Author: kono
Date: 2011-05-09 14:04:03 -0700 (Mon, 09 May 2011)
New Revision: 24969
Modified:
core3/network-analyzer-impl/trunk/pom.xml
core3/network-analyzer-impl/trunk/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/BatchAnalysisAction.java
core3/network-analyzer-impl/trunk/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/BatchNetworkAnalyzer.java
core3/network-analyzer-impl/trunk/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/BatchResultsDialog.java
core3/network-analyzer-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
Log:
Fixed to make it compatible with new network IO API.
Modified: core3/network-analyzer-impl/trunk/pom.xml
===================================================================
--- core3/network-analyzer-impl/trunk/pom.xml 2011-05-09 19:54:43 UTC (rev
24968)
+++ core3/network-analyzer-impl/trunk/pom.xml 2011-05-09 21:04:03 UTC (rev
24969)
@@ -89,27 +89,27 @@
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>session-api</artifactId>
- <version>3.0.0-alpha2</version>
+ <version>3.0.0-alpha3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>viewmodel-api</artifactId>
- <version>3.0.0-alpha3</version>
+ <version>3.0.0-alpha4-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>swing-application-api</artifactId>
- <version>3.0.0-alpha1</version>
+ <version>3.0.0-alpha2-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>core-task-api</artifactId>
- <version>3.0.0-alpha2</version>
+ <version>3.0.0-alpha3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>io-api</artifactId>
- <version>3.0.0-alpha2</version>
+ <version>3.0.0-alpha3-SNAPSHOT</version>
</dependency>
<dependency>
Modified:
core3/network-analyzer-impl/trunk/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/BatchAnalysisAction.java
===================================================================
---
core3/network-analyzer-impl/trunk/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/BatchAnalysisAction.java
2011-05-09 19:54:43 UTC (rev 24968)
+++
core3/network-analyzer-impl/trunk/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/BatchAnalysisAction.java
2011-05-09 21:04:03 UTC (rev 24969)
@@ -21,16 +21,14 @@
import java.awt.event.ActionEvent;
import java.io.File;
import java.io.FileFilter;
-import java.io.InputStream;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
-import org.cytoscape.io.read.CyNetworkViewReader;
-import org.cytoscape.io.read.CyNetworkViewReaderManager;
-import org.cytoscape.model.CyNetworkManager;
-
import org.cytoscape.application.swing.CySwingApplication;
+import org.cytoscape.io.read.CyNetworkReader;
+import org.cytoscape.io.read.CyNetworkReaderManager;
+import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.session.CyApplicationManager;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -52,13 +50,13 @@
private static final Logger logger =
LoggerFactory.getLogger(BatchAnalysisAction.class);
- private final CyNetworkViewReaderManager cyNetworkViewReaderMgr;
+ private final CyNetworkReaderManager cyNetworkViewReaderMgr;
private final CyNetworkManager netMgr;
/**
* Constructs a new batch analysis action.
*/
- protected BatchAnalysisAction(CyApplicationManager
appMgr,CySwingApplication swingApp, CyNetworkManager netMgr,
CyNetworkViewReaderManager cyNetworkViewReaderMgr) {
+ protected BatchAnalysisAction(CyApplicationManager
appMgr,CySwingApplication swingApp, CyNetworkManager netMgr,
CyNetworkReaderManager cyNetworkViewReaderMgr) {
super(Messages.AC_BATCH_ANALYSIS,appMgr,swingApp);
this.netMgr = netMgr;
this.cyNetworkViewReaderMgr = cyNetworkViewReaderMgr;
@@ -118,7 +116,7 @@
public boolean accept(File aPathname) {
if (aPathname.isFile() && aPathname.canRead()) {
final String name =
aPathname.getAbsolutePath();
- CyNetworkViewReader reader =
cyNetworkViewReaderMgr.getReader(aPathname.toURI());
+ CyNetworkReader reader =
cyNetworkViewReaderMgr.getReader(aPathname.toURI(), name);
if (reader != null) {
return true;
}
Modified:
core3/network-analyzer-impl/trunk/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/BatchNetworkAnalyzer.java
===================================================================
---
core3/network-analyzer-impl/trunk/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/BatchNetworkAnalyzer.java
2011-05-09 19:54:43 UTC (rev 24968)
+++
core3/network-analyzer-impl/trunk/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/BatchNetworkAnalyzer.java
2011-05-09 21:04:03 UTC (rev 24969)
@@ -24,16 +24,15 @@
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashSet;
-import java.util.Iterator;
import java.util.List;
import java.util.Set;
-import org.cytoscape.io.read.CyNetworkViewReader;
-import org.cytoscape.io.read.CyNetworkViewReaderManager;
-import org.cytoscape.model.CyNetworkManager;
-import org.cytoscape.model.CyTable;
+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.CyNode;
+
import de.mpg.mpi_inf.bioinf.netanalyzer.data.AnalysisError;
import de.mpg.mpi_inf.bioinf.netanalyzer.data.Interpretations;
import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
@@ -55,7 +54,7 @@
public class BatchNetworkAnalyzer extends SwingWorker {
private final CyNetworkManager netMgr;
- private final CyNetworkViewReaderManager cyNetworkViewReaderMgr;
+ private final CyNetworkReaderManager cyNetworkViewReaderMgr;
/**
* Initializes a new instance of <code>BatchNetworkAnalyzer</code>.
