkBuilder.class);
-
- private final CyNetworkFactory networkFactory;
-
- volatile boolean cancel = false;
-
- public CyNetworkBuilder(final CyNetworkFactory networkFactory) {
- this.networkFactory = networkFactory;
- }
-
- public CyNetwork buildNetwork(final InputStream is) throws IOException {
- CyNetwork network = networkFactory.createNetwork();
-
- final Mitab25Mapper mapper = new Mitab25Mapper(network);
-
- String line = null;
- final BufferedReader br = new BufferedReader(new
InputStreamReader(is));
- while ((line = br.readLine()) != null) {
- if(cancel) {
- br.close();
- logger.warn("Network bulilder interrupted.");
- network = null;
- return null;
- }
-
- mapper.parse(line);
- }
-
- br.close();
- logger.info("Import Done: " + network.getSUID());
- return network;
- }
-
- public void cancel() {
- this.cancel = true;
- }
-}
Modified:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/mapper/InteractionClusterMapper.java
===================================================================
---
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/mapper/InteractionClusterMapper.java
2012-07-26 21:45:23 UTC (rev 30010)
+++
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/mapper/InteractionClusterMapper.java
2012-07-26 22:15:36 UTC (rev 30011)
@@ -15,12 +15,11 @@
import javax.xml.bind.JAXBException;
import javax.xml.bind.Unmarshaller;
-import org.cytoscape.event.CyEventHelper;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyRow;
import org.cytoscape.webservice.psicquic.miriam.Miriam;
-import org.cytoscape.webservice.psicquic.miriam.Synonyms;
import org.cytoscape.webservice.psicquic.miriam.Miriam.Datatype;
+import org.cytoscape.webservice.psicquic.miriam.Synonyms;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
Deleted:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/mapper/Mitab25Mapper.java
===================================================================
---
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/mapper/Mitab25Mapper.java
2012-07-26 21:45:23 UTC (rev 30010)
+++
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/mapper/Mitab25Mapper.java
2012-07-26 22:15:36 UTC (rev 30011)
@@ -1,284 +0,0 @@
-package org.cytoscape.webservice.psicquic.mapper;
-
-import java.util.HashMap;
-import java.util.Map;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyRow;
-
-/**
- * Map minimal set of information from MITAB25.
- *
- */
-public class Mitab25Mapper {
-
- // Separator for multiple entries.
- private static final String SEPARATOR = "\\|";
- private static final String ATTR_PREFIX = "PSI-MI-25: ";
-
- private static final int COLUMN_COUNT = 15;
-
- // Reg.Ex for parsing entry
- private final static Pattern miPttr = Pattern.compile("MI:\\d{4}");
- private final static Pattern miNamePttr = Pattern.compile("\\(.+\\)");
-
- private static final String TAB = "\t";
-
- // Attr Names
- private static final String DATABASE_UNIQUE_ID = ATTR_PREFIX +
"database-unique ID";
- private static final String DETECTION_METHOD = ATTR_PREFIX +
"interaction detection method";
- private static final String INTERACTION_TYPE = ATTR_PREFIX +
"interaction type";
- private static final String SOURCE_DB = ATTR_PREFIX + "source database";
- private static final String INTERACTION_ID = ATTR_PREFIX + "Interaction
ID";
- private static final String EDGE_SCORE = ATTR_PREFIX + "confidence
score";
-
- // Stable IDs which maybe used for mapping later
- private static final String UNIPROT = "uniprotkb";
- private static final String ENTREZ_GENE = "entrezgene/locuslink";
- private static final String ENTREZ_GENE_SYN = "entrez gene/locuslink";
-
- private static final String CHEBI = "chebi";
-
- private static final String INTERACTOR_TYPE = ATTR_PREFIX + "interactor
type";
- private static final String COMPOUND = "compound";
-
- private Matcher matcher;
-
-
-
- private final CyNetwork network;
- private final Map<String, CyNode> nodeMap;
-
- public Mitab25Mapper(final CyNetwork network) {
- this.network = network;
- this.nodeMap = new HashMap<String, CyNode>();
-
- // Create Columns
- network.getDefaultNodeTable().createColumn(INTERACTOR_TYPE,
String.class, true);
- network.getDefaultNodeTable().createColumn(DATABASE_UNIQUE_ID,
String.class, true);
- network.getDefaultEdgeTable().createColumn(INTERACTION_ID,
String.class, true);
- }
-
- public void parse(final String line) {
-
- String[] sourceID;
- String[] targetID;
-
- String[] detectionMethods;
- CyNode source;
- CyNode target;
- CyEdge e;
-
- String[] sourceDB;
- String[] interactionID;
- String[] interactionType;
-
- String[] edgeScore;
-
-
- final String[] entry = line.split(TAB);
-
- // Validate entry list.
