Author: pwang
Date: 2009-06-10 17:03:57 -0700 (Wed, 10 Jun 2009)
New Revision: 16910
Added:
csplugins/trunk/ucsd/pwang/jActiveModules3/src/csplugins/jActiveModules/dialogs/ConditionsVsPathwaysTable2.java
Log:
use CyGroup in the result panel
Added:
csplugins/trunk/ucsd/pwang/jActiveModules3/src/csplugins/jActiveModules/dialogs/ConditionsVsPathwaysTable2.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules3/src/csplugins/jActiveModules/dialogs/ConditionsVsPathwaysTable2.java
(rev 0)
+++
csplugins/trunk/ucsd/pwang/jActiveModules3/src/csplugins/jActiveModules/dialogs/ConditionsVsPathwaysTable2.java
2009-06-11 00:03:57 UTC (rev 16910)
@@ -0,0 +1,339 @@
+// ConditionsVsPathwaysTable
+//------------------------------------------------------------------------------------------
+// $Revision: 14177 $
+// $Date: 2008-06-10 15:16:57 -0700 (Tue, 10 Jun 2008) $
+// $Author: rmkelley $
+//---------------------------------------------------------------------------------------
+package csplugins.jActiveModules.dialogs;
+//---------------------------------------------------------------------------------------
+import giny.model.Node;
+
+import java.awt.BorderLayout;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.List;
+import java.util.Vector;
+import java.util.Iterator;
+import java.util.Set;
+import java.util.HashSet;
+
+import javax.swing.AbstractAction;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JFileChooser;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.ListSelectionModel;
+import javax.swing.SwingConstants;
+import javax.swing.table.AbstractTableModel;
+import javax.swing.table.TableCellRenderer;
+
+import csplugins.jActiveModules.ActivePathViewer;
+import csplugins.jActiveModules.ActivePaths;
+import csplugins.jActiveModules.Component;
+import csplugins.jActiveModules.ActiveModulesUI;
+import cytoscape.CyNetwork;
+import cytoscape.util.CyNetworkNaming;
+import cytoscape.Cytoscape;
+import cytoscape.CyEdge;
+import cytoscape.view.cytopanels.CytoPanel;
+import cytoscape.groups.CyGroup;
+
+
+//---------------------------------------------------------------------------------------
+public class ConditionsVsPathwaysTable2 extends JPanel {
+ JTable table;
+ //JPanel topTable, bottomTable;
+ ActivePathViewer pathViewer;
+ csplugins.jActiveModules.Component[] activePaths;
+ String[] conditionNames;
+ CyNetwork cyNetwork;
+ ActiveModulesUI parentUI;
+ Vector tableData;
+
+ //
-----------------------------------------------------------------------------------------
+ public ConditionsVsPathwaysTable2(CyNetwork cyNetwork,
+ String[] conditionNames,
+ Vector tableData,
+ ActivePathViewer pathViewer,
+ ActiveModulesUI parentUI)
+
+ {
+ this.cyNetwork = cyNetwork;
+ this.activePaths = activePaths;
+ this.conditionNames = conditionNames;
+ this.pathViewer = pathViewer;
+ this.parentUI = parentUI;
+ this.tableData = tableData;
+ init();
+ } // ConditionsVsPathwaysTable ctor
+
+ private String[] getTableColuimnNames() {
+ String[] columnNames = new String[3+conditionNames.length];
+
+ columnNames[0] = "Network";
+ columnNames[1] = "Size";
+ columnNames[2] = "Score";
+
+ for (int i=0; i<conditionNames.length; i++ ){
+ columnNames[3+i] = conditionNames[i];
+ }
+ return columnNames;
+ }
+
+ private void init() {
+
+ String[] columnNames= getTableColuimnNames();
+
+ table = new JTable(new ActivePathsTableModel2(tableData,
+ columnNames));
+ table.setDefaultRenderer(Boolean.class, new ColorRenderer2());
+ JScrollPane scrollpane = new JScrollPane(table);
+
+
table.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
+ setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+// JPanel tablePanel = new JPanel();
+// tablePanel.setLayout(new BoxLayout(tablePanel,
BoxLayout.Y_AXIS));
+//
+// topTable = new ConditionsVsPathwaysTopTable(activePaths);
+// tablePanel.add(topTable);
+// bottomTable = new
ConditionsVsPathwaysBottomTable(conditionNames,
+// activePaths, pathViewer);
+// tablePanel.add(bottomTable);
+// JScrollPane scrollPane = new JScrollPane(tablePanel);
+ c.fill = GridBagConstraints.BOTH;
+ c.gridx = 0; c.gridy = 0;
+ c.weightx = 1.0; c.weighty = 1.0;
+ add(scrollpane, c);
+
+ JPanel buttonPanel = new JPanel();
+
+
+ final CyNetwork parentNetwork = Cytoscape.getCurrentNetwork();
+
+ final JButton createNetworkButton = new JButton(new
AbstractAction("Create Network")
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ for (int i=0; i< table.getSelectedRowCount();
i++) {
+ int[] rows = table.getSelectedRows();
+
+ parentNetwork.unselectAllNodes();
+ parentNetwork.unselectAllEdges();
+
+
ConditionsVsPathwaysTable2.this.pathViewer.displayPath(activePaths[rows[i]],
"");
+
+ Set nodes =
parentNetwork.getSelectedNodes();
+ Set edges = new HashSet();
+ Iterator iterator =
parentNetwork.edgesIterator();
+ while (iterator.hasNext())
+ {
+ CyEdge edge = (CyEdge)
iterator.next();
+ if
(nodes.contains(edge.getSource()) && nodes.contains(edge.getTarget()))
+ edges.add(edge);
+ }
+ CyNetwork newNetwork =
Cytoscape.createNetwork(nodes, edges,
+
CyNetworkNaming.getSuggestedSubnetworkTitle(parentNetwork),
+ parentNetwork);
+ Cytoscape.createNetworkView(newNetwork,
" results");
+
Cytoscape.getNetworkView(newNetwork.getIdentifier())
+
.setVisualStyle(Cytoscape.getNetworkView(parentNetwork.getIdentifier()).getVisualStyle().getName());
+ }
+ }
+ });
+ createNetworkButton.setEnabled(false);
+ table.addMouseListener(new MouseAdapter() {
+ public void mousePressed(MouseEvent me) {
+ //System.err.println("Mouse pressed");
+ if (table.getSelectedRowCount() ==0) {
+ return;
+ }
+
ConditionsVsPathwaysTable2.this.pathViewer.displayPath(
+
activePaths[table.getSelectedRow()], "");
+
createNetworkButton.setEnabled(table.getSelectedRow() != -1);
+ }
+ });
+ JButton dismissButton = new JButton("Close");
+ dismissButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent ae) {
+ CytoPanel cytoPanel =
Cytoscape.getDesktop().getCytoPanel(SwingConstants.EAST);
+
cytoPanel.remove(ConditionsVsPathwaysTable2.this);
+ }
+ });
+
+ final JButton saveButton = new JButton("Save All Results");
+ saveButton.setEnabled(true);
+ saveButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent ae) {
+ ConditionsVsPathwaysTable2.this.saveState();
+ }
+ });
+
+
+ JButton saveScoreDistributions = new JButton(new
AbstractAction("Save Score Distributions")
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ parentUI.startRandomizeAndRun(cyNetwork);
+ }
+ });
+ buttonPanel.add(dismissButton, BorderLayout.CENTER);
+ buttonPanel.add(createNetworkButton, BorderLayout.CENTER);
+ buttonPanel.add(saveButton, BorderLayout.CENTER);
+ buttonPanel.add(saveScoreDistributions, BorderLayout.CENTER);
+
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.gridx = 0; c.gridy = 1;
+ c.weightx = 1.0; c.weighty = 0.0;
+ add(buttonPanel, c);
+ //mainPanel.setPreferredSize(new Dimension(500, 500));
+ //setSize(800, 600);
+
+ }
+
+ public csplugins.jActiveModules.Component[] getActivePaths() {
+ return activePaths;
+ }
+
+
+ public void saveState(String filename) {
+ try {
+ FileWriter fileWriter = new FileWriter(filename);
+ for (int i = 0; i < activePaths.length; i++) {
+ StringBuffer sb = new StringBuffer();
