Author: kono
Date: 2011-05-09 15:05:49 -0700 (Mon, 09 May 2011)
New Revision: 24979
Modified:
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/CPath2Factory.java
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/LoadNetworkFromUrlTask.java
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/MergeNetworkTask.java
Log:
Fixed to make this bundle compatible with new network IO API.
Modified:
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/CPath2Factory.java
===================================================================
---
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/CPath2Factory.java
2011-05-09 21:56:50 UTC (rev 24978)
+++
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/CPath2Factory.java
2011-05-09 22:05:49 UTC (rev 24979)
@@ -31,7 +31,7 @@
import org.cytoscape.cpath2.internal.view.model.PathwayTableModel;
import org.cytoscape.cpath2.internal.web_service.CPathResponseFormat;
import org.cytoscape.cpath2.internal.web_service.CPathWebService;
-import org.cytoscape.io.read.CyNetworkViewReaderManager;
+import org.cytoscape.io.read.CyNetworkReaderManager;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
@@ -56,7 +56,7 @@
private final CyNetworkManager networkManager;
private final CyApplicationManager applicationManager;
private final CyNetworkViewManager networkViewManager;
- private final CyNetworkViewReaderManager networkViewReaderManager;
+ private final CyNetworkReaderManager networkViewReaderManager;
private final CyNetworkNaming naming;
private final CyNetworkFactory networkFactory;
private final CyLayoutAlgorithmManager layoutManager;
@@ -65,7 +65,7 @@
private final MapBioPaxToCytoscapeFactory mapperFactory;
private final NetworkListener networkListener;
- public CPath2Factory(CySwingApplication application, TaskManager
taskManager, OpenBrowser openBrowser, CyNetworkManager networkManager,
CyApplicationManager applicationManager, CyNetworkViewManager
networkViewManager, CyNetworkViewReaderManager networkViewReaderManager,
CyNetworkNaming naming, CyNetworkFactory networkFactory,
CyLayoutAlgorithmManager layouts, UndoSupport undoSupport, BioPaxContainer
bpContainer, MapBioPaxToCytoscapeFactory mapperFactory, NetworkListener
networkListener) {
+ public CPath2Factory(CySwingApplication application, TaskManager
taskManager, OpenBrowser openBrowser, CyNetworkManager networkManager,
CyApplicationManager applicationManager, CyNetworkViewManager
networkViewManager, CyNetworkReaderManager networkViewReaderManager,
CyNetworkNaming naming, CyNetworkFactory networkFactory,
CyLayoutAlgorithmManager layouts, UndoSupport undoSupport, BioPaxContainer
bpContainer, MapBioPaxToCytoscapeFactory mapperFactory, NetworkListener
networkListener) {
this.application = application;
this.taskManager = taskManager;
this.openBrowser = openBrowser;
@@ -157,7 +157,7 @@
return networkViewManager;
}
- public CyNetworkViewReaderManager getCyNetworkViewReaderManager() {
+ public CyNetworkReaderManager getCyNetworkViewReaderManager() {
return networkViewReaderManager;
}
Modified:
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
===================================================================
---
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
2011-05-09 21:56:50 UTC (rev 24978)
+++
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
2011-05-09 22:05:49 UTC (rev 24979)
@@ -34,7 +34,7 @@
import org.cytoscape.cpath2.internal.web_service.CPathResponseFormat;
import org.cytoscape.cpath2.internal.web_service.CPathWebService;
import org.cytoscape.cpath2.internal.web_service.EmptySetException;
-import org.cytoscape.io.read.CyNetworkViewReader;
+import org.cytoscape.io.read.CyNetworkReader;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
@@ -50,506 +50,532 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-
/**
* Controller for Executing a Get Record(s) by CPath ID(s) command.
- *
+ *
* @author Ethan Cerami.
*/
public class ExecuteGetRecordByCPathId extends AbstractTask {
- private CPathWebService webApi;
- private long ids[];
- private String networkTitle;
- private boolean haltFlag = false;
- private CyNetwork mergedNetwork;
- private CPathResponseFormat format;
- private final static String CPATH_SERVER_NAME_ATTRIBUTE =
"CPATH_SERVER_NAME";
- private final static String CPATH_SERVER_DETAILS_URL =
"CPATH_SERVER_DETAILS_URL";
+ private CPathWebService webApi;
+ private long ids[];
+ private String networkTitle;
+ private boolean haltFlag = false;
+ private CyNetwork mergedNetwork;
+ private CPathResponseFormat format;
+ private final static String CPATH_SERVER_NAME_ATTRIBUTE =
"CPATH_SERVER_NAME";
+ private final static String CPATH_SERVER_DETAILS_URL =
"CPATH_SERVER_DETAILS_URL";
private Logger logger =
LoggerFactory.getLogger(ExecuteGetRecordByCPathId.class);
private final CPath2Factory cPathFactory;
private final BioPaxContainer bpContainer;
private final MapBioPaxToCytoscapeFactory mapperFactory;
private final NetworkListener networkListener;
-
- /**
- * Constructor.
- *
- * @param webApi cPath Web API.
- * @param ids Array of cPath IDs.
- * @param format CPathResponseFormat Object.
- * @param networkTitle Tentative Network Title.
- * @param bpContainer
- * @param application
- */
- public ExecuteGetRecordByCPathId(CPathWebService webApi, long ids[],
CPathResponseFormat format,
- String networkTitle, CPath2Factory cPathFactory, BioPaxContainer
bpContainer, MapBioPaxToCytoscapeFactory mapperFactory,
- NetworkListener networkListener) {
- this.webApi = webApi;
- this.ids = ids;
- this.format = format;
- this.networkTitle = networkTitle;
- this.cPathFactory = cPathFactory;
- this.bpContainer = bpContainer;
- this.mapperFactory = mapperFactory;
- this.networkListener = networkListener;
- }
- /**
- * Constructor.
- *
- * @param webApi cPath Web API.
- * @param ids Array of cPath IDs.
- * @param format CPathResponseFormat Object.