- if (entry == null || entry.length < COLUMN_COUNT)
- return;
-
- sourceID = entry[0].split(SEPARATOR);
- final String sourceIDHalf = sourceID[0].split(":")[1];
- targetID = entry[1].split(SEPARATOR);
- final String targetIDHalf = targetID[0].split(":")[1];
-
- // Create source and target node if necessary.
- source = nodeMap.get(sourceID[0]);
- if(source == null) {
- source = network.addNode();
- network.getRow(source).set(CyNetwork.NAME,
sourceIDHalf);
- network.getRow(source).set(DATABASE_UNIQUE_ID,
sourceID[0]);
- nodeMap.put(sourceID[0], source);
- }
- target = nodeMap.get(targetID[0]);
- if (target == null) {
- target = network.addNode();
- network.getRow(target).set(CyNetwork.NAME,
targetIDHalf);
- network.getRow(target).set(DATABASE_UNIQUE_ID,
targetID[0]);
- nodeMap.put(targetID[0], target);
- }
-
- // Set type if not protein
- if (sourceID[0].contains(CHEBI))
- network.getRow(source).set(INTERACTOR_TYPE, COMPOUND);
- if (targetID[0].contains(CHEBI))
- network.getRow(target).set(INTERACTOR_TYPE, COMPOUND);
-
-// // Aliases
-// setAliases(nodeAttr, source.getIdentifier(),
entry[0].split(SEPARATOR));
-// setAliases(nodeAttr, target.getIdentifier(),
entry[1].split(SEPARATOR));
-// setAliases(nodeAttr, source.getIdentifier(),
entry[2].split(SEPARATOR));
-// setAliases(nodeAttr, target.getIdentifier(),
entry[3].split(SEPARATOR));
-// setAliases(nodeAttr, source.getIdentifier(),
entry[4].split(SEPARATOR));
-// setAliases(nodeAttr, target.getIdentifier(),
entry[5].split(SEPARATOR));
-//
- // Tax ID (pick first one only)
- setTaxID(network.getRow(source), entry[9].split(SEPARATOR)[0]);
- setTaxID(network.getRow(target), entry[10].split(SEPARATOR)[0]);
-
-// sourceDB = entry[12].split(SEPARATOR);
- interactionID = entry[13].split(SEPARATOR);
- edgeScore = entry[14].split(SEPARATOR);
-
- detectionMethods = entry[6].split(SEPARATOR);
- interactionType = entry[11].split(SEPARATOR);
- e = network.addEdge(source, target, true);
- network.getRow(e).set(
- CyNetwork.NAME,
- network.getRow(source).get(CyNetwork.NAME,
String.class) + " (" + interactionID[0] + ") "
- +
network.getRow(target).get(CyNetwork.NAME, String.class));
- network.getRow(e).set(CyEdge.INTERACTION, interactionID[0]);
-
-// setEdgeListAttribute(edgeAttr, e.getIdentifier(),
interactionType, INTERACTION_TYPE);
-// setEdgeListAttribute(edgeAttr, e.getIdentifier(),
detectionMethods, DETECTION_METHOD);
-// setEdgeListAttribute(edgeAttr, e.getIdentifier(), sourceDB,
SOURCE_DB);
-//
-// // Map scores
-// setEdgeScoreListAttribute(edgeAttr, e.getIdentifier(),
edgeScore, EDGE_SCORE);
-//
- network.getRow(e).set(INTERACTION_ID, interactionID[0]);
-//
-// setPublication(edgeAttr, e.getIdentifier(),
entry[8].split(SEPARATOR), entry[7].split(SEPARATOR));
-
- }
-
-
- private void setTaxID(final CyRow row, String value) {
- String[] buf = value.split(":", 2);
- String attrName;
- String taxonName;
- if (buf != null && buf.length == 2) {
- attrName = ATTR_PREFIX + buf[0];
-
- if(row.getTable().getColumn(attrName) == null)
- row.getTable().createColumn(attrName,
String.class, false);
- if(row.getTable().getColumn(attrName+ ".name") == null)
- row.getTable().createColumn(attrName+ ".name",
String.class, false);
-
- matcher = miNamePttr.matcher(buf[1]);
- if (matcher.find()) {
