Author: kozo
Date: 2009-08-12 12:25:51 -0700 (Wed, 12 Aug 2009)
New Revision: 17795
Modified:
csplugins/trunk/soc/kozo/layer-plugin/layer-builder-plugin/src/main/java/org/cytoscape/layer/internal/MultiLayerNetworkBuilderImpl.java
Log:
added test output code (refs ticket:24)
Modified:
csplugins/trunk/soc/kozo/layer-plugin/layer-builder-plugin/src/main/java/org/cytoscape/layer/internal/MultiLayerNetworkBuilderImpl.java
===================================================================
---
csplugins/trunk/soc/kozo/layer-plugin/layer-builder-plugin/src/main/java/org/cytoscape/layer/internal/MultiLayerNetworkBuilderImpl.java
2009-08-12 18:26:59 UTC (rev 17794)
+++
csplugins/trunk/soc/kozo/layer-plugin/layer-builder-plugin/src/main/java/org/cytoscape/layer/internal/MultiLayerNetworkBuilderImpl.java
2009-08-12 19:25:51 UTC (rev 17795)
@@ -19,15 +19,12 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.model.View;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.VisualStyle;
import org.cytoscape.view.vizmap.mappings.DiscreteMapping;
-import org.cytoscape.view.model.CyNetworkViewFactory;
-import org.cytoscape.view.model.CyNetworkView;
-import cytoscape.internal.view.NetworkViewManager;
-
/**
* Build actual network here
*
@@ -40,25 +37,26 @@
private static final String NODE_TITLE = "name";
private static final String EDGE_TITLE = "name";
private static final String LAYER_INDEX = "layer index";
-
+
private static final String VISUAL_STYLE_TITLE = "Layer Style";
-
+
private Map<String, CyDataTable> netAttrMgr;
-
+
private CyNetworkManager manager;
private CyNetwork layeredNetwork;
private CyNetworkFactory factory;
private CyNetworkViewFactory networkViewFactory;
private CyNetworkView networkView;
-
+
private VisualMappingManager vmm;
private VisualStyle layerVS;
-
+
private List<CyNetwork> layers;
private List<CyNetwork> connectors;
public MultiLayerNetworkBuilderImpl(CyNetworkManager manager,
- CyNetworkFactory factory, VisualMappingManager vmm,
CyNetworkViewFactory networkViewFactory) {
+ CyNetworkFactory factory, VisualMappingManager vmm,
+ CyNetworkViewFactory networkViewFactory) {
this.manager = manager;
this.factory = factory;
this.vmm = vmm;
@@ -67,59 +65,62 @@
public CyNetwork buildLayeredNetwork(List<CyNetwork> layers,
List<CyNetwork> connectors) {
-
+
layeredNetwork = factory.getInstance();
layeredNetwork.attrs().set(NETWORK_TITLE, "Layered Network");
netAttrMgr = layeredNetwork.getCyDataTables(NODE);
-
netAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(LAYER_INDEX, String.class,
false);
+
netAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(LAYER_INDEX,
+ String.class, false);
// HashSet cumulatedNodes = new HashSet();
Map<String, CyNode> nodeMap = new HashMap<String, CyNode>();
Map<String, CyEdge> edgeMap = new HashMap<String, CyEdge>();
// Connect layers here...
