Author: mes
Date: 2012-02-28 11:53:01 -0800 (Tue, 28 Feb 2012)
New Revision: 28385
Added:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loadnetwork/GenerateNetworkViewsTask.java
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTaskTest.java
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTaskTest.java
Log:
simplified some code by separating out a class
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
2012-02-28 17:07:42 UTC (rev 28384)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
2012-02-28 19:53:01 UTC (rev 28385)
@@ -111,83 +111,4 @@
return threshold;
}
-
- protected class GenerateNetworkViewsTask extends AbstractTask {
- private final String name;
- private final CyNetworkReader viewReader;
- private final CyNetworkManager networkManager;
- private final CyNetworkViewManager networkViewManager;
- private final CyNetworkNaming namingUtil;
- private final int viewThreshold;
-
-
- public GenerateNetworkViewsTask(final String name, final
CyNetworkReader viewReader,
- final CyNetworkManager networkManager, final
CyNetworkViewManager networkViewManager,
- final CyNetworkNaming namingUtil, final int
viewThreshold) {
- this.name = name;
- this.viewReader = viewReader;
- this.networkManager = networkManager;
- this.networkViewManager = networkViewManager;
- this.namingUtil = namingUtil;
- this.viewThreshold = viewThreshold;
- }
-
- public void run(final TaskMonitor taskMonitor) throws Exception
{
- if (taskMonitor != null)
- taskMonitor.setProgress(0.0);
-
- final CyNetwork[] networks = viewReader.getNetworks();
-
- for (CyNetwork network : networks) {
-
- // Use original name if exists
- String networkName =
network.getRow(network).get(CyTableEntry.NAME, String.class);
- if(networkName == null ||
networkName.trim().length() == 0) {
- networkName = name;
- if(networkName == null)
- networkName = "? (Name is
missing)";
-
-
network.getRow(network).set(CyTableEntry.NAME,
namingUtil.getSuggestedNetworkTitle(networkName));
- }
- networkManager.addNetwork(network);
-
- final int numGraphObjects =
network.getNodeCount() + network.getEdgeCount();
- if (numGraphObjects < viewThreshold) {
- final CyNetworkView view =
viewReader.buildCyNetworkView(network);
- networkViewManager.addNetworkView(view);
- view.fitContent();
- }
-
- informUserOfGraphStats(network,
numGraphObjects, taskMonitor);
- }
- }
-
- /**
- * Inform User of Network Stats.
- */
- private void informUserOfGraphStats(final CyNetwork newNetwork,
final int objectCount,
- final TaskMonitor taskMonitor) {
- NumberFormat formatter = new DecimalFormat("#,###,###");
- StringBuffer sb = new StringBuffer();
-
- // Give the user some confirmation
- sb.append("Successfully loaded network from: ");
- sb.append(name);
- sb.append("\n\nNetwork contains " +
formatter.format(newNetwork.getNodeCount()));
- sb.append(" nodes and " +
formatter.format(newNetwork.getEdgeCount()));
- sb.append(" edges.\n\n");
-
- if (objectCount < viewThreshold) {
- sb.append("Network is under " + viewThreshold
- + " graph objects. A view will
be automatically created.");
- } else {
- sb.append("Network is over " + viewThreshold +
" graph objects. A view has not been created."