- taxonName = matcher.group();
- row.set(attrName, buf[1].split("\\(")[0]);
- row.set(attrName + ".name",
taxonName.substring(1, taxonName.length() - 1));
- } else {
- row.set(attrName, buf[1]);
- }
- }
- }
-//
-// private void setPublication(CyAttributes attr, String id, String[]
pubID, String[] authors) {
-// String key = null;
-// String[] temp;
-//
-// for (String val : pubID) {
-// temp = val.split(":", 2);
-// if (temp == null || temp.length < 2)
-// continue;
-//
-// key = ATTR_PREFIX + temp[0];
-// listAttrMapper(attr, key, id, temp[1]);
-// }
-//
-// for (String val : authors) {
-// key = ATTR_PREFIX + "author";
-// listAttrMapper(attr, key, id, val);
-// }
-// }
-//
-// private void setAliases(final String id, final String[] entry) {
-// String key = null;
-// String[] temp;
-// String value;
-//
-// for (String val : entry) {
-// temp = val.split(":", 2);
-// if (temp == null || temp.length < 2)
-// continue;
-//
-// key = ATTR_PREFIX + temp[0];
-// value = temp[1].replaceAll("\\(.+\\)", "");
-// listAttrMapper(attr, key, id, value);
-// }
-// }
-//
-// private void setEdgeListAttribute(CyAttributes attr, String id,
String[] entry, String key) {
-//
-// String value;
-// String name;
-//
-// for (String val : entry) {
-// value = trimPSITerm(val);
-// name = trimPSIName(val);
-//
-// listAttrMapper(attr, key, id, value);
-// listAttrMapper(attr, key + ".name", id, name);
-// }
-// }
-//
-// // Special case for edge scores
-// private void setEdgeScoreListAttribute(CyAttributes attr, String id,
String[] entry, String key) {
-//
-// String scoreString;
-// String scoreType;
-//
-// for (String val : entry) {
-// final String[] parts = val.split(":");
-// if (parts == null || parts.length != 2)
-// continue;
-//
-// scoreString = parts[1];
-// scoreType = parts[0];
-//
-// try {
-// final Double score =
Double.parseDouble(scoreString);
-// edgeAttr.setAttribute(id, key + "." +
scoreType, score);
-// } catch (Exception e) {
-// if (scoreString != null &&
scoreString.trim().equals("") == false)
-// edgeAttr.setAttribute(id, key + "." +
scoreType, scoreString);
-//
-// continue;
-// }
-// }
-// }
-//
-
-//
-// private String trimPSITerm(String original) {
-// String miID = null;
-//
-// matcher = miPttr.matcher(original);
-//
-// if (matcher.find()) {
-// miID = matcher.group();
-// } else {
-// miID = "-";
-// }
-//
-// return miID;
-// }
-//
-// private String trimPSIName(String original) {
-// String miName = null;
-//
-// matcher = miNamePttr.matcher(original);
-//
-// if (matcher.find()) {
-// miName = matcher.group();
-// miName = miName.substring(1, miName.length() - 1);
-// } else {
-// miName = "-";
-// }
-//
-// return miName;
-// }
-
-}
Modified:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/simpleclient/PSICQUICSimpleClient.java
===================================================================
---
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/simpleclient/PSICQUICSimpleClient.java
2012-07-26 21:45:23 UTC (rev 30010)
+++
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/simpleclient/PSICQUICSimpleClient.java
2012-07-26 22:15:36 UTC (rev 30011)
@@ -108,6 +108,8 @@
String strCount = streamToString(result);
strCount = strCount.replaceAll("\n", "");
+ result.close();
+
return Long.parseLong(strCount);