+ sb.append("#Subnetwork " + i + "\n");
+ csplugins.jActiveModules.Component ap =
activePaths[i];
+ List nodeNames = ap.getDisplayNodes();
+ String[] condNames = ap.getConditions();
+ double score = ap.getScore();
+ sb.append("#Score\n");
+ sb.append(score + "\n");
+ sb.append("#Nodes\n");
+ for (int j = 0; j < nodeNames.size(); j++)
+ sb.append(((Node)
nodeNames.get(j)).getIdentifier() + "\n");
+ sb.append("#Conditions\n");
+ for (int j = 0; j < condNames.length; j++)
+ sb.append(condNames[j] + "\n");
+ sb.append("\n");
+ fileWriter.write(sb.toString());
+ }
+ fileWriter.close();
+ } catch (IOException ioe) {
+ System.err.println("Error while writing " + filename);
+ ioe.printStackTrace();
+ } // catch
+ } // saveState
+
+ //
--------------------------------------------------------------------------------
+
+ public void saveState() {
+ JFileChooser chooser = new JFileChooser();
+ if (chooser.showSaveDialog(null) == chooser.APPROVE_OPTION) {
+ String name = chooser.getSelectedFile().toString();
+ saveState(name);
+ }
+ }
+
+
+} // class ConditionsVsPathwaysTable
+
+class ActivePathsTableModel2 extends AbstractTableModel {
+ //Component[] activePaths;
+ String[] columnNames;
+ Vector data;
+ protected static int HEADER_COLUMNS = 3;
+ public ActivePathsTableModel2(Vector tableData,String[] columnNames) {
+ this.data = tableData;
+ this.columnNames = columnNames;
+ }
+
+ public Class getColumnClass(int column) {
+ switch (column) {
+ case 0: return Integer.class;
+ case 1: return Integer.class;
+ case 2: return Double.class;
+ default: return Boolean.class;
+ }
+ }
+
+ public int getColumnCount() {
+ return columnNames.length;
+ }
+
+ public String getColumnName(int column) {
+ return columnNames[column];
+ }
+ public int getRowCount() {
+ return data.size();
+ }
+
+ public Object getValueAt(int rowIndex, int columnIndex) {
+ // TODO Auto-generated method stub
+ Vector groupVector = (Vector) data.elementAt(0);
+ CyGroup theGroup = (CyGroup) groupVector.elementAt(rowIndex);
+
+ Double[] scores = (Double[]) data.elementAt(1);
+ Boolean[][] values = (Boolean[][])data.elementAt(2);
+
+ switch (columnIndex) {
+ case 0 :
+ return new Integer(rowIndex + 1);
+ case 1 :
+ return new Integer(theGroup.getNodes().size());
+ case 2 :
+ return scores[rowIndex];
+ default :
+ return values[rowIndex][columnIndex-3];
+ }
+ }
+
+}
+
+class ColorRenderer2 extends JLabel implements TableCellRenderer {
+ public ColorRenderer2() {
+ setOpaque(true);
+ }
+
+ // public java.awt.Component getTableCellRendererComponent (JTable
table,
+ // Object value,
+ // boolean isSelected, boolean hasFocus,
+ // int row, int column) {
+ // float cell_value = ((Double)value).floatValue();
+ // float MAX = 1;
+ // float MID = .5f;
+ // float MIN = 0;
+ // float green_fraction =
+ // Math.min(1f,Math.max(0f,(cell_value-MID)/(MAX-MID)));
+ // float red_fraction =
+ // Math.min(1f,Math.max(0f,(MID-cell_value)/(MID-MIN)));
+ // setBackground(new Color(red_fraction,green_fraction,0f));
+ // setText(String.valueOf(cell_value));
+ // setForeground(Color.WHITE);
+ // return this;
+ // } // getTableCellRendererComponent
+ public java.awt.Component getTableCellRendererComponent(JTable table,
+ Object value, boolean isSelected, boolean hasFocus, int
row,
+ int column) {
+ boolean cell_value = ((Boolean) value).booleanValue();
+ if (cell_value) {
+ setBackground(Color.RED);
+ } else {
+ setBackground(Color.WHITE);
+ }
+
+ setForeground(Color.WHITE);
+ return this;
+ } // getTableCellRendererComponent
+}
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