Author: pwang
Date: 2011-06-22 17:19:31 -0700 (Wed, 22 Jun 2011)
New Revision: 25888
Added:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ImportNetworkTableReaderFactory.java
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ImportNetworkTableReaderTask.java
Log:
original creation
Added:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ImportNetworkTableReaderFactory.java
===================================================================
---
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ImportNetworkTableReaderFactory.java
(rev 0)
+++
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ImportNetworkTableReaderFactory.java
2011-06-23 00:19:31 UTC (rev 25888)
@@ -0,0 +1,71 @@
+package org.cytoscape.tableimport.internal;
+
+import java.io.InputStream;
+import java.util.Properties;
+
+import org.cytoscape.session.CyApplicationManager;
+import org.cytoscape.session.CyNetworkNaming;
+import org.cytoscape.tableimport.internal.util.CytoscapeServices;
+import org.cytoscape.util.swing.FileUtil;
+import org.cytoscape.util.swing.OpenBrowser;
+import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.work.TaskIterator;
+import org.cytoscape.work.swing.GUITaskManager;
+import org.cytoscape.application.swing.CySwingApplication;
+import org.cytoscape.io.CyFileFilter;
+import org.cytoscape.io.read.CyNetworkReaderManager;
+import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.model.CyTableFactory;
+import org.cytoscape.model.CyTableManager;
+import org.cytoscape.property.CyProperty;
+import org.cytoscape.property.bookmark.Bookmarks;
+import org.cytoscape.property.bookmark.BookmarksUtil;
+import org.cytoscape.work.TaskFactory;
+
+public class ImportNetworkTableReaderFactory extends
AbstractNetworkReaderFactory {
+ private final static long serialVersionUID = 12023139869460154L;
+
+ private final String fileFormat;
+
+ /**
+ * Creates a new ImportNetworkTableReaderFactory object.
+ */
+ public ImportNetworkTableReaderFactory(CyFileFilter filter,
+ CySwingApplication desktop, CyApplicationManager appMgr,
+ CyNetworkManager netMgr,
+ GUITaskManager guiTaskManagerServiceRef,
+ CyProperty<?> cytoscapePropertiesServiceRef,
+ FileUtil fileUtilService,
+ CyNetworkViewFactory cyNetworkViewFactory,
CyNetworkFactory cyNetworkFactory, String fileFormat,
+ CyNetworkNaming cyNetworkNaming, CyNetworkViewManager
networkViewManager) {
+ super(filter, cyNetworkViewFactory, cyNetworkFactory);
+
+
+ CytoscapeServices.networkViewManager = networkViewManager;
+ CytoscapeServices.cyNetworkNaming = cyNetworkNaming;
+ CytoscapeServices.cyNetworkViewFactoryServiceRef =
cyNetworkViewFactory;
+ CytoscapeServices.cyNetworkFactoryServiceRef = cyNetworkFactory;
+
+ CytoscapeServices.desktop = desktop;
+ CytoscapeServices.cytoscapePropertiesServiceRef =
cytoscapePropertiesServiceRef;
+ CytoscapeServices.guiTaskManagerServiceRef =
guiTaskManagerServiceRef;
+ CytoscapeServices.fileUtil = fileUtilService;
+ CytoscapeServices.appMgr = appMgr;
+ CytoscapeServices.netMgr = netMgr;
+
+ this.fileFormat = fileFormat;
+
+ }
+
+ public TaskIterator getTaskIterator() {
+ return new TaskIterator(new
ImportNetworkTableReaderTask(this.inputStream, fileFormat, this.inputName));
+ }
+
+ @Override
+ public void setInputStream(InputStream is, String inputName) {
+ this.inputStream = is;
+ this.inputName = inputName;
+ }
+}
Added:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ImportNetworkTableReaderTask.java
===================================================================
---
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ImportNetworkTableReaderTask.java
(rev 0)
+++
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ImportNetworkTableReaderTask.java
2011-06-23 00:19:31 UTC (rev 25888)
@@ -0,0 +1,79 @@
+package org.cytoscape.tableimport.internal;
+
+import java.io.InputStream;
+import javax.swing.JPanel;
+import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.io.read.CyNetworkReader;
+import org.cytoscape.io.read.CyTableReader;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.model.CyTable;
+import org.cytoscape.tableimport.internal.ui.ImportAttributeTableTask;
+import org.cytoscape.tableimport.internal.ui.ImportTablePanel;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.ProvidesGUI;
+import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.tableimport.internal.util.CytoscapeServices;
+
+public class ImportNetworkTableReaderTask extends AbstractTask implements
CyNetworkReader {
+
+ private ImportTablePanel importTablePanel;
+
+ private final InputStream is;
+ private final String fileType;
+ private CyNetwork[] networks;
+ private final String inputName;
+
+ public ImportNetworkTableReaderTask(final InputStream is, final String
fileType, final String inputName) {
+
+ this.is = is;
+ this.fileType = fileType;
+ this.inputName = inputName;
+
+ this.importTablePanel = null;
+ }
+
+ @ProvidesGUI
+ public JPanel getGUI() {
+ if (importTablePanel == null) {
+ try {
+ this.importTablePanel =
+ new
ImportTablePanel(ImportTablePanel.NETWORK_IMPORT, is, fileType, inputName,null,
null, null, null, null, null);
+ } catch (Exception e) {
+ throw new IllegalStateException("Could not
initialize ImportTablePanel.", e);
+ }
+ }
+
+ return importTablePanel;
+ }
+
+ @Override
+ public void run(TaskMonitor monitor) throws Exception {
+
+ monitor.setTitle("Loading network from table");
+ monitor.setProgress(0.0);
+ monitor.setStatusMessage("Loading network...");
+
+ // Load network data here.
+ this.importTablePanel.importTable();
+
+ //monitor.setStatusMessage("Mapping data table to local
ones...");
+
+
this.insertTasksAfterCurrentTask(importTablePanel.getLoadTask());
+
+ monitor.setProgress(1.0);
+ }
+
+ @Override
+ public CyNetworkView buildCyNetworkView(CyNetwork arg0) {
+ final CyNetworkView view =
CytoscapeServices.cyNetworkViewFactoryServiceRef.getNetworkView(arg0);
+ return view;
+ }
+
+ @Override
+ public CyNetwork[] getCyNetworks() {
+ return networks;
+ }
+}
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