- * @param networkTitle Tentative Network Title.
- * @param mergedNetwork Network to merge into.
- * @param mapperFactory
- * @param mapBioPaxToCytoscape
- * @param viewManager
- * @param application
- */
- public ExecuteGetRecordByCPathId(CPathWebService webApi, long ids[],
CPathResponseFormat format,
- String networkTitle, CyNetwork mergedNetwork, CPath2Factory
cPathFactory,
- BioPaxContainer bpContainer, MapBioPaxToCytoscapeFactory
mapperFactory,
- NetworkListener networkListener) {
- this.webApi = webApi;
- this.ids = ids;
- this.format = format;
- this.networkTitle = networkTitle;
- this.mergedNetwork = mergedNetwork;
- this.cPathFactory = cPathFactory;
- this.bpContainer = bpContainer;
- this.mapperFactory = mapperFactory;
- this.networkListener = networkListener;
- }
+ /**
+ * Constructor.
+ *
+ * @param webApi
+ * cPath Web API.
+ * @param ids
+ * Array of cPath IDs.
+ * @param format
+ * CPathResponseFormat Object.
+ * @param networkTitle
+ * Tentative Network Title.
+ * @param bpContainer
+ * @param application
+ */
+ public ExecuteGetRecordByCPathId(CPathWebService webApi, long ids[],
CPathResponseFormat format,
+ String networkTitle, CPath2Factory cPathFactory,
BioPaxContainer bpContainer,
+ MapBioPaxToCytoscapeFactory mapperFactory,
NetworkListener networkListener) {
+ this.webApi = webApi;
+ this.ids = ids;
+ this.format = format;
+ this.networkTitle = networkTitle;
+ this.cPathFactory = cPathFactory;
+ this.bpContainer = bpContainer;
+ this.mapperFactory = mapperFactory;
+ this.networkListener = networkListener;
+ }
- /**
- * Our implementation of Task.abort()
- */
- public void cancel() {
- webApi.abort();
- haltFlag = true;
- }
+ /**
+ * Constructor.
+ *
+ * @param webApi
+ * cPath Web API.
+ * @param ids
+ * Array of cPath IDs.
+ * @param format
+ * CPathResponseFormat Object.
+ * @param networkTitle
+ * Tentative Network Title.
+ * @param mergedNetwork
+ * Network to merge into.
+ * @param mapperFactory
+ * @param mapBioPaxToCytoscape
+ * @param viewManager
+ * @param application
+ */
+ public ExecuteGetRecordByCPathId(CPathWebService webApi, long ids[],
CPathResponseFormat format,
+ String networkTitle, CyNetwork mergedNetwork,
CPath2Factory cPathFactory, BioPaxContainer bpContainer,
+ MapBioPaxToCytoscapeFactory mapperFactory,
NetworkListener networkListener) {
+ this.webApi = webApi;
+ this.ids = ids;
+ this.format = format;
+ this.networkTitle = networkTitle;
+ this.mergedNetwork = mergedNetwork;
+ this.cPathFactory = cPathFactory;
+ this.bpContainer = bpContainer;
+ this.mapperFactory = mapperFactory;
+ this.networkListener = networkListener;
+ }
- /**
- * Our implementation of Task.getTitle.
- *
- * @return Task Title.
- */
- public String getTitle() {
- return "Retrieving " + networkTitle + " from "
- + CPathProperties.getInstance().getCPathServerName() + "...";
- }
+ /**
+ * Our implementation of Task.abort()
+ */
+ public void cancel() {
+ webApi.abort();
+ haltFlag = true;
+ }
- /**
- * Our implementation of Task.run().
- * @throws Exception
- */
- public void run(TaskMonitor taskMonitor) throws Exception {
- String title = "Retrieving " + networkTitle + " from "
- + CPathProperties.getInstance().getCPathServerName() + "...";
- taskMonitor.setTitle(title);
- try {
- // read the network from cpath instance
- if (taskMonitor != null) {
- taskMonitor.setProgress(0);
- taskMonitor.setStatusMessage("Retrieving " + networkTitle +
".");
- }
+ /**
+ * Our implementation of Task.getTitle.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return "Retrieving " + networkTitle + " from " +
CPathProperties.getInstance().getCPathServerName() + "...";
+ }
- // Store BioPAX to Temp File
- String tmpDir = System.getProperty("java.io.tmpdir");
- // Branch based on download mode setting.
- File tmpFile;
- if (format == CPathResponseFormat.BIOPAX) {
- tmpFile = File.createTempFile("temp", ".xml", new
File(tmpDir));
- } else {
- tmpFile = File.createTempFile("temp", ".sif", new
File(tmpDir));
- }
- tmpFile.deleteOnExit();
+ /**
+ * Our implementation of Task.run().
+ *
+ * @throws Exception
+ */
+ public void run(TaskMonitor taskMonitor) throws Exception {
+ String title = "Retrieving " + networkTitle + " from " +
CPathProperties.getInstance().getCPathServerName()
+ + "...";
+ taskMonitor.setTitle(title);
+ try {
+ // read the network from cpath instance
+ if (taskMonitor != null) {
+ taskMonitor.setProgress(0);
+ taskMonitor.setStatusMessage("Retrieving " +
networkTitle + ".");
+ }
- // Get Data, and write to temp file.
- String data = webApi.getRecordsByIds(ids, format, taskMonitor);
- FileWriter writer = new FileWriter(tmpFile);
- writer.write(data);
- writer.close();
+ // Store BioPAX to Temp File
+ String tmpDir = System.getProperty("java.io.tmpdir");
+ // Branch based on download mode setting.