}
Modified:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/task/ImportNetworkFromPSICQUICTask.java
===================================================================
---
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/task/ImportNetworkFromPSICQUICTask.java
2012-07-26 21:45:23 UTC (rev 30010)
+++
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/task/ImportNetworkFromPSICQUICTask.java
2012-07-26 22:15:36 UTC (rev 30011)
@@ -11,7 +11,6 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.task.create.CreateNetworkViewTaskFactory;
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.webservice.psicquic.PSICQUICRestClient;
import org.cytoscape.webservice.psicquic.PSICQUICRestClient.SearchMode;
import org.cytoscape.webservice.psicquic.RegistryManager;
@@ -21,6 +20,7 @@
import org.slf4j.LoggerFactory;
public class ImportNetworkFromPSICQUICTask extends AbstractTask {
+
private static final Logger logger =
LoggerFactory.getLogger(ImportNetworkFromPSICQUICTask.class);
private final PSICQUICRestClient client;
@@ -31,7 +31,6 @@
private final CreateNetworkViewTaskFactory createViewTaskFactory;
private String query;
-
private Collection<String> targetServices;
private Set<String> searchResult;
@@ -40,23 +39,20 @@
private SearchRecoredsTask searchTask;
private final SearchMode mode;
- private final boolean toCluster;
- private final CyNetworkView parentNetworkView;
+ private final boolean mergeNetworks;
private volatile boolean canceled = false;
public ImportNetworkFromPSICQUICTask(final String query, final
PSICQUICRestClient client,
final CyNetworkManager manager, final RegistryManager
registryManager, final Set<String> searchResult,
- final SearchMode mode, final
CreateNetworkViewTaskFactory createViewTaskFactory, final boolean toCluster,
final CyNetworkView parentNetworkView) {
+ final SearchMode mode, final
CreateNetworkViewTaskFactory createViewTaskFactory, final boolean toCluster) {
this.client = client;
this.manager = manager;
this.registryManager = registryManager;
this.query = query;
- this.toCluster = toCluster;
- this.parentNetworkView = parentNetworkView;
+ this.mergeNetworks = toCluster;
-
this.searchResult = searchResult;
this.mode = mode;
this.createViewTaskFactory = createViewTaskFactory;
@@ -65,16 +61,15 @@
public ImportNetworkFromPSICQUICTask(final String query, final
PSICQUICRestClient client,
final CyNetworkManager manager, final RegistryManager
registryManager, final SearchRecoredsTask searchTask,
final SearchMode mode, final
CreateNetworkViewTaskFactory createViewTaskFactory) {
+
this.client = client;
this.manager = manager;
this.registryManager = registryManager;
this.query = query;
- this.toCluster = false;
-
+ this.mergeNetworks = false;
this.searchTask = searchTask;
this.mode = mode;
this.createViewTaskFactory = createViewTaskFactory;
- this.parentNetworkView = null;
}
@Override
@@ -85,62 +80,46 @@
if(searchResult == null)
processSearchResult();
- else {
+ else
targetServices = searchResult;
- }
if(searchResult == null)
throw new NullPointerException("Could not find search
result");
-
if (query == null)
throw new NullPointerException("Query is null");
if (targetServices == null)
throw new NullPointerException("Target service set is
null");
// Switch task type based on the user option.