- + " If you wish to view this
network, use " + "\"Create View\" from the \"Edit\" menu.");
- }
-
- if (taskMonitor != null)
- taskMonitor.setStatusMessage(sb.toString());
- }
- }
-
}
Added:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loadnetwork/GenerateNetworkViewsTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loadnetwork/GenerateNetworkViewsTask.java
(rev 0)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loadnetwork/GenerateNetworkViewsTask.java
2012-02-28 19:53:01 UTC (rev 28385)
@@ -0,0 +1,127 @@
+/*
+ File: GenerateNetworkViewsTask.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ 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.task.internal.loadnetwork;
+
+import java.net.URI;
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
+import java.util.Properties;
+
+import org.cytoscape.io.read.CyNetworkReader;
+import org.cytoscape.io.read.CyNetworkReaderManager;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.session.CyNetworkNaming;
+import org.cytoscape.task.creation.ImportNetworksTaskFactory;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.ProvidesTitle;
+import org.cytoscape.work.TaskMonitor;
+
+class GenerateNetworkViewsTask extends AbstractTask {
+ private final String name;
+ private final CyNetworkReader viewReader;
+ private final CyNetworkManager networkManager;
+ private final CyNetworkViewManager networkViewManager;
+ private final CyNetworkNaming namingUtil;
+ private final int viewThreshold;
+
+ public GenerateNetworkViewsTask(final String name, final
CyNetworkReader viewReader,
+ final CyNetworkManager networkManager, final
CyNetworkViewManager networkViewManager,
+ final CyNetworkNaming namingUtil, final int
viewThreshold) {
+ this.name = name;
+ this.viewReader = viewReader;
+ this.networkManager = networkManager;
+ this.networkViewManager = networkViewManager;
+ this.namingUtil = namingUtil;
+ this.viewThreshold = viewThreshold;
+ }
+
+ public void run(final TaskMonitor taskMonitor) throws Exception {
+ taskMonitor.setProgress(0.0);
+
+ final CyNetwork[] networks = viewReader.getNetworks();
+ double numNets = (double)(networks.length);
+ int i = 0;
+
+ for (CyNetwork network : networks) {
+
+ // Use original name if exists
+ String networkName =
network.getRow(network).get(CyTableEntry.NAME, String.class);
+ if(networkName == null || networkName.trim().length()
== 0) {
+ networkName = name;
+ if(networkName == null)
+ networkName = "? (Name is missing)";
+
+ network.getRow(network).set(CyTableEntry.NAME,
namingUtil.getSuggestedNetworkTitle(networkName));
+ }
+ networkManager.addNetwork(network);
+
+ final int numGraphObjects = network.getNodeCount() +
network.getEdgeCount();
+ if (numGraphObjects < viewThreshold) {
+ final CyNetworkView view =
viewReader.buildCyNetworkView(network);
+ networkViewManager.addNetworkView(view);
+ view.fitContent();
+ }
+
+ taskMonitor.setProgress((double)(++i)/numNets);
+
+ informUserOfGraphStats(network, numGraphObjects,
taskMonitor);
+ }
+ }
+
+ /**
+ * Inform User of Network Stats.
+ */
+ private void informUserOfGraphStats(final CyNetwork newNetwork, final
int objectCount,
+ final TaskMonitor taskMonitor) {
+ NumberFormat formatter = new DecimalFormat("#,###,###");
+ StringBuffer sb = new StringBuffer();
+
+ // Give the user some confirmation
+ sb.append("Successfully loaded network from: ");
+ sb.append(name);
+ sb.append("\n\nNetwork contains " +
formatter.format(newNetwork.getNodeCount()));
+ sb.append(" nodes and " +
formatter.format(newNetwork.getEdgeCount()));
+ sb.append(" edges.\n\n");
+
+ if (objectCount < viewThreshold) {
+ sb.append("Network is under " + viewThreshold
+ + " graph objects. A view will be
automatically created.");
+ } else {
+ sb.append("Network is over " + viewThreshold + " graph
objects. A view has not been created."
+ + " If you wish to view this network,
use " + "\"Create View\" from the \"Edit\" menu.");
+ }
+
+ taskMonitor.setStatusMessage(sb.toString());
+ }
+}
Modified:
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTaskTest.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTaskTest.java
2012-02-28 17:07:42 UTC (rev 28384)
+++
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTaskTest.java
2012-02-28 19:53:01 UTC (rev 28385)
@@ -35,8 +35,7 @@
package org.cytoscape.task.internal.loadnetwork;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.*;
import java.io.File;
@@ -74,7 +73,7 @@
}
verify(netmgr).addNetwork(net);
// verify(networkViewManager).addNetworkView(view);
- verify(tm).setProgress(1.0);
+ verify(tm,atLeast(1)).setProgress(1.0);
}
@Test(expected = NullPointerException.class)
Modified:
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTaskTest.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTaskTest.java
2012-02-28 17:07:42 UTC (rev 28384)
+++
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTaskTest.java
2012-02-28 19:53:01 UTC (rev 28385)
@@ -29,10 +29,7 @@
package org.cytoscape.task.internal.loadnetwork;
import static org.junit.Assert.assertNotNull;
-import static org.mockito.Mockito.doThrow;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.verify;
-import static org.mockito.Mockito.when;
+import static org.mockito.Mockito.*;
import java.io.IOException;
import java.net.URL;
@@ -79,7 +76,7 @@
}
verify(netmgr).addNetwork(net);
// verify(networkViewManager).addNetworkView(view);
- verify(tm).setProgress(1.0);
+ verify(tm,atLeast(1)).setProgress(1.0);
}
@Test(expected = Exception.class)
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