+ File tmpFile;
+ if (format == CPathResponseFormat.BIOPAX) {
+ tmpFile = File.createTempFile("temp", ".xml",
new File(tmpDir));
+ } else {
+ tmpFile = File.createTempFile("temp", ".sif",
new File(tmpDir));
+ }
+ tmpFile.deleteOnExit();
- // Load up File via ImportHandler Framework
- // the biopax graph reader is going to be called
- // it will look for the network view title
- // via system properties, so lets set it now
- if (networkTitle != null && networkTitle.length() > 0) {
- System.setProperty("biopax.network_view_title", networkTitle);
- }
-
- CyNetworkViewReader reader =
cPathFactory.getCyNetworkViewReaderManager().getReader(tmpFile.toURI(),
tmpFile.getName());
- if (taskMonitor != null) {
- taskMonitor.setStatusMessage("Creating Cytoscape Network...");
- taskMonitor.setProgress(0);
- }
+ // Get Data, and write to temp file.
+ String data = webApi.getRecordsByIds(ids, format,
taskMonitor);
+ FileWriter writer = new FileWriter(tmpFile);
+ writer.write(data);
+ writer.close();
- reader.run(taskMonitor);
- CyNetworkView view = reader.getNetworkViews()[0];
- CyNetwork cyNetwork = view.getModel();
+ // Load up File via ImportHandler Framework
+ // the biopax graph reader is going to be called
+ // it will look for the network view title
+ // via system properties, so lets set it now
+ if (networkTitle != null && networkTitle.length() > 0) {
+ System.setProperty("biopax.network_view_title",
networkTitle);
+ }
+ CyNetworkReader reader =
cPathFactory.getCyNetworkViewReaderManager().getReader(tmpFile.toURI(),
+ tmpFile.getName());
+ if (taskMonitor != null) {
+ taskMonitor.setStatusMessage("Creating
Cytoscape Network...");
+ taskMonitor.setProgress(0);
+ }
+
+ reader.run(taskMonitor);
+ final CyNetwork cyNetwork = reader.getCyNetworks()[0];
+ final CyNetworkView view = reader.buildCyNetworkView(cyNetwork);
+
cPathFactory.getCyNetworkManager().addNetwork(cyNetwork);
cPathFactory.getCyNetworkViewManager().addNetworkView(view);
-
- // Branch, based on download mode.
- if (format == CPathResponseFormat.BINARY_SIF) {
- postProcessingBinarySif(view, taskMonitor);
- } else {
- postProcessingBioPAX(view, taskMonitor);
- }
- // Fire appropriate network event.
- // TODO: Port this?
-// if (mergedNetwork == null) {
-// // Fire a Network Loaded Event
-// Object[] ret_val = new Object[2];
-// ret_val[0] = cyNetwork;
-// ret_val[1] = networkTitle;
-// Cytoscape.firePropertyChange(Cytoscape.NETWORK_LOADED, null,
ret_val);
-// } else {
-// // Fire a Network Modified Event; causes Quick Find to
Re-Index.
-// Object[] ret_val = new Object[2];
-// ret_val[0] = mergedNetwork;
-// ret_val[1] = networkTitle;
-// Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED,
null,
-// ret_val);
-// }
+
cPathFactory.getCyNetworkManager().addNetwork(cyNetwork);
+
cPathFactory.getCyNetworkViewManager().addNetworkView(view);
- // Add Links Back to cPath Instance
- addLinksToCPathInstance (cyNetwork);
+ // Branch, based on download mode.
+ if (format == CPathResponseFormat.BINARY_SIF) {
+ postProcessingBinarySif(view, taskMonitor);
+ } else {
+ postProcessingBioPAX(view, taskMonitor);
+ }
- if (taskMonitor != null) {
- taskMonitor.setStatusMessage("Done");
- taskMonitor.setProgress(1.0);
- }
-
- CyLayoutAlgorithmManager layoutManager =
cPathFactory.getCyLayoutAlgorithmManager();
- TaskFactory tf = layoutManager.getDefaultLayout();
- TaskIterator ti = tf.getTaskIterator();
- Task task = ti.next();
- insertTasksAfterCurrentTask(task);
-
- } catch (IOException e) {
- throw new Exception("Failed to retrieve records.", e);
- } catch (EmptySetException e) {
- throw new Exception("No matches found for your request. ", e);
- } catch (CPathException e) {
- if (e.getErrorCode() != CPathException.ERROR_CANCELED_BY_USER) {
- throw e;
- }
- }
- }
+ // Fire appropriate network event.
+ // TODO: Port this?
+ // if (mergedNetwork == null) {
+ // // Fire a Network Loaded Event
+ // Object[] ret_val = new Object[2];
+ // ret_val[0] = cyNetwork;
+ // ret_val[1] = networkTitle;
+ //
Cytoscape.firePropertyChange(Cytoscape.NETWORK_LOADED, null,
+ // ret_val);
+ // } else {
+ // // Fire a Network Modified Event; causes Quick Find
to Re-Index.
+ // Object[] ret_val = new Object[2];
+ // ret_val[0] = mergedNetwork;
+ // ret_val[1] = networkTitle;
+ //
Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED, null,
+ // ret_val);
+ // }
- /**
- * Add Node Links Back to cPath Instance.
- * @param cyNetwork CyNetwork.
- */
- private void addLinksToCPathInstance(CyNetwork cyNetwork) {
- CPathProperties props = CPathProperties.getInstance();
- String serverName = props.getCPathServerName();
- String serverURL = props.getCPathUrl();
- CyRow row = cyNetwork.getCyRow();
- 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);
- String url = serverURL.replaceFirst("webservice.do",
"record2.do?id=");
- AttributeUtil.set(cyNetwork,
ExecuteGetRecordByCPathId.CPATH_SERVER_DETAILS_URL, url, String.class);
- }
- }
+ // Add Links Back to cPath Instance
+ addLinksToCPathInstance(cyNetwork);
- /**
- * Execute Post-Processing on BINARY SIF Network.
- *
- * @param cyNetwork Cytoscape Network Object.
- */
- private void postProcessingBinarySif(final CyNetworkView view, TaskMonitor
taskMonitor) {
- // Init the node attribute meta data, e.g. description, visibility,
etc.
- // TODO: What happened to attribute descriptions?