- if(toCluster) {
- final CyNetwork network =
client.importClusteredNetwork(query, targetServices, mode, taskMonitor);
- result = new HashMap<String, CyNetwork>();
- result.put("clustered", network);
- } else
- result = client.importNetwork(query, targetServices,
mode, taskMonitor);
- if(canceled) {
- result.clear();
- result = null;
- return;
- }
-
final Date date = new Date();
final SimpleDateFormat timestamp = new
SimpleDateFormat("yyyy/MM/dd K:mm:ss a, z");
final String suffix = "(" + timestamp.format(date) + ")";
-
- // Register networks to the manager
- final Set<CyNetwork> networks = new HashSet<CyNetwork>();
-
- if (toCluster) {
- final CyNetwork network =
result.values().iterator().next();
- if(network != null) {
- network.getRow(network).set(CyNetwork.NAME,
"Merged Network " + suffix);
- addNetworkData(network);
- manager.addNetwork(network);
- networks.add(network);
- }
+ result = new HashMap<String, CyNetwork>();
+ if(mergeNetworks) {
+ final CyNetwork network =
client.importMergedNetwork(query, targetServices, mode, taskMonitor);
+ network.getRow(network).set(CyNetwork.NAME, "Merged
Network " + suffix);
+ addNetworkData(network);
+ manager.addNetwork(network);
+ result.put("clustered", network);
} else {
- for (String sourceURL : result.keySet()) {
- final CyNetwork network = result.get(sourceURL);
- network.getRow(network).set(CyNetwork.NAME,
-
registryManager.getSource2NameMap().get(sourceURL) + " " + suffix);
+ final Collection<CyNetwork> networks =
client.importNetworks(query, targetServices, mode, taskMonitor);
+ for(CyNetwork network: networks) {
+ final String networkName =
network.getRow(network).get(CyNetwork.NAME, String.class) + " " + suffix;
+ network.getRow(network).set(CyNetwork.NAME,
networkName);
addNetworkData(network);
manager.addNetwork(network);
- networks.add(network);
+ result.put(networkName, network);
}
}
-
- logger.debug(networks.size() + " networks created.");
+ if(canceled) {
+ result.clear();
+ result = null;
+ return;
+ }
if (!canceled)
-
insertTasksAfterCurrentTask(createViewTaskFactory.createTaskIterator(networks));
+
insertTasksAfterCurrentTask(createViewTaskFactory.createTaskIterator(result.values()));
}
@Override
Deleted:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/ui/ResultDialog.java
===================================================================
---
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/ui/ResultDialog.java
2012-07-26 21:45:23 UTC (rev 30010)
+++
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/ui/ResultDialog.java
2012-07-26 22:15:36 UTC (rev 30011)
@@ -1,195 +0,0 @@
-package org.cytoscape.webservice.psicquic.ui;
-
-import java.awt.Frame;
-import java.net.URI;
-import java.util.Map;
-
-import javax.swing.GroupLayout;
-import javax.swing.JDialog;
-import javax.swing.LayoutStyle;
-import javax.swing.table.DefaultTableModel;
-
-/**
- * Display result of the query.
- *
- */
-public class ResultDialog extends JDialog {
-
- private static final long serialVersionUID = 6996385373168492882L;
-
- private Map<URI, String> dbNames;
- private DefaultTableModel model;
-
- private boolean mergeNetworks;
-
- /**
- * Creates new form PSICQUICResultDialog
- *
- */
- public ResultDialog(Frame parent, boolean modal, Map<URI, String>
dbNames) {
- super(parent, modal);
- this.dbNames = dbNames;
- setTableModel();
- initComponents();
- mergeNetworks = false;
- }
-
- private void setTableModel() {
- resultTable = new javax.swing.JTable(new DefaultTableModel() {
- @Override
- public boolean isCellEditable(int row, int column) {
- if (column == 0)
- return false;
- else
- return true;
- }
- });
-
- model = (DefaultTableModel) resultTable.getModel();
- model.addColumn("Service URL", dbNames.keySet().toArray());
- model.addColumn("Network Name (Please edit these if
necessary)");
- for (int i = 0; i < model.getRowCount(); i++) {
- model.setValueAt(dbNames.get(model.getValueAt(i, 0)),
i, 1);
- }
-
- resultTable.getTableHeader().setReorderingAllowed(false);
- }
-
- /**
- * This method is called from within the constructor to initialize the
form.
