Author: kono
Date: 2011-10-26 16:21:12 -0700 (Wed, 26 Oct 2011)
New Revision: 27315
Modified:
csplugins/trunk/ucsd/kono/bingo3/src/BiNGO/DisplayBiNGOWindow.java
csplugins/trunk/ucsd/kono/bingo3/src/BiNGO/GOlorize/GoBin.java
csplugins/trunk/ucsd/kono/bingo3/src/BiNGO/GOlorize/ResultPanel.java
csplugins/trunk/ucsd/kono/bingo3/src/BiNGO/GOlorize/ZSelectNodes.java
csplugins/trunk/ucsd/kono/bingo3/src/BiNGO/SettingsPanelActionListener.java
Log:
Selection function fixed.
Modified: csplugins/trunk/ucsd/kono/bingo3/src/BiNGO/DisplayBiNGOWindow.java
===================================================================
--- csplugins/trunk/ucsd/kono/bingo3/src/BiNGO/DisplayBiNGOWindow.java
2011-10-26 22:05:35 UTC (rev 27314)
+++ csplugins/trunk/ucsd/kono/bingo3/src/BiNGO/DisplayBiNGOWindow.java
2011-10-26 23:21:12 UTC (rev 27315)
@@ -59,6 +59,7 @@
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.TaskManager;
import org.cytoscape.work.TaskMonitor;
import BiNGO.ontology.Ontology;
@@ -216,8 +217,13 @@
buildNodeAttributes(network);
buildEdgeAttributes(network);
- final CyNetworkViewFactory viewFactory =
adapter.getCyNetworkViewFactory();
- final CyNetworkView bingoCyNetworkView =
viewFactory.getNetworkView(network);
+
+ // Create View
+ final TaskManager tm = adapter.getTaskManager();
+ tm.execute(new GenericTaskFactory(new CreateViewTask(network)));
+
+// final CyNetworkViewFactory viewFactory =
adapter.getCyNetworkViewFactory();
+// final CyNetworkView bingoCyNetworkView =
viewFactory.getNetworkView(network);
//
// // from MCODE plugin, MCODEResultsDialog class layout graph and
fit it to window
// // randomize node positions before layout so that they don't
all layout in a line
Modified: csplugins/trunk/ucsd/kono/bingo3/src/BiNGO/GOlorize/GoBin.java
===================================================================
--- csplugins/trunk/ucsd/kono/bingo3/src/BiNGO/GOlorize/GoBin.java
2011-10-26 22:05:35 UTC (rev 27314)
+++ csplugins/trunk/ucsd/kono/bingo3/src/BiNGO/GOlorize/GoBin.java
2011-10-26 23:21:12 UTC (rev 27315)
@@ -47,6 +47,7 @@
import javax.swing.JTable;
import org.cytoscape.model.CyNetwork;
+import org.cytoscape.plugin.CyPluginAdapter;
import org.cytoscape.view.model.CyNetworkView;
import BiNGO.SettingsPanel;
@@ -92,9 +93,11 @@
// private JFrame bingoWindow = new JFrame("BiNGO Settings");
private SettingsPanel settingsPanel;
private CyNetworkView networkView;
+
+ private final CyPluginAdapter adapter;
- public GoBin(BiNGO.SettingsPanel settingsPanel, CyNetworkView
networkView) {
-
+ public GoBin(BiNGO.SettingsPanel settingsPanel, CyNetworkView
networkView, final CyPluginAdapter adapter) {
+ this.adapter = adapter;
this.setTitle("BiNGO output");
this.settingsPanel = settingsPanel;
this.networkView = networkView;
@@ -289,7 +292,7 @@
ResultPanel result = new ResultPanel(testMap, correctionMap,
mapSmallX, mapSmallN, mapBigX, mapBigN,
alphaString, annotation, alias, ontology,
annotationFile, ontologyFile, testString, correctionString,
overUnderString, dirName, fileName,
clusterVsString, catString, selectedCanonicalNameVector,
- currentNetwork, currentNetworkview, this);
+ currentNetwork, currentNetworkview, this,
adapter);
if (getResultPanelCount() != 0)
result.setTabName(trouveBonNom(result.getTabName()));
Modified: csplugins/trunk/ucsd/kono/bingo3/src/BiNGO/GOlorize/ResultPanel.java
===================================================================
--- csplugins/trunk/ucsd/kono/bingo3/src/BiNGO/GOlorize/ResultPanel.java
2011-10-26 22:05:35 UTC (rev 27314)
+++ csplugins/trunk/ucsd/kono/bingo3/src/BiNGO/GOlorize/ResultPanel.java