-// MapBioPaxToCytoscape.initAttributes(nodeAttributes);
+ if (taskMonitor != null) {
+ taskMonitor.setStatusMessage("Done");
+ taskMonitor.setProgress(1.0);
+ }
- final CyNetwork cyNetwork = view.getModel();
-
- // Set the Quick Find Default Index
- AttributeUtil.set(cyNetwork, "quickfind.default_index",
"biopax.node_label", String.class);
+ CyLayoutAlgorithmManager layoutManager =
cPathFactory.getCyLayoutAlgorithmManager();
+ TaskFactory tf = layoutManager.getDefaultLayout();
+ TaskIterator ti = tf.getTaskIterator();
+ Task task = ti.next();
+ insertTasksAfterCurrentTask(task);
- // Specify that this is a BINARY_NETWORK
- AttributeUtil.set(cyNetwork, BinarySifVisualStyleUtil.BINARY_NETWORK,
Boolean.TRUE, Boolean.class);
+ } catch (IOException e) {
+ throw new Exception("Failed to retrieve records.", e);
+ } catch (EmptySetException e) {
+ throw new Exception("No matches found for your request.
", e);
+ } catch (CPathException e) {
+ if (e.getErrorCode() !=
CPathException.ERROR_CANCELED_BY_USER) {
+ throw e;
+ }
+ }
+ }
- // Get all node details.
- getNodeDetails(cyNetwork, taskMonitor);
+ /**
+ * Add Node Links Back to cPath Instance.
+ *
+ * @param cyNetwork
+ * CyNetwork.
+ */
+ private void addLinksToCPathInstance(CyNetwork cyNetwork) {
+ CPathProperties props = CPathProperties.getInstance();
+ String serverName = props.getCPathServerName();
+ String serverURL = props.getCPathUrl();
+ CyRow row = cyNetwork.getCyRow();
+ 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);
+ String url = serverURL.replaceFirst("webservice.do",
"record2.do?id=");
+ AttributeUtil.set(cyNetwork,
ExecuteGetRecordByCPathId.CPATH_SERVER_DETAILS_URL, url, String.class);
+ }
+ }
- if (haltFlag == false) {
- if (mergedNetwork != null) {
- mergeNetworks(cyNetwork, taskMonitor);
- } else {
-// } else if (cyNetwork.getNodeCount() <
Integer.parseInt(CytoscapeInit.getProperties()
-// .getProperty("viewThreshold"))) {
- if (taskMonitor != null) {
- taskMonitor.setStatusMessage("Creating Network View...");
- taskMonitor.setProgress(0);
- }
+ /**
+ * Execute Post-Processing on BINARY SIF Network.
+ *
+ * @param cyNetwork
+ * Cytoscape Network Object.
+ */
+ private void postProcessingBinarySif(final CyNetworkView view,
TaskMonitor taskMonitor) {
+ // Init the node attribute meta data, e.g. description,
visibility, etc.
+ // TODO: What happened to attribute descriptions?
+ // MapBioPaxToCytoscape.initAttributes(nodeAttributes);
- // Set up the right visual style
-// VisualStyle visualStyle =
BinarySifVisualStyleUtil.getVisualStyle();
+ final CyNetwork cyNetwork = view.getModel();
- // Set up the right layout algorithm.
-// LayoutUtil layoutAlgorithm = new LayoutUtil();
+ // Set the Quick Find Default Index
+ AttributeUtil.set(cyNetwork, "quickfind.default_index",
"biopax.node_label", String.class);
- // Now, create the view.
- // Use local create view option, so that we don't mess up the
visual style.
-// final CyNetworkView view = createNetworkView
-// (cyNetwork, cyNetwork.getCyRow().get(CyNetwork.NAME,
String.class), layoutAlgorithm, null);
-
- networkListener.registerNetwork(view);
+ // Specify that this is a BINARY_NETWORK
+ AttributeUtil.set(cyNetwork,
BinarySifVisualStyleUtil.BINARY_NETWORK, Boolean.TRUE, Boolean.class);
- SwingUtilities.invokeLater(new Runnable() {
+ // Get all node details.
+ getNodeDetails(cyNetwork, taskMonitor);
+
+ if (haltFlag == false) {
+ if (mergedNetwork != null) {
+ mergeNetworks(cyNetwork, taskMonitor);
+ } else {
+ // } else if (cyNetwork.getNodeCount() <
+ //
Integer.parseInt(CytoscapeInit.getProperties()
+ // .getProperty("viewThreshold"))) {
+ if (taskMonitor != null) {
+ taskMonitor.setStatusMessage("Creating
Network View...");
+ taskMonitor.setProgress(0);
+ }
+
+ // Set up the right visual style
+ // VisualStyle visualStyle =
+ // BinarySifVisualStyleUtil.getVisualStyle();
+
+ // Set up the right layout algorithm.
+ // LayoutUtil layoutAlgorithm = new
LayoutUtil();
+
+ // Now, create the view.
+ // Use local create view option, so that we
don't mess up the
+ // visual style.
+ // final CyNetworkView view = createNetworkView
+ // (cyNetwork,
cyNetwork.getCyRow().get(CyNetwork.NAME,
+ // String.class), layoutAlgorithm, null);
+
+ networkListener.registerNetwork(view);
+
+ SwingUtilities.invokeLater(new Runnable() {
public void run() {
-//
CytoscapeWrapper.activateBioPaxPlugInTab(bpContainer);
- bpContainer.showLegend();
-// view.fitContent();
- String networkTitleWithUnderscores =
networkTitle.replaceAll(": ", "");
- networkTitleWithUnderscores =
networkTitleWithUnderscores.replaceAll(" ", "_");
- CyNetworkNaming naming =
cPathFactory.getCyNetworkNaming();
- networkTitleWithUnderscores =
naming.getSuggestedNetworkTitle(networkTitleWithUnderscores);
- AttributeUtil.set(cyNetwork, CyNetwork.NAME,
networkTitleWithUnderscores, String.class);
- }
- });
- }
- } else {
- // If we have requested a halt, and we have a network, destroy it.
