Author: pwang
Date: 2011-01-21 17:27:49 -0800 (Fri, 21 Jan 2011)
New Revision: 23562
Added:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ui/ImportAttributeTableTask.java
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ui/ImportAttributeTableTaskFactory.java
Log:
Original creation
Added:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ui/ImportAttributeTableTask.java
===================================================================
---
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ui/ImportAttributeTableTask.java
(rev 0)
+++
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ui/ImportAttributeTableTask.java
2011-01-22 01:27:49 UTC (rev 23562)
@@ -0,0 +1,139 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package org.cytoscape.tableimport.internal.ui;
+
+import org.cytoscape.io.read.CyNetworkViewReader;
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.tableimport.internal.reader.GraphReader;
+import org.cytoscape.tableimport.internal.util.CytoscapeServices;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.view.vizmap.VisualStyle;
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.Task;
+import org.cytoscape.work.TaskFactory;
+import org.cytoscape.work.TaskIterator;
+import org.cytoscape.work.TaskMonitor;
+import java.io.IOException;
+import java.net.URL;
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
+import java.util.HashMap;
+import java.util.Map;
+import org.cytoscape.tableimport.internal.reader.TextTableReader;
+
+/**
+ *
+ */
+public class ImportAttributeTableTask extends AbstractTask {
+
+ protected CyNetworkView[] cyNetworkViews;
+ protected VisualStyle[] visualstyles;
+
+ private final TextTableReader reader;
+ private final String source;
+
+ /**
+ * Creates a new ImportNetworkTask object.
+ *
+ * @param reader DOCUMENT ME!
+ * @param source DOCUMENT ME!
+ */
+ public ImportAttributeTableTask(final TextTableReader reader, String
source) {
+ this.reader = reader;
+ this.source = source;
+ }
+
+
+ @Override
+ public void run(TaskMonitor tm) throws IOException {
+
+ tm.setProgress(0.10);
+ //this.reader.setNetwork(network);
+
+ if (this.cancelled){
+ return;
+ }
+
+ this.reader.readTable();
+
+ //tm.setProgress(0.80);
+
+ //if (this.cancelled){
+ // return;
+ //}
+
+
+ tm.setProgress(1.0);
+
+ //informUserOfGraphStats(network, tm);
+ }
+
+ /**
+ * Inform User of Network Stats.
+ */
+ private void informUserOfGraphStats(final CyNetwork newNetwork, final
TaskMonitor taskMonitor) {
+ NumberFormat formatter = new DecimalFormat("#,###,###");
+ StringBuffer sb = new StringBuffer();
+
+ // Give the user some confirmation
+ sb.append("Successfully loaded network from: ");
+ sb.append(newNetwork.getCyRow().get("title", String.class));
+ sb.append("\n\nNetwork contains "
+ + formatter.format(newNetwork.getNodeCount()));
+ sb.append(" nodes and " +
formatter.format(newNetwork.getEdgeCount()));
+ sb.append(" edges.\n\n");
+
+ String thresh = "0";
//CytoscapeServices.cytoscapePropertiesServiceRef.getProperties().getProperty("viewThreshold");
+
+ if (newNetwork.getNodeCount() < Integer.parseInt(thresh)) {
+ sb.append("Network is under " + thresh
+ + " nodes. A view will be
automatically created.");
+ } else {
+ sb.append("Network is over " + thresh
+ + " nodes. A view has not been
created."
+ + " If you wish to view this network,
use "
+ + "\"Create View\" from the \"Edit\"
menu.");
+ }
+
+ taskMonitor.setStatusMessage(sb.toString());
+ }
+
+}
Added:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ui/ImportAttributeTableTaskFactory.java
===================================================================
---
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ui/ImportAttributeTableTaskFactory.java
(rev 0)
+++
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ui/ImportAttributeTableTaskFactory.java
2011-01-22 01:27:49 UTC (rev 23562)
@@ -0,0 +1,18 @@
+package org.cytoscape.tableimport.internal.ui;
+
+
+import org.cytoscape.work.TaskFactory;
+import org.cytoscape.work.TaskIterator;
+
+public class ImportAttributeTableTaskFactory implements TaskFactory
+{
+ ImportAttributeTableTask task;
+
+ public ImportAttributeTableTaskFactory(ImportAttributeTableTask task){
+ this.task = task;
+ }
+ public TaskIterator getTaskIterator() {
+ return new TaskIterator(task);
+ }
+
+}
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