2011-10-26 23:21:12 UTC (rev 27315)
@@ -66,6 +66,7 @@
import javax.swing.table.TableColumnModel;
import org.cytoscape.model.CyNetwork;
+import org.cytoscape.plugin.CyPluginAdapter;
import org.cytoscape.view.model.CyNetworkView;
import BiNGO.Browser;
@@ -169,6 +170,8 @@
final static int SELECT_COLUMN = 0;
final static int GO_TERM_COLUMN = 1;
final static int DESCRIPTION_COLUMN = 2;
+
+ private final CyPluginAdapter adapter;
/**
* Creates a new instance of ResultPanel
@@ -178,9 +181,10 @@
Map mapBigN, String alphaString, Annotation annotation,
Map alias, Ontology ontology,
String annotationFile, String ontologyFile, String
testString, String correctionString,
String overUnderString, String dirName, String fileNam,
String clusterVsString, String catString,
- Set selectedCanonicalNameVector, CyNetwork
currentNetwork, CyNetworkView currentNetworkview, GoBin goB) {
+ Set selectedCanonicalNameVector, CyNetwork
currentNetwork, CyNetworkView currentNetworkview, GoBin goB, final
CyPluginAdapter adapter) {
this.fileName = fileNam.substring(0, fileNam.length() - 4);
-
+
+ this.adapter = adapter;
this.testMap = testMap;
this.correctionMap = correctionMap;
this.mapSmallX = mapSmallX;
@@ -376,7 +380,7 @@
constr.weightx = 100;
constr.anchor = constr.EAST;
JButton jButton4 = new JButton("Select nodes");
- jButton4.addActionListener(new
ZSelectNodes((ResultAndStartPanel) this));
+ jButton4.addActionListener(new
ZSelectNodes((ResultAndStartPanel) this, adapter));
jPanelApplyButtons.add(jButton4, constr);
jPanelDeBase.add(jPanelApplyButtons,
java.awt.BorderLayout.SOUTH);
Modified: csplugins/trunk/ucsd/kono/bingo3/src/BiNGO/GOlorize/ZSelectNodes.java
===================================================================
--- csplugins/trunk/ucsd/kono/bingo3/src/BiNGO/GOlorize/ZSelectNodes.java
2011-10-26 22:05:35 UTC (rev 27314)
+++ csplugins/trunk/ucsd/kono/bingo3/src/BiNGO/GOlorize/ZSelectNodes.java
2011-10-26 23:21:12 UTC (rev 27315)
@@ -45,9 +45,12 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.plugin.CyPluginAdapter;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
+import com.sun.xml.internal.bind.v2.model.core.Adapter;
+
import BiNGO.ontology.Annotation;
public class ZSelectNodes implements ActionListener {
@@ -55,69 +58,81 @@
ResultAndStartPanel result;
Annotation annotation;
+ private final CyPluginAdapter adapter;
+
/** Creates a new instance of ZSelectNodes */
- public ZSelectNodes(ResultAndStartPanel result) {
+ public ZSelectNodes(ResultAndStartPanel result, final CyPluginAdapter
adapter) {
this.result = result;
-
+ this.adapter = adapter;
}
public void actionPerformed(ActionEvent ev) {
- // TODO: FIXME
- System.out.println("Not implemented yet!!");
+ System.out.println("Selection start!!");
-// this.annotation = result.getAnnotation();
-// Map<String, HashSet<String>> alias = result.getAlias();
-// JTable jTable = result.getJTable();
-// // goSelected = ZDisplayGoNodes3.getSelectedGoSet(jTable);
-// goSelected = getSelectedGoSet(jTable);
-// CyNetworkView currentNetworkView = result.getNetworkView();
-// if (currentNetworkView != null) {
-// final CyNetwork model = currentNetworkView.getModel();
-// final List<CyNode> nodes = model.getNodeList();
-// for (final CyNode node : nodes)
-// node.getCyRow().set(CyNetwork.SELECTED, false);
-//
-// currentNetworkView.updateView();
-//
-// HashSet selectedNodesSet = new HashSet();
-//
-// if (result instanceof ResultPanel) {
-// this.annotation = result.getAnnotation();
-// final Collection<View<CyNode>> nodeViews =
currentNetworkView.getNodeViews();
-// for(View<CyNode> nodeView: nodeViews) {