@@ -67,7 +66,7 @@
* @param aInterpr
* Parameter specifying which interpretations to be applied
to each network.
*/
- public BatchNetworkAnalyzer(File aOutputDir, List<File> aInputFiles,
Interpretations aInterpr, CyNetworkManager netMgr, CyNetworkViewReaderManager
cyNetworkViewReaderMgr) {
+ public BatchNetworkAnalyzer(File aOutputDir, List<File> aInputFiles,
Interpretations aInterpr, CyNetworkManager netMgr, CyNetworkReaderManager
cyNetworkViewReaderMgr) {
analyzer = null;
cancelled = false;
dialog = null;
@@ -117,8 +116,8 @@
if (!inputFile.isFile()) {
throw new RuntimeException();
}
- CyNetworkViewReader reader =
cyNetworkViewReaderMgr.getReader(inputFile.toURI());
- network =
reader.getNetworkViews()[0].getModel();
+ CyNetworkReader reader =
cyNetworkViewReaderMgr.getReader(inputFile.toURI(), inputFile.getName());
+ network = reader.getCyNetworks()[0];
} catch (RuntimeException e) {
writeLine(Messages.SM_READERROR);
reports.add(new
NetworkAnalysisReport(inputFile, null, AnalysisError.NETWORK_NOT_OPENED));
Modified:
core3/network-analyzer-impl/trunk/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/BatchResultsDialog.java
===================================================================
---
core3/network-analyzer-impl/trunk/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/BatchResultsDialog.java
2011-05-09 19:54:43 UTC (rev 24968)
+++
core3/network-analyzer-impl/trunk/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/BatchResultsDialog.java
2011-05-09 21:04:03 UTC (rev 24969)
@@ -40,9 +40,9 @@
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
-import org.cytoscape.io.read.CyNetworkViewReader;
-import org.cytoscape.io.read.CyNetworkViewReaderManager;
-import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.io.read.CyNetworkReader;
+import org.cytoscape.io.read.CyNetworkReaderManager;
+import org.cytoscape.model.CyNetwork;
import de.mpg.mpi_inf.bioinf.netanalyzer.LoadNetstatsAction;
import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
@@ -56,7 +56,7 @@
*/
public class BatchResultsDialog extends JDialog implements ActionListener,
ListSelectionListener {
- private final CyNetworkViewReaderManager cyNetworkViewReaderMgr;
+ private final CyNetworkReaderManager cyNetworkViewReaderMgr;
private final Frame aOwner;
/**
@@ -67,7 +67,7 @@
* @param aReports
* List of analysis reports to be visualized.
*/
- public BatchResultsDialog(Frame aOwner, List<NetworkAnalysisReport>
aReports, CyNetworkViewReaderManager cyNetworkViewReaderMgr) {
+ public BatchResultsDialog(Frame aOwner, List<NetworkAnalysisReport>
aReports, CyNetworkReaderManager cyNetworkViewReaderMgr) {
super(aOwner, Messages.DT_BATCHRESULTS, false);
init(aReports);
setLocationRelativeTo(aOwner);
@@ -111,8 +111,8 @@
} else if (c == 0) {
final File file = model.getNetwork(r);
if (file != null && file.isFile()) {
- CyNetworkViewReader reader =
cyNetworkViewReaderMgr.getReader(file.toURI());
- CyNetworkView[] views =
reader.getNetworkViews();
+ CyNetworkReader reader =
cyNetworkViewReaderMgr.getReader(file.toURI(), file.getName());
+ CyNetwork[] networks =
reader.getCyNetworks();
// TODO do something with the
networks?
}
}
Modified:
core3/network-analyzer-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/network-analyzer-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-05-09 19:54:43 UTC (rev 24968)
+++
core3/network-analyzer-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-05-09 21:04:03 UTC (rev 24969)
@@ -15,7 +15,7 @@
interface="org.cytoscape.model.CyNetworkManager"/>
<osgi:reference id="cyNetworkViewReaderManagerServiceRef"
- interface="org.cytoscape.io.read.CyNetworkViewReaderManager"/>
+ interface="org.cytoscape.io.read.CyNetworkReaderManager"/>
<osgi:service id="analyzeNetworkActionService"
ref="analyzeNetworkAction"
interface="org.cytoscape.application.swing.CyAction"/>
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