-// if (cyNetwork != null) {
-// Cytoscape.destroyNetwork(cyNetwork);
-// }
- }
- }
+ //
CytoscapeWrapper.activateBioPaxPlugInTab(bpContainer);
+ bpContainer.showLegend();
+ // view.fitContent();
+ String
networkTitleWithUnderscores = networkTitle.replaceAll(": ", "");
+ networkTitleWithUnderscores =
networkTitleWithUnderscores.replaceAll(" ", "_");
+ CyNetworkNaming naming =
cPathFactory.getCyNetworkNaming();
+ networkTitleWithUnderscores =
naming.getSuggestedNetworkTitle(networkTitleWithUnderscores);
+ AttributeUtil.set(cyNetwork,
CyNetwork.NAME, networkTitleWithUnderscores, String.class);
+ }
+ });
+ }
+ } else {
+ // If we have requested a halt, and we have a network,
destroy it.
+ // if (cyNetwork != null) {
+ // Cytoscape.destroyNetwork(cyNetwork);
+ // }
+ }
+ }
- /**
- * Execute Post-Processing on BioPAX Network.
- *
- * @param cyNetwork Cytoscape Network Object.
- */
- private void postProcessingBioPAX(final CyNetworkView view, TaskMonitor
taskMonitor) {
- final CyNetwork cyNetwork = view.getModel();
-
- if (haltFlag == false) {
- if (mergedNetwork != null) {
- mergeNetworks(cyNetwork, taskMonitor);
- } else {
-// } else if (cyNetwork.getNodeCount() <
Integer.parseInt(CytoscapeInit.getProperties()
-// .getProperty("viewThreshold"))) {
- if (taskMonitor != null) {
- taskMonitor.setStatusMessage("Creating Network View...");
- taskMonitor.setProgress(0);
- }
+ /**
+ * Execute Post-Processing on BioPAX Network.
+ *
+ * @param cyNetwork
+ * Cytoscape Network Object.
+ */
+ private void postProcessingBioPAX(final CyNetworkView view, TaskMonitor
taskMonitor) {
+ final CyNetwork cyNetwork = view.getModel();
- // Set up the right visual style
-// VisualStyle visualStyle =
BioPaxVisualStyleUtil.getBioPaxVisualStyle();
+ if (haltFlag == false) {
+ if (mergedNetwork != null) {
+ mergeNetworks(cyNetwork, taskMonitor);
+ } else {
+ // } else if (cyNetwork.getNodeCount() <
+ //
Integer.parseInt(CytoscapeInit.getProperties()
+ // .getProperty("viewThreshold"))) {
+ if (taskMonitor != null) {
+ taskMonitor.setStatusMessage("Creating
Network View...");
+ taskMonitor.setProgress(0);
+ }
- // Set up the right layout algorithm.
-// LayoutUtil layoutAlgorithm = new LayoutUtil();
+ // Set up the right visual style
+ // VisualStyle visualStyle =
+ // BioPaxVisualStyleUtil.getBioPaxVisualStyle();
- // Now, create the view.
- // Use local create view option, so that we don't mess up the
visual style.
-// CyNetworkView view = createNetworkView(cyNetwork,
-// cyNetwork.getCyRow().get(CyNetwork.NAME,
String.class), layoutAlgorithm, null);
+ // Set up the right layout algorithm.
+ // LayoutUtil layoutAlgorithm = new
LayoutUtil();
- // Now apply the visual style;
- // Doing this as a separate step ensures that the visual
style appears
- // in the visual style drop-down menu.
-// view.applyVizmapper(visualStyle);
- }
- } else {
- // If we have requested a halt, and we have a network, destroy it.
- // TODO: Review: Network hasn't been added to manager at this
point
- // so we don't need to do the following, right?
-// if (cyNetwork != null) {
-// Cytoscape.destroyNetwork(cyNetwork);
-// }
- }
- }
+ // Now, create the view.
+ // Use local create view option, so that we
don't mess up the
+ // visual style.
+ // CyNetworkView view =
createNetworkView(cyNetwork,
+ // cyNetwork.getCyRow().get(CyNetwork.NAME,
String.class),
+ // layoutAlgorithm, null);
+ // Now apply the visual style;
+ // Doing this as a separate step ensures that
the visual style
+ // appears
+ // in the visual style drop-down menu.
+ // view.applyVizmapper(visualStyle);
+ }
+ } else {
+ // If we have requested a halt, and we have a network,
destroy it.
+ // TODO: Review: Network hasn't been added to manager
at this point
+ // so we don't need to do the following, right?
+ // if (cyNetwork != null) {
+ // Cytoscape.destroyNetwork(cyNetwork);
+ // }
+ }
+ }
- private void mergeNetworks(CyNetwork cyNetwork, TaskMonitor taskMonitor) {
- // TODO: Do we need to clone nodes/edges when merging?
- taskMonitor.setStatusMessage("Merging Network...");
- Map<String, CyNode> nodes = new HashMap<String, CyNode>();
- for (CyNode node : cyNetwork.getNodeList()) {
- CyNode newNode = mergedNetwork.addNode();
- AttributeUtil.copyAttributes(node, newNode);
- String name = node.getCyRow().get(CyNode.NAME, String.class);
- nodes.put(name, newNode);
- }
- Set<CyEdge> edges = new HashSet<CyEdge>();
- for (CyEdge edge : cyNetwork.getEdgeList()) {
- String sourceName =
edge.getSource().getCyRow().get(CyNode.NAME, String.class);
- String targetName =
edge.getTarget().getCyRow().get(CyNode.NAME, String.class);
- CyNode source = nodes.get(sourceName);
- CyNode target = nodes.get(targetName);
- CyEdge newEdge = mergedNetwork.addEdge(source, target, true);
- AttributeUtil.copyAttributes(edge, newEdge);
- edges.add(newEdge);
- }
+ private void mergeNetworks(CyNetwork cyNetwork, TaskMonitor
taskMonitor) {
+ // TODO: Do we need to clone nodes/edges when merging?