-// Set goAnnot = new HashSet();
-//
-// String nodeName =
nodeView.getNode().getIdentifier().toUpperCase();
-// HashSet identifiers = alias.get(node);
-// if (identifiers != null) {
-// Iterator it =
identifiers.iterator();
-// while (it.hasNext()) {
-// int[] goID =
annotation.getClassifications(it.next() + "");
-// for (int t = 0; t <
goID.length; t++) {
-//
goAnnot.add(goID[t] + "");
-// }
-// }
-// }
-//
-// if (goAnnot != null) {
-// Iterator it =
goAnnot.iterator();
-// while (it.hasNext()) {
-// if
(goSelected.contains((new Integer(it.next() + "")).toString())) {
-//
selectedNodesSet.add(nodeView.getNode());
-// continue;
-// }
-// }
-// }
-//
-// // this.annotation=null;
-// }
-//
currentNetworkView.getNetwork().setSelectedNodeState(selectedNodesSet, true);
-// currentNetworkView.updateView();
-// }
-//
-// this.annotation = null;
-// }
+ this.annotation = result.getAnnotation();
+ Map<String, Set<String>> alias = result.getAlias();
+ JTable jTable = result.getJTable();
+ goSelected = getSelectedGoSet(jTable);
+ CyNetworkView currentNetworkView = result.getNetworkView();
+ if (currentNetworkView != null) {
+ final CyNetwork model = currentNetworkView.getModel();
+ final List<CyNode> nodes = model.getNodeList();
+ for (final CyNode node : nodes)
+ node.getCyRow().set(CyNetwork.SELECTED, false);
+
+ //currentNetworkView.updateView();
+
+ System.out.println("Selection cleared!!----------" +
model.getCyRow().get(CyTableEntry.NAME, String.class));
+
+ final Set<CyNode> selectedNodesSet = new
HashSet<CyNode>();
+
+ if (result instanceof ResultPanel) {
+ this.annotation = result.getAnnotation();
+ final Collection<View<CyNode>> nodeViews =
currentNetworkView.getNodeViews();
+ for(View<CyNode> nodeView: nodeViews) {
+ Set goAnnot = new HashSet();
+
+ final CyNode node = nodeView.getModel();
+ final String nodeName =
node.getCyRow().get(CyTableEntry.NAME, String.class);
+ Set identifiers = alias.get(nodeName);
+ if (identifiers != null) {
+ Iterator it =
identifiers.iterator();
+ while (it.hasNext()) {
+ int[] goID =
annotation.getClassifications(it.next() + "");
+ for (int t = 0; t <
goID.length; t++) {
+
goAnnot.add(goID[t] + "");
+ }
+ }
+ System.out.println("Selected
Node name = " + nodeName);
+ }
+
+
+ if (goAnnot != null) {
+ Iterator it =
goAnnot.iterator();
+ while (it.hasNext()) {
+ if
(goSelected.contains((new Integer(it.next() + "")).toString())) {
+
selectedNodesSet.add(nodeView.getModel());
+ continue;
+ }
+ }
+ }
+ // this.annotation=null;
+ }
+
+ System.out.println("Nodes selected = " +
selectedNodesSet.size());
+
+ for(final CyNode node: selectedNodesSet)
+ node.getCyRow().set(CyNetwork.SELECTED,
true);
+
+ adapter.getCyEventHelper().flushPayloadEvents();
+ currentNetworkView.updateView();
+ }
+
+ this.annotation = null;
+ }
+
+ System.out.println("Selection DONE!!");
}
private HashSet getSelectedGoSet(JTable jTable1) {
Modified:
csplugins/trunk/ucsd/kono/bingo3/src/BiNGO/SettingsPanelActionListener.java
===================================================================
--- csplugins/trunk/ucsd/kono/bingo3/src/BiNGO/SettingsPanelActionListener.java
2011-10-26 22:05:35 UTC (rev 27314)
+++ csplugins/trunk/ucsd/kono/bingo3/src/BiNGO/SettingsPanelActionListener.java
2011-10-26 23:21:12 UTC (rev 27315)
@@ -1059,7 +1059,7 @@
display.makeWindow();
}
if ((goBin == null) || goBin.isWindowClosed()) {
- goBin = new BiNGO.GOlorize.GoBin(settingsPanel,
startNetworkView);
+ goBin = new BiNGO.GOlorize.GoBin(settingsPanel,
startNetworkView, adapter);
}
if (params.getAnnotationFile() == null) {
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