Author: pwang
Date: 2012-05-11 15:17:12 -0700 (Fri, 11 May 2012)
New Revision: 29248
Modified:
core3/samples/trunk/sample27a/pom.xml
core3/samples/trunk/sample27a/src/main/java/org/cytoscape/sample/internal/Sample27aApp.java
core3/samples/trunk/sample27a/src/main/java/org/cytoscape/sample/internal/TCReader.java
Log:
Updated
Modified: core3/samples/trunk/sample27a/pom.xml
===================================================================
--- core3/samples/trunk/sample27a/pom.xml 2012-05-11 21:24:21 UTC (rev
29247)
+++ core3/samples/trunk/sample27a/pom.xml 2012-05-11 22:17:12 UTC (rev
29248)
@@ -4,7 +4,7 @@
<properties>
<bundle.symbolicName>sample27s</bundle.symbolicName>
<bundle.namespace>org.cytoscape.sample.internal</bundle.namespace>
-
<cytoscape.api.version>3.0.0-alpha8-SNAPSHOT</cytoscape.api.version>
+
<cytoscape.api.version>3.0.0-beta2-SNAPSHOT</cytoscape.api.version>
<maven-jar-plugin.version>2.3.1</maven-jar-plugin.version>
<maven-surefire-plugin.version>2.7.1</maven-surefire-plugin.version>
</properties>
@@ -14,7 +14,7 @@
<packaging>jar</packaging>
<name>${bundle.symbolicName}</name>
- <version>3.0.0-alpha8-SNAPSHOT</version>
+ <version>3.0.0-beta2-SNAPSHOT</version>
<build>
<plugins>
@@ -69,11 +69,6 @@
</repositories>
<dependencies>
- <dependency>
- <groupId>org.cytoscape</groupId>
- <artifactId>plugin-api</artifactId>
- <version>${cytoscape.api.version}</version>
- </dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>core-task-api</artifactId>
Modified:
core3/samples/trunk/sample27a/src/main/java/org/cytoscape/sample/internal/Sample27aApp.java
===================================================================
---
core3/samples/trunk/sample27a/src/main/java/org/cytoscape/sample/internal/Sample27aApp.java
2012-05-11 21:24:21 UTC (rev 29247)
+++
core3/samples/trunk/sample27a/src/main/java/org/cytoscape/sample/internal/Sample27aApp.java
2012-05-11 22:17:12 UTC (rev 29248)
@@ -17,9 +17,6 @@
public Sample27aApp(CySwingAppAdapter swingAdapter){
super(swingAdapter);
- //a.get
- StreamUtil streamUtil = null;
-
// Define a filter
HashSet<String> extensions = new HashSet<String>();
extensions.add("tc");
@@ -27,9 +24,9 @@
contentTypes.add("txt");
String description = "My test filter";
DataCategory category = DataCategory.NETWORK;
- BasicCyFileFilter filter = new
BasicCyFileFilter(extensions,contentTypes, description, category, streamUtil);
+ BasicCyFileFilter filter = new
BasicCyFileFilter(extensions,contentTypes, description, category,
swingAdapter.getStreamUtil());
- // Create an instance of the TaskFactory
+ // Create an instance of the ReaderFactory
TCReaderFactory factory = new TCReaderFactory(filter,
swingAdapter.getCyNetworkFactory(), swingAdapter.getCyNetworkViewFactory());
//register the ReaderFactory as an InputStreamTaskFactory.
Modified:
core3/samples/trunk/sample27a/src/main/java/org/cytoscape/sample/internal/TCReader.java
===================================================================
---
core3/samples/trunk/sample27a/src/main/java/org/cytoscape/sample/internal/TCReader.java
2012-05-11 21:24:21 UTC (rev 29247)
+++
core3/samples/trunk/sample27a/src/main/java/org/cytoscape/sample/internal/TCReader.java
2012-05-11 22:17:12 UTC (rev 29248)
@@ -14,7 +14,9 @@
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
+import java.util.HashMap;
+
public class TCReader extends AbstractTask implements CyNetworkReader {
// reads the file and creates a CyNetwork.
private static final int BUFFER_SIZE = 16384;
@@ -34,19 +36,56 @@
public void run(TaskMonitor taskMonitor) throws Exception {
String text = readString(stream);
-
+ String[] lines = text.split("\n");
+
+ if (lines.length == 0){
+ return;
+ }
+
network = networkFactory.createNetwork();
+
+ HashMap<String, CyNode> nodeNameMap = new HashMap<String,
CyNode>();
-
- CyNode node = network.addNode();
- CyRow attributes = network.getRow(node);
- attributes.set("name", "NAMENAME");
-
-
-
-
-
+ for (int i=0; i< lines.length; i++){
+ String line = lines[i];
+ String[] items = line.split("\t");
+ String name1 = items[0].trim();
+ String name2 = items[1].trim();
+
+ CyNode node1 = null;
+ CyNode node2 = null;
+
+ // for Node1
+ if (nodeNameMap.containsKey(name1)){
+ // Node already existed, get a reference to it
+ node1 = nodeNameMap.get(name1);
+ }
+ else {
+ // Node does not exist, create new one
+ node1 = network.addNode();
+ CyRow attributes = network.getRow(node1);
+ attributes.set("name", name1);
+ nodeNameMap.put(name1, node1);
+ }
+
+ // for Node2
+ if (nodeNameMap.containsKey(name2)){
+ // Node already existed, get a reference to it
+ node2 = nodeNameMap.get(name2);
+ }
+ else {
+ // Node does not exist, create new one
+ node2 = network.addNode();
+ CyRow attributes = network.getRow(node2);
+ attributes.set("name", name2);
+ nodeNameMap.put(name2, node2);
+ }
+
+ // Create an edge between node1 and node2
+ network.addEdge(node1, node2, true);
+ }
}
+
public CyNetwork[] getNetworks() {
return new CyNetwork[] { network };
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