+ taskMonitor.setStatusMessage("Merging Network...");
+ Map<String, CyNode> nodes = new HashMap<String, CyNode>();
+ for (CyNode node : cyNetwork.getNodeList()) {
+ CyNode newNode = mergedNetwork.addNode();
+ AttributeUtil.copyAttributes(node, newNode);
+ String name = node.getCyRow().get(CyNode.NAME,
String.class);
+ nodes.put(name, newNode);
+ }
+ Set<CyEdge> edges = new HashSet<CyEdge>();
+ for (CyEdge edge : cyNetwork.getEdgeList()) {
+ String sourceName =
edge.getSource().getCyRow().get(CyNode.NAME, String.class);
+ String targetName =
edge.getTarget().getCyRow().get(CyNode.NAME, String.class);
+ CyNode source = nodes.get(sourceName);
+ CyNode target = nodes.get(targetName);
+ CyEdge newEdge = mergedNetwork.addEdge(source, target,
true);
+ AttributeUtil.copyAttributes(edge, newEdge);
+ edges.add(newEdge);
+ }
-// // Select this view
-// final CyNetworkView networkView =
viewManager.getNetworkView((mergedNetwork.getSUID());
-// Cytoscape.setCurrentNetwork(mergedNetwork.getIdentifier());
-// Cytoscape.setCurrentNetworkView(mergedNetwork.getIdentifier());
+ // // Select this view
+ // final CyNetworkView networkView =
+ // viewManager.getNetworkView((mergedNetwork.getSUID());
+ // Cytoscape.setCurrentNetwork(mergedNetwork.getIdentifier());
+ //
Cytoscape.setCurrentNetworkView(mergedNetwork.getIdentifier());
-// final BioPaxContainer bpContainer = BioPaxContainer.getInstance();
- SwingUtilities.invokeLater(new Runnable() {
- public void run() {
-// CytoscapeWrapper.activateBioPaxPlugInTab(bpContainer);
- bpContainer.showLegend();
-// VisualMappingManager vizmapper =
Cytoscape.getVisualMappingManager();
-// vizmapper.applyAppearances();
- }
- });
+ // final BioPaxContainer bpContainer =
BioPaxContainer.getInstance();
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ //
CytoscapeWrapper.activateBioPaxPlugInTab(bpContainer);
+ bpContainer.showLegend();
+ // VisualMappingManager vizmapper =
+ // Cytoscape.getVisualMappingManager();
+ // vizmapper.applyAppearances();
+ }
+ });
- // Select only the new nodes
- SelectUtil.unselectAllNodes(mergedNetwork);
- SelectUtil.unselectAllEdges(mergedNetwork);
- SelectUtil.setSelectedNodeState(nodes.values(), true);
- SelectUtil.setSelectedEdgeState(edges, true);
+ // Select only the new nodes
+ SelectUtil.unselectAllNodes(mergedNetwork);
+ SelectUtil.unselectAllEdges(mergedNetwork);
+ SelectUtil.setSelectedNodeState(nodes.values(), true);
+ SelectUtil.setSelectedEdgeState(edges, true);
- // Delete the temp network.
-// Cytoscape.destroyNetwork(cyNetwork);
+ // Delete the temp network.
+ // Cytoscape.destroyNetwork(cyNetwork);
- // Apply Layout
- Object[] options = {"Yes", "No"};
- int n =
JOptionPane.showOptionDialog(cPathFactory.getCySwingApplication().getJFrame(),
- "Would you like to layout the modified network?",
- "Adjust Layout?",
- JOptionPane.YES_NO_CANCEL_OPTION,
- JOptionPane.QUESTION_MESSAGE,
- null,
- options, options[0]);
- if (n==0) {
-// SwingUtilities.invokeLater(new Runnable() {
-// public void run() {
-// LayoutUtil layoutAlgorithm = new LayoutUtil();
-// networkView.applyLayout(layoutAlgorithm);
-// networkView.fitContent();
-// }
-// });
- }
- }
+ // Apply Layout
+ Object[] options = { "Yes", "No" };
+ int n =
JOptionPane.showOptionDialog(cPathFactory.getCySwingApplication().getJFrame(),
+ "Would you like to layout the modified
network?", "Adjust Layout?", JOptionPane.YES_NO_CANCEL_OPTION,
+ JOptionPane.QUESTION_MESSAGE, null, options,
options[0]);
+ if (n == 0) {
+ // SwingUtilities.invokeLater(new Runnable() {
+ // public void run() {
+ // LayoutUtil layoutAlgorithm = new LayoutUtil();
+ // networkView.applyLayout(layoutAlgorithm);
+ // networkView.fitContent();
+ // }
+ // });
+ }
+ }
- /**
- * Gets Details for Each Node from Web Service API.
- */
- private void getNodeDetails (CyNetwork cyNetwork, TaskMonitor taskMonitor)
{
- if (taskMonitor != null) {
- taskMonitor.setStatusMessage("Retrieving node details...");
- taskMonitor.setProgress(0);
- }
- List<List<CyNode>> batchList = createBatchArray(cyNetwork);
- if (batchList.size()==0) {
- logger.info ("Skipping node
details. Already have all the details new need.");
- }
- MapBioPaxToCytoscape mapBioPaxToCytoscape =
mapperFactory.getInstance(cyNetwork, taskMonitor);
- for (int i=0; i<batchList.size(); i++) {
- if (haltFlag == true) {
- break;
- }
- List<CyNode> currentList = batchList.get(i);
- logger.debug ("Getting node details, batch: " + i);
- long ids[] = new long [currentList.size()];
- 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);
- nodes.put(name, node);
- ids[j] = Long.valueOf(name);
- }
- try {
- final String xml = webApi.getRecordsByIds(ids,
CPathResponseFormat.BIOPAX, new NullTaskMonitor());
- //StringReader reader = new StringReader(xml);
- //BioPaxUtil bpUtil = new BioPaxUtil(reader, new
NullTaskMonitor());
- Model model = new SimpleReader().convertFromOWL(new
ByteArrayInputStream(xml.getBytes()));
- //ArrayList peList = bpUtil.getPhysicalEntityList();
- //Namespace ns =
Namespace.getNamespace("http://www.w3.org/1999/02/22-rdf-syntax-ns#";);
- //for (int j=0; j<peList.size(); j++) {
- for(BioPAXElement pe: BioPaxUtil.getObjects(model,
physicalEntity.class, PhysicalEntity.class)) {
- //Element element = (Element) peList.get(j);
- //String id = element.getAttributeValue("ID", ns);
- String id = BioPaxUtil.getLocalPartRdfId(pe);
- if (id != null) {
- id = id.replaceAll("CPATH-", "");
- mapBioPaxToCytoscape.mapNodeAttribute(pe, model,
cyNetwork, nodes.get(id));
- }
- }
- double percentComplete = i / (double) batchList.size();
- if (taskMonitor != null) {
- taskMonitor.setProgress(percentComplete);
- }
- } catch (EmptySetException e) {
- e.printStackTrace();
- } catch (CPathException e) {
- e.printStackTrace();
- }
- }
- }
+ /**
+ * Gets Details for Each Node from Web Service API.