-
- for (int i = 0; i < layers.size()-1; i++) {
+
+ for (int i = 0; i < layers.size() - 1; i++) {
CyNetwork topLayer = layers.get(i);
- CyNetwork connector=connectors.get(i);
- CyNetwork bottomLayer = layers.get(i+1);
-
- connect(topLayer, connector, bottomLayer, nodeMap,
edgeMap, i, i+1);
-
+ CyNetwork connector = connectors.get(i);
+ CyNetwork bottomLayer = layers.get(i + 1);
+
+ connect(topLayer, connector, bottomLayer, nodeMap,
edgeMap, i,
+ i + 1);
+
}
-
+
nodeMap.clear();
nodeMap = null;
manager.addNetwork(layeredNetwork);
-
+
setNetworkView(layeredNetwork);
manager.addNetworkView(networkView);
System.out.println("layer index attribute test start!!");
-
- try {
- PrintWriter fout = new PrintWriter(new
BufferedWriter(new FileWriter("nodeAttribute.txt")));
-
- for (CyNode cyNode : layeredNetwork.getNodeList()){
-
- fout.println("NODE_NAME");
- fout.println(cyNode.attrs().get(NODE_TITLE,
String.class));
- fout.println("NODE_LAYER_INDEX");
- fout.println(cyNode.attrs().get(LAYER_INDEX,
String.class));
- }
-
- } catch (IOException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
-
+ // try {
+ // PrintWriter fout = new PrintWriter(new BufferedWriter(new
+ // FileWriter("nodeAttribute.txt")));
+ //
+ // for (CyNode cyNode : layeredNetwork.getNodeList()){
+ //
+ // fout.println("NODE_NAME");
+ // fout.println(cyNode.attrs().get(NODE_TITLE, String.class));
+ // fout.println("NODE_LAYER_INDEX");
+ // fout.println(cyNode.attrs().get(LAYER_INDEX, String.class));
+ //
+ // }
+ //
+ // } catch (IOException e) {
+ // // TODO Auto-generated catch block
+ // e.printStackTrace();
+ // }
+
buildVisualStyle();
-
+
System.out.println("OK!");
-
+
return layeredNetwork;
}
@@ -134,12 +135,13 @@
for (CyNode cyNode : topLayer.getNodeList()) {
String nodeName = cyNode.attrs().get(NODE_TITLE,
String.class);
-
+
if (nodeMap.containsKey(nodeName) == false) {
CyNode newNode = layeredNetwork.addNode();
newNode.attrs().set(NODE_TITLE, nodeName);
- newNode.attrs().set(LAYER_INDEX,
Integer.toString(topLayerIndex));
+ newNode.attrs().set(LAYER_INDEX,
+
Integer.toString(topLayerIndex));
nodeMap.put(nodeName, newNode);
}
@@ -149,9 +151,11 @@
String edgeName = edge.attrs().get(NETWORK_TITLE,
String.class);
CyNode sourceNode = edge.getSource();
- String sourceName = sourceNode.attrs().get(NODE_TITLE,
String.class);
+ String sourceName = sourceNode.attrs()
+ .get(NODE_TITLE, String.class);
CyNode targetNode = edge.getTarget();
- String targetName = targetNode.attrs().get(NODE_TITLE,
String.class);
+ String targetName = targetNode.attrs()
+ .get(NODE_TITLE, String.class);
if (edgeMap.containsKey(edgeName) == false) {
CyEdge newEdge = layeredNetwork.addEdge(
@@ -166,12 +170,13 @@
for (CyNode cyNode : bottomLayer.getNodeList()) {
String nodeName = cyNode.attrs().get(NODE_TITLE,
String.class);
-
+
if (nodeMap.containsKey(nodeName) == false) {
CyNode newNode = layeredNetwork.addNode();
newNode.attrs().set(NODE_TITLE, nodeName);
- newNode.attrs().set(LAYER_INDEX,
Integer.toString(bottomLayerIndex));
+ newNode.attrs().set(LAYER_INDEX,
+
Integer.toString(bottomLayerIndex));
nodeMap.put(nodeName, newNode);
}
@@ -182,9 +187,11 @@
String edgeName = edge.attrs().get(EDGE_TITLE,
String.class);
CyNode sourceNode = edge.getSource();
- String sourceName = sourceNode.attrs().get(NODE_TITLE,
String.class);
+ String sourceName = sourceNode.attrs()
+ .get(NODE_TITLE, String.class);
CyNode targetNode = edge.getTarget();
- String targetName = targetNode.attrs().get(NODE_TITLE,
String.class);
+ String targetName = targetNode.attrs()
+ .get(NODE_TITLE, String.class);
if (edgeMap.containsKey(edgeName) == false) {
CyEdge newEdge = layeredNetwork.addEdge(