- * WARNING: Do NOT modify this code. The content of this method is
always
- * regenerated by the Form Editor.
- */
- @SuppressWarnings("unchecked")
- // <editor-fold defaultstate="collapsed" desc="Generated Code">
- private void initComponents() {
- setTitle("PSICQUIC Import Result");
-
- titlePanel = new javax.swing.JPanel();
- titleLabel = new javax.swing.JLabel();
- resultScrollPane = new javax.swing.JScrollPane();
-
- buttonPanel = new javax.swing.JPanel();
- okButton = new javax.swing.JButton();
- mergeButton = new javax.swing.JButton();
- mergeButton = new javax.swing.JButton();
-
-
setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
-
- titlePanel.setBackground(java.awt.Color.white);
-
- titleLabel.setFont(new java.awt.Font("SansSerif", 1, 14)); //
NOI18N
- titleLabel.setText("PSICQUIC Data Import Result");
-
- GroupLayout titlePanelLayout = new GroupLayout(titlePanel);
- titlePanel.setLayout(titlePanelLayout);
-
titlePanelLayout.setHorizontalGroup(titlePanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
- .addGroup(
-
titlePanelLayout.createSequentialGroup().addContainerGap().addComponent(titleLabel)
-
.addContainerGap(390, Short.MAX_VALUE)));
-
titlePanelLayout.setVerticalGroup(titlePanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING).addGroup(
-
titlePanelLayout.createSequentialGroup().addContainerGap().addComponent(titleLabel)
-
.addContainerGap(GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)));
-
- resultScrollPane.setBackground(java.awt.Color.white);
-
- resultScrollPane.setViewportView(resultTable);
-
- buttonPanel.setBackground(java.awt.Color.white);
-
- okButton.setText("OK");
- okButton.setPreferredSize(new java.awt.Dimension(70, 26));
- okButton.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(java.awt.event.ActionEvent
evt) {
- okButtonActionPerformed(evt);
- }
- });
-
- mergeButton.setText("Merge");
- mergeButton.setPreferredSize(new java.awt.Dimension(70, 26));
- mergeButton.addActionListener(new
java.awt.event.ActionListener() {
- public void actionPerformed(java.awt.event.ActionEvent
evt) {
- mergeButtonActionPerformed(evt);
- }
- });
-
- GroupLayout buttonPanelLayout = new GroupLayout(buttonPanel);
- buttonPanel.setLayout(buttonPanelLayout);
-
buttonPanelLayout.setHorizontalGroup(buttonPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
- .addGroup(
- GroupLayout.Alignment.TRAILING,
- buttonPanelLayout
-
.createSequentialGroup()
-
.addContainerGap(491, Short.MAX_VALUE)
-
.addComponent(mergeButton, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE,
-
GroupLayout.PREFERRED_SIZE)
-
.addPreferredGap(LayoutStyle.ComponentPlacement.RELATED)
-
.addComponent(okButton, GroupLayout.PREFERRED_SIZE, 55,
GroupLayout.PREFERRED_SIZE)
-
.addContainerGap()));
-
buttonPanelLayout.setVerticalGroup(buttonPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
- .addGroup(
- GroupLayout.Alignment.TRAILING,
- buttonPanelLayout
-
.createSequentialGroup()
-
.addContainerGap(GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
- .addGroup(
-
buttonPanelLayout
-
.createParallelGroup(GroupLayout.Alignment.BASELINE)
-
.addComponent(okButton, GroupLayout.PREFERRED_SIZE,
-
GroupLayout.DEFAULT_SIZE,
GroupLayout.PREFERRED_SIZE)
-
.addComponent(mergeButton, GroupLayout.PREFERRED_SIZE,
-
GroupLayout.DEFAULT_SIZE,
GroupLayout.PREFERRED_SIZE))
-
.addContainerGap()));
-
- GroupLayout layout = new GroupLayout(getContentPane());
