Author: kono
Date: 2011-05-03 16:03:30 -0700 (Tue, 03 May 2011)
New Revision: 24911
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
Log:
Broken format are fixed.
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
2011-05-03 21:31:16 UTC (rev 24910)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
2011-05-03 23:03:30 UTC (rev 24911)
@@ -50,112 +50,112 @@
* Task to load a new network.
*/
abstract public class AbstractLoadNetworkTask extends AbstractTask {
- protected CyNetworkViewReader reader;
- protected URI uri;
- protected TaskMonitor taskMonitor;
- protected String name;
- protected boolean interrupted = false;
- protected CyNetworkViewReaderManager mgr;
- protected CyNetworkManager networkManager;
- protected CyNetworkViewManager networkViewManager;
- protected Properties props;
- protected CyNetworkNaming namingUtil;
+ protected CyNetworkViewReader reader;
+ protected URI uri;
+ protected TaskMonitor taskMonitor;
+ protected String name;
+ protected boolean interrupted = false;
+ protected CyNetworkViewReaderManager mgr;
+ protected CyNetworkManager networkManager;
+ protected CyNetworkViewManager networkViewManager;
+ protected Properties props;
+ protected CyNetworkNaming namingUtil;
- public AbstractLoadNetworkTask(final CyNetworkViewReaderManager mgr, final
CyNetworkManager networkManager,
- final CyNetworkViewManager networkViewManager, final Properties
props, final CyNetworkNaming namingUtil) {
- this.mgr = mgr;
- this.networkManager = networkManager;
- this.networkViewManager = networkViewManager;
- this.props = props;
- this.namingUtil = namingUtil;
- }
+ public AbstractLoadNetworkTask(final CyNetworkViewReaderManager mgr,
final CyNetworkManager networkManager,
+ final CyNetworkViewManager networkViewManager, final
Properties props, final CyNetworkNaming namingUtil) {
+ this.mgr = mgr;
+ this.networkManager = networkManager;
+ this.networkViewManager = networkViewManager;
+ this.props = props;
+ this.namingUtil = namingUtil;
+ }
- protected void loadNetwork(final CyNetworkViewReader viewReader) throws
Exception {
- if (viewReader == null)
- throw new IllegalArgumentException("Could not read file: Network
View Reader is null.");
+ protected void loadNetwork(final CyNetworkViewReader viewReader) throws
Exception {
+ if (viewReader == null)
+ throw new IllegalArgumentException("Could not read
file: Network View Reader is null.");
- taskMonitor.setStatusMessage("Reading in Network Data...");
- taskMonitor.setProgress(-1.0);
- taskMonitor.setStatusMessage("Creating Cytoscape Network...");
+ taskMonitor.setStatusMessage("Reading in Network Data...");
+ taskMonitor.setProgress(-1.0);
+ taskMonitor.setStatusMessage("Creating Cytoscape Network...");
- insertTasksAfterCurrentTask(viewReader, new
GenerateNetworkViewsTask(name, viewReader, networkManager,
- networkViewManager, namingUtil, props));
- }
+ insertTasksAfterCurrentTask(viewReader, new
GenerateNetworkViewsTask(name, viewReader, networkManager,
+ networkViewManager, namingUtil, props));
+ }
- @Override
- abstract public void run(TaskMonitor taskMonitor) throws Exception;
+ @Override
+ abstract public void run(TaskMonitor taskMonitor) throws Exception;
}
class GenerateNetworkViewsTask extends AbstractTask {
- private final String name;
- private final CyNetworkViewReader viewReader;
- private final CyNetworkManager networkManager;
- private final CyNetworkViewManager networkViewManager;
- private final CyNetworkNaming namingUtil;
- private final Properties props;
+ private final String name;
+ private final CyNetworkViewReader viewReader;
+ private final CyNetworkManager networkManager;
+ private final CyNetworkViewManager networkViewManager;
+ private final CyNetworkNaming namingUtil;
+ private final Properties props;
- GenerateNetworkViewsTask(final String name, final CyNetworkViewReader
viewReader,
- final CyNetworkManager networkManager, final CyNetworkViewManager
networkViewManager,
- final CyNetworkNaming namingUtil, final Properties props) {
- this.name = name;
- this.viewReader = viewReader;
- this.networkManager = networkManager;
- this.networkViewManager = networkViewManager;
- this.namingUtil = namingUtil;
- this.props = props;
- }
+ GenerateNetworkViewsTask(final String name, final CyNetworkViewReader
viewReader,
+ final CyNetworkManager networkManager, final
CyNetworkViewManager networkViewManager,
+ final CyNetworkNaming namingUtil, final Properties
props) {
+ this.name = name;
+ this.viewReader = viewReader;
+ this.networkManager = networkManager;
+ this.networkViewManager = networkViewManager;
+ this.namingUtil = namingUtil;
+ this.props = props;
+ }
- public void run(final TaskMonitor taskMonitor) throws Exception {
- final CyNetworkView[] cyNetworkViews = viewReader.getNetworkViews();
+ public void run(final TaskMonitor taskMonitor) throws Exception {
+ final CyNetworkView[] cyNetworkViews =
viewReader.getNetworkViews();
- if (cyNetworkViews == null || cyNetworkViews.length < 0)
- throw new IOException("Could not create network for the producer.");
+ if (cyNetworkViews == null || cyNetworkViews.length < 0)
+ throw new IOException("Could not create network for the
producer.");
- for (CyNetworkView view : cyNetworkViews) {
- if (cancelled)
- return;
+ for (CyNetworkView view : cyNetworkViews) {
+ if (cancelled)
+ return;
- final CyNetwork cyNetwork = view.getModel();
- cyNetwork.getCyRow().set(CyTableEntry.NAME,
namingUtil.getSuggestedNetworkTitle(name));
- networkManager.addNetwork(cyNetwork);
-
- // Do the following only for non-null views.
- if (view.isEmptyView() == false) {
- networkViewManager.addNetworkView(view);
- view.fitContent();
- } else {
- view = null;
- }
+ final CyNetwork cyNetwork = view.getModel();
+ cyNetwork.getCyRow().set(CyTableEntry.NAME,
namingUtil.getSuggestedNetworkTitle(name));
+ networkManager.addNetwork(cyNetwork);
- informUserOfGraphStats(cyNetwork, taskMonitor);
+ // Do the following only for non-null views.
+ if (view.isEmptyView() == false) {
+ networkViewManager.addNetworkView(view);
+ view.fitContent();
+ } else {
+ view = null;
+ }
+
+ informUserOfGraphStats(cyNetwork, taskMonitor);
+ }
+
+ taskMonitor.setProgress(1.0);
}
- taskMonitor.setProgress(1.0);
- }
+ /**
+ * Inform User of Network Stats.
+ */
+ private void informUserOfGraphStats(final CyNetwork newNetwork, final
TaskMonitor taskMonitor) {
+ NumberFormat formatter = new DecimalFormat("#,###,###");
+ StringBuffer sb = new StringBuffer();
- /**
- * 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(name);
+ sb.append("\n\nNetwork contains " +
formatter.format(newNetwork.getNodeCount()));
+ sb.append(" nodes and " +
formatter.format(newNetwork.getEdgeCount()));
+ sb.append(" edges.\n\n");
- // 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");
+ String thresh = props.getProperty("viewThreshold");
- String thresh = props.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.");
+ }
- 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());
}
-
- taskMonitor.setStatusMessage(sb.toString());
- }
}
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