@@ -194,12 +201,12 @@
}
}
-
+
// 3rd Phase: append nodes only included in connector
for (CyNode cyNode : connector.getNodeList()) {
String nodeName = cyNode.attrs().get(NODE_TITLE,
String.class);
-
+
if (nodeMap.containsKey(nodeName) == false) {
CyNode newNode = layeredNetwork.addNode();
newNode.attrs().set(NODE_TITLE, nodeName);
@@ -212,9 +219,11 @@
String edgeName = edge.attrs().get(EDGE_TITLE,
String.class);
CyNode sourceNode = edge.getSource();
- String sourceName = sourceNode.attrs().get(NODE_TITLE,
String.class);
+ String sourceName = sourceNode.attrs()
+ .get(NODE_TITLE, String.class);
CyNode targetNode = edge.getTarget();
- String targetName = targetNode.attrs().get(NODE_TITLE,
String.class);
+ String targetName = targetNode.attrs()
+ .get(NODE_TITLE, String.class);
if (edgeMap.containsKey(edgeName) == false) {
CyEdge newEdge = layeredNetwork.addEdge(
@@ -240,40 +249,66 @@
this.layers = layers;
this.connectors = connectors;
}
-
- public void buildVisualStyle(){
+
+ public void buildVisualStyle() {
layerVS = vmm.createVisualStyle(VISUAL_STYLE_TITLE);
- final DiscreteMapping<String, Double> index2zLocation = new
DiscreteMapping<String, Double>(LAYER_INDEX, String.class, NODE_Z_LOCATION);
-
-// CyNetworkView view = (CyNetworkView)
manager.getCurrentPresentation().getViewModel();
-// CyNetworkView view =
manager.getNetworkView(layeredNetwork.getSUID());
-
+ final DiscreteMapping<String, Double> index2zLocation = new
DiscreteMapping<String, Double>(
+ LAYER_INDEX, String.class, NODE_Z_LOCATION);
+
+ // CyNetworkView view = (CyNetworkView)
+ // manager.getCurrentPresentation().getViewModel();
+ // CyNetworkView view =
+ // manager.getNetworkView(layeredNetwork.getSUID());
+
final List<View<CyNode>> nodeViews = networkView.getNodeViews();
-
+
String indexString;
- for(View<CyNode> nv: nodeViews) {
-
System.out.println(nv.getSource().attrs().get(NODE_TITLE, String.class));
+
+ // try {
+ // PrintWriter fout = new PrintWriter(new BufferedWriter(
+ // new FileWriter("node_layer_index.txt")));
+
+ for (View<CyNode> nv : nodeViews) {
+
System.out.println(nv.getSource().attrs().get(NODE_TITLE,
+ String.class));
indexString = nv.getSource().attrs().get(LAYER_INDEX,
String.class);
System.out.println(indexString);
- index2zLocation.putMapValue(indexString,
Integer.parseInt(indexString) * 300d);
+ index2zLocation.putMapValue(indexString, Integer
+ .parseInt(indexString) * 300d);
}
-
+
+ // } catch (IOException e) {
+ // e.printStackTrace();
+ // }
+
layerVS.addVisualMappingFunction(index2zLocation);
-
+
vmm.setVisualStyle(layerVS, networkView);
layerVS.apply(networkView);
-
+
// for test
- for(View<CyNode> nv: nodeViews){
- indexString = nv.getSource().attrs().get(LAYER_INDEX,
String.class);
-
System.out.println(nv.getSource().attrs().get(NODE_TITLE, String.class));
-
System.out.println(nv.getVisualProperty(NODE_Z_LOCATION));
-//
System.out.println(index2zLocation.getMapValue(indexString));
+
+ try {
+ PrintWriter fout = new PrintWriter(new BufferedWriter(
+ new FileWriter("node_z_location.txt")));
+
+ for (View<CyNode> nv : nodeViews) {
+ indexString =
nv.getSource().attrs().get(LAYER_INDEX,
+ String.class);
+
fout.println(nv.getSource().attrs().get(NODE_TITLE,
+ String.class));
+
fout.println(nv.getVisualProperty(NODE_Z_LOCATION));
+ //
System.out.println(index2zLocation.getMapValue(indexString));
+ }
+
+ } catch (IOException e) {
+ e.printStackTrace();
}
+
}
-
- public void setNetworkView(CyNetwork cyNetwork){
+
+ public void setNetworkView(CyNetwork cyNetwork) {
this.networkView =
networkViewFactory.getNetworkViewFor(cyNetwork);
}
-
+
}
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