- getContentPane().setLayout(layout);
-
layout.setHorizontalGroup(layout.createParallelGroup(GroupLayout.Alignment.LEADING)
- .addComponent(titlePanel,
GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
- .addComponent(resultScrollPane,
GroupLayout.DEFAULT_SIZE, 614, Short.MAX_VALUE)
- .addComponent(buttonPanel,
GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE));
-
layout.setVerticalGroup(layout.createParallelGroup(GroupLayout.Alignment.LEADING).addGroup(
- layout.createSequentialGroup()
- .addComponent(titlePanel,
GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE,
-
GroupLayout.PREFERRED_SIZE)
-
.addPreferredGap(LayoutStyle.ComponentPlacement.RELATED)
- .addComponent(resultScrollPane,
GroupLayout.DEFAULT_SIZE, 173, Short.MAX_VALUE)
-
.addPreferredGap(LayoutStyle.ComponentPlacement.RELATED)
- .addComponent(buttonPanel,
GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE,
-
GroupLayout.PREFERRED_SIZE)));
-
- pack();
- }// </editor-fold>
-
- private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {
- this.dispose();
- }
-
- private void mergeButtonActionPerformed(java.awt.event.ActionEvent evt)
{
- mergeNetworks = true;
- this.dispose();
- }
-
- public boolean isMerge() {
- return mergeNetworks;
- }
-
- public Map<URI, String> getNewNames() {
- for (int i = 0; i < resultTable.getModel().getRowCount(); i++) {
- // TODO: FIXME use suggested network naming utility.
- final String newName =
resultTable.getModel().getValueAt(i, 1).toString();
- dbNames.put((URI) resultTable.getModel().getValueAt(i,
0), newName);
- }
- return dbNames;
- }
-
- // Variables declaration - do not modify
- private javax.swing.JPanel buttonPanel;
- private javax.swing.JButton mergeButton;
- private javax.swing.JButton okButton;
- private javax.swing.JScrollPane resultScrollPane;
- private javax.swing.JTable resultTable;
- private javax.swing.JLabel titleLabel;
- private javax.swing.JPanel titlePanel;
- // End of variables declaration
-
-}
Modified:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/ui/SourceStatusPanel.java
===================================================================
---
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/ui/SourceStatusPanel.java
2012-07-26 21:45:23 UTC (rev 30010)
+++
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/ui/SourceStatusPanel.java
2012-07-26 22:15:36 UTC (rev 30011)
@@ -337,20 +337,20 @@
private void importButtonActionPerformed(ActionEvent evt) {
- final boolean toBeClustered =
clusterResultCheckBox.isSelected();
+ final boolean mergeNetwork = clusterResultCheckBox.isSelected();
+
final Set<String> targetSources = getSelected();
final Set<String> sourceURLs = new HashSet<String>();
- for (String source : targetSources) {
+ for (String source : targetSources)
sourceURLs.add(manager.getActiveServices().get(source));
- }
// Execute Import Task
final ImportNetworkFromPSICQUICTask networkTask = new
ImportNetworkFromPSICQUICTask(query, client,
- networkManager, manager, sourceURLs, mode,
createViewTaskFactory, toBeClustered, null);
+ networkManager, manager, sourceURLs, mode,
createViewTaskFactory, mergeNetwork);
taskManager.execute(new TaskIterator(networkTask));
- Window parentWindow = ((Window) getRootPane().getParent());
+ final Window parentWindow = ((Window)
getRootPane().getParent());
parentWindow.pack();
repaint();
--
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