+ */
+ private void getNodeDetails(CyNetwork cyNetwork, TaskMonitor
taskMonitor) {
+ if (taskMonitor != null) {
+ taskMonitor.setStatusMessage("Retrieving node
details...");
+ taskMonitor.setProgress(0);
+ }
+ List<List<CyNode>> batchList = createBatchArray(cyNetwork);
+ if (batchList.size() == 0) {
+ logger.info("Skipping node details. Already have all
the details new need.");
+ }
+ MapBioPaxToCytoscape mapBioPaxToCytoscape =
mapperFactory.getInstance(cyNetwork, taskMonitor);
+ for (int i = 0; i < batchList.size(); i++) {
+ if (haltFlag == true) {
+ break;
+ }
+ List<CyNode> currentList = batchList.get(i);
+ logger.debug("Getting node details, batch: " + i);
+ long ids[] = new long[currentList.size()];
+ 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);
+ nodes.put(name, node);
+ ids[j] = Long.valueOf(name);
+ }
+ try {
+ final String xml = webApi.getRecordsByIds(ids,
CPathResponseFormat.BIOPAX, new NullTaskMonitor());
+ // StringReader reader = new StringReader(xml);
+ // BioPaxUtil bpUtil = new BioPaxUtil(reader,
new
+ // NullTaskMonitor());
+ Model model = new
SimpleReader().convertFromOWL(new ByteArrayInputStream(xml.getBytes()));
+ // ArrayList peList =
bpUtil.getPhysicalEntityList();
+ // Namespace ns =
+ //
Namespace.getNamespace("http://www.w3.org/1999/02/22-rdf-syntax-ns#";);
+ // for (int j=0; j<peList.size(); j++) {
+ for (BioPAXElement pe :
BioPaxUtil.getObjects(model, physicalEntity.class, PhysicalEntity.class)) {
+ // Element element = (Element)
peList.get(j);
+ // String id =
element.getAttributeValue("ID", ns);
+ String id =
BioPaxUtil.getLocalPartRdfId(pe);
+ if (id != null) {
+ id = id.replaceAll("CPATH-",
"");
+
mapBioPaxToCytoscape.mapNodeAttribute(pe, model, cyNetwork, nodes.get(id));
+ }
+ }
+ double percentComplete = i / (double)
batchList.size();
+ if (taskMonitor != null) {
+
taskMonitor.setProgress(percentComplete);
+ }
+ } catch (EmptySetException e) {
+ e.printStackTrace();
+ } catch (CPathException e) {
+ e.printStackTrace();
+ }
+ }
+ }
- private List<List<CyNode>> createBatchArray(CyNetwork cyNetwork) {
- int max_ids_per_request = 50;
- List<List<CyNode>> masterList = new ArrayList<List<CyNode>>();
- List<CyNode> currentList = new ArrayList<CyNode>();
- int counter = 0;
- for (CyNode node : cyNetwork.getNodeList()) {
- CyRow row = node.getCyRow();
- String label = row.get(BioPaxVisualStyleUtil.BIOPAX_NODE_LABEL,
String.class);
+ private List<List<CyNode>> createBatchArray(CyNetwork cyNetwork) {
+ int max_ids_per_request = 50;
+ List<List<CyNode>> masterList = new ArrayList<List<CyNode>>();
+ List<CyNode> currentList = new ArrayList<CyNode>();
+ int counter = 0;
+ for (CyNode node : cyNetwork.getNodeList()) {
+ CyRow row = node.getCyRow();
+ String label =
row.get(BioPaxVisualStyleUtil.BIOPAX_NODE_LABEL, String.class);
- // If we already have details on this node, skip it.
- if (label == null) {
- currentList.add(node);
- counter++;
- }
- if (counter > max_ids_per_request) {
- masterList.add(currentList);
- currentList = new ArrayList<CyNode>();
- counter = 0;
- }
- }
- if (currentList.size() > 0) {
- masterList.add(currentList);
- }
- return masterList;
- }
+ // If we already have details on this node, skip it.
+ if (label == null) {
+ currentList.add(node);
+ counter++;
+ }
+ if (counter > max_ids_per_request) {
+ masterList.add(currentList);
+ currentList = new ArrayList<CyNode>();
+ counter = 0;
+ }
+ }
+ if (currentList.size() > 0) {
+ masterList.add(currentList);
+ }
+ return masterList;
+ }
-// private CyNetworkView createNetworkView (CyNetwork network, String
title, CyLayoutAlgorithm
-// layout, VisualStyle vs) {
-//
-// if (viewManager.viewExists((network.getSUID()))) {
-// return
Cytoscape.getNetworkView(network.getIdentifier());
-// }
-//
-// final DingNetworkView view = new DingNetworkView(network,
title);
-// view.setGraphLOD(new CyGraphLOD());
-// view.setIdentifier(network.getIdentifier());
-// view.setTitle(network.getTitle());
-// Cytoscape.getNetworkViewMap().put(network.getIdentifier(),
view);
-// Cytoscape.setSelectionMode(Cytoscape.getSelectionMode(), view);
-//
-// VisualMappingManager VMM = Cytoscape.getVisualMappingManager();
-// if (vs != null) {
-// view.setVisualStyle(vs.getName());
-// VMM.setVisualStyle(vs);
-// VMM.setNetworkView(view);
-// }
-//
-// if (layout == null) {
-// layout = CyLayouts.getDefaultLayout();
-// }
-//
-//
Cytoscape.firePropertyChange(cytoscape.view.CytoscapeDesktop.NETWORK_VIEW_CREATED,
-// null, view);
-// layout.doLayout(view);
-// view.fitContent();
-// view.redrawGraph(false, true);
-// return view;
-// }
+ // private CyNetworkView createNetworkView (CyNetwork network, String
title,
+ // CyLayoutAlgorithm
+ // layout, VisualStyle vs) {
+ //
+ // if (viewManager.viewExists((network.getSUID()))) {
+ // return Cytoscape.getNetworkView(network.getIdentifier());
+ // }
+ //
+ // final DingNetworkView view = new DingNetworkView(network, title);
+ // view.setGraphLOD(new CyGraphLOD());
+ // view.setIdentifier(network.getIdentifier());
+ // view.setTitle(network.getTitle());
+ // Cytoscape.getNetworkViewMap().put(network.getIdentifier(), view);
+ // Cytoscape.setSelectionMode(Cytoscape.getSelectionMode(), view);
+ //
+ // VisualMappingManager VMM = Cytoscape.getVisualMappingManager();
+ // if (vs != null) {
+ // view.setVisualStyle(vs.getName());
+ // VMM.setVisualStyle(vs);
+ // VMM.setNetworkView(view);
+ // }
+ //
+ // if (layout == null) {
+ // layout = CyLayouts.getDefaultLayout();
+ // }
+ //
+ //
Cytoscape.firePropertyChange(cytoscape.view.CytoscapeDesktop.NETWORK_VIEW_CREATED,
+ // null, view);
+ // layout.doLayout(view);
+ // view.fitContent();
+ // view.redrawGraph(false, true);
+ // return view;
+ // }
}
class NullTaskMonitor implements TaskMonitor {
Modified:
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/LoadNetworkFromUrlTask.java
===================================================================
---
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/LoadNetworkFromUrlTask.java
2011-05-09 21:56:50 UTC (rev 24978)
+++
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/LoadNetworkFromUrlTask.java
2011-05-09 22:05:49 UTC (rev 24979)
@@ -48,10 +48,9 @@
import javax.swing.JOptionPane;
import org.cytoscape.cpath2.internal.CPath2Factory;
-import org.cytoscape.io.read.CyNetworkViewReader;
-import org.cytoscape.io.read.CyNetworkViewReaderManager;
+import org.cytoscape.io.read.CyNetworkReader;
+import org.cytoscape.io.read.CyNetworkReaderManager;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.Task;
import org.cytoscape.work.TaskMonitor;
@@ -78,8 +77,8 @@
taskMonitor.setStatusMessage("Reading in Network Data...");
try {
- CyNetworkViewReaderManager readerManager =
factory.getCyNetworkViewReaderManager();
- CyNetworkViewReader reader =
readerManager.getReader(url.toURI(), url.getFile());
+ CyNetworkReaderManager readerManager =
factory.getCyNetworkViewReaderManager();
+ CyNetworkReader reader =
readerManager.getReader(url.toURI(), url.getFile());
if (reader == null) {
JOptionPane.showMessageDialog(factory.getCySwingApplication().getJFrame(),
@@ -89,8 +88,8 @@
}
taskMonitor.setStatusMessage("Creating Cytoscape
Network...");
reader.run(taskMonitor);
- CyNetworkView[] views = reader.getNetworkViews();
- CyNetwork cyNetwork = views[0].getModel();
+ CyNetwork[] networks = reader.getCyNetworks();
+ CyNetwork cyNetwork = networks[0];
// TODO: Does CPath2 listen for this?
// Object[] ret_val = new Object[2];
Modified:
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/MergeNetworkTask.java
===================================================================
---
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/MergeNetworkTask.java
2011-05-09 21:56:50 UTC (rev 24978)
+++
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/MergeNetworkTask.java
2011-05-09 22:05:49 UTC (rev 24979)
@@ -46,12 +46,11 @@
import org.cytoscape.cpath2.internal.util.AttributeUtil;
import org.cytoscape.cpath2.internal.util.SelectUtil;
import org.cytoscape.cpath2.internal.web_service.CPathProperties;
-import org.cytoscape.io.read.CyNetworkViewReader;
-import org.cytoscape.io.read.CyNetworkViewReaderManager;
+import org.cytoscape.io.read.CyNetworkReader;
+import org.cytoscape.io.read.CyNetworkReaderManager;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.Task;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.undo.UndoSupport;
@@ -103,12 +102,11 @@
taskMonitor.setStatusMessage("Reading in Network Data from "
+ CPathProperties.getInstance().getCPathServerName() + "...");
- CyNetworkViewReaderManager manager =
factory.getCyNetworkViewReaderManager();
- CyNetworkViewReader reader =
manager.getReader(cpathInstanceURL.toURI(), cpathInstanceURL.getFile());
+ CyNetworkReaderManager manager =
factory.getCyNetworkViewReaderManager();
+ CyNetworkReader reader = manager.getReader(cpathInstanceURL.toURI(),
cpathInstanceURL.getFile());
reader.run(taskMonitor);
- CyNetworkView networkView = reader.getNetworkViews()[0];
- CyNetwork network = networkView.getModel();
+ CyNetwork network = reader.getCyNetworks()[0];
// unselect all nodes / edges
SelectUtil.unselectAllNodes(mergedNetwork);
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