Author: pwang
Date: 2011-10-20 16:03:50 -0700 (Thu, 20 Oct 2011)
New Revision: 27256
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/dialogs/ActivePathsParameterPanel.java
Log:
Refactored to work with Cy3
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/dialogs/ActivePathsParameterPanel.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/dialogs/ActivePathsParameterPanel.java
2011-10-20 22:46:50 UTC (rev 27255)
+++
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/dialogs/ActivePathsParameterPanel.java
2011-10-20 23:03:50 UTC (rev 27256)
@@ -54,19 +54,22 @@
import javax.swing.table.TableCellRenderer;
import javax.swing.table.DefaultTableCellRenderer;
import org.jdesktop.layout.GroupLayout;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import javax.swing.JTable;
import csplugins.jActiveModules.ActiveModulesUI;
+import csplugins.jActiveModules.CyHelpBrokerImpl;
import csplugins.jActiveModules.data.ActivePathFinderParameters;
-import cytoscape.CyNetwork;
-import cytoscape.Cytoscape;
-import cytoscape.data.CyAttributes;
-import cytoscape.data.CyAttributesUtils;
-import cytoscape.logger.CyLogger;
-import cytoscape.view.CyHelpBroker;
-import cytoscape.view.cytopanels.CytoPanel;
-import cytoscape.util.swing.NetworkSelectorPanel;
+import org.cytoscape.application.CyApplicationManager;
+import org.cytoscape.application.swing.CySwingApplication;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.model.CyTable;
+//import cytoscape.view.CyHelpBroker;
+import org.cytoscape.util.swing.NetworkSelectorPanel;
import java.awt.Component;
import javax.swing.table.TableColumn;
@@ -81,16 +84,20 @@
import javax.swing.event.CellEditorListener;
import javax.swing.event.ChangeEvent;
import java.util.Comparator;
-import cytoscape.util.swing.ColumnResizer;
+import org.cytoscape.util.swing.ColumnResizer;
//import cytoscape.util.swing.CyCollapsiblePanel;
+import org.cytoscape.model.CyColumn;
+import java.util.Iterator;
+import org.cytoscape.model.CyTableUtil;
-public class ActivePathsParameterPanel extends JPanel {
+public class ActivePathsParameterPanel extends JPanel implements ItemListener {
private static final long serialVersionUID = -6759180275710507653L;
- private static final CyLogger logger =
CyLogger.getLogger(ActivePathsParameterPanel.class);
-
+ private static final Logger logger =
LoggerFactory.getLogger(ActivePathsParameterPanel.class);
+
+
JTextField readout;
ActivePathFinderParameters apfParams;
@@ -164,22 +171,28 @@
private ActiveModulesUI pluginMainClass;
JDialog helpDialog;
- private NetworkSelectorPanel networkPanel = new NetworkSelectorPanel();
+ private NetworkSelectorPanel networkPanel;
-
+ private final CySwingApplication cySwingApplicationServiceRef;
+ private CyHelpBrokerImpl cyHelpBroker = new CyHelpBrokerImpl();
+
//
-----------------------------------------------------------------------------
public ActivePathsParameterPanel(
- ActivePathFinderParameters incomingApfParams,
- ActiveModulesUI parentUI) {
+ ActivePathFinderParameters incomingApfParams,
CySwingApplication cySwingApplicationServiceRef,
+ CyApplicationManager cyApplicationManager,
CyNetworkManager cyNetworkManager,
+ NetworkSelectorPanel networkSelectorPanel){
+ this.cySwingApplicationServiceRef =
cySwingApplicationServiceRef;
// Set global parameters
this.setLayout(new BorderLayout());
this.setMinimumSize(new Dimension(320, 420));
this.setPreferredSize(new Dimension(320, 420));
+ this.networkPanel = networkSelectorPanel;
+ this.networkPanel.getJCombobox().addItemListener(this);
+
// uses copy constructor so that changes aren't committed if
you dismiss.
apfParams = incomingApfParams;
- this.pluginMainClass = parentUI;
if (apfParams == null)
throw new IllegalStateException(
@@ -237,13 +250,11 @@
private void initComponents() {
java.awt.GridBagConstraints gridBagConstraints;
- //networkPanel = new javax.swing.JPanel();
jSplitPane1 = new javax.swing.JSplitPane();
attrSelectionPanel = new javax.swing.JPanel();
jScrollPane1 = new javax.swing.JScrollPane();
tblAttrSelection = new javax.swing.JTable();
jScrollPane2 = new javax.swing.JScrollPane();
- //collapsiblePanel = new javax.swing.JPanel();
buttonPanel = new javax.swing.JPanel();
helpButton = new javax.swing.JButton();
aboutButton = new javax.swing.JButton();
@@ -298,7 +309,7 @@
buttonPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
helpButton.setText("Help");
helpButton.setPreferredSize(new java.awt.Dimension(67, 23));
- CyHelpBroker.getHelpBroker().enableHelpOnButton(helpButton,
"jActiveModules", null);
+ //cyHelpBroker.getHelpBroker().enableHelpOnButton(helpButton,
"jActiveModules", null);
buttonPanel.add(helpButton);
@@ -486,34 +497,45 @@
private Vector<Object[]> getDataVect(){
- Vector<Object[]> dataVect = new Vector<Object[]>();
- CyAttributes nodeAttrs = Cytoscape.getNodeAttributes();
- String[] names = nodeAttrs.getAttributeNames();
- for ( String name : names ) {
- if ( nodeAttrs.getType(name) ==
CyAttributes.TYPE_FLOATING ) {
- Map attrMap =
CyAttributesUtils.getAttribute(name,nodeAttrs);
+ Vector<Object[]> dataVect = new Vector<Object[]>();
- if ( attrMap == null )
+ if (this.networkPanel.getSelectedNetwork() == null){
+ return dataVect;
+ }
+
+ System.out.println("Entering
ActivePathsParameterPanel.getDataVector()...");
+
+
+ CyTable table =
this.networkPanel.getSelectedNetwork().getDefaultNodeTable();
+
+ String[] names = (String[])
CyTableUtil.getColumnNames(table).toArray();
+
+ for (String name: names){
+
+ CyColumn col = table.getColumn(name);
+
+ if ( col.getType() == Float.class || col.getType() ==
Double.class) {
+ List<Float> vals = (List<Float>)
col.getValues(Float.class);
+
+ if ( vals == null )
continue; // no values have been
defined for the attr yet
Object[] row = new Object[5];
row[0] = name;
boolean isPValue = true;
- for ( Object value : attrMap.values() ) {
- double d =
((Double)value).doubleValue();
- if ( d < 0 || d > 1 ) {
+ for ( Object value : vals ) {
+ double d =
((Double)value).doubleValue();
+ if ( d < 0 || d > 1 ) {
isPValue = false;
break;
}
}
-
- Collection<Double> values = attrMap.values();
- row[1] = Collections.min(values);
- row[2] = Collections.max(values);
+ row[1] = Collections.min(vals);
+ row[2] = Collections.max(vals);
row[3] = false;
if (!isPValue) {
@@ -1095,11 +1117,11 @@
} // createRegionalScoringController
private void createHelpDialog() {
- helpDialog = new JDialog(Cytoscape.getDesktop(),
"jActiveModules Help");
+ helpDialog = new
JDialog(this.cySwingApplicationServiceRef.getJFrame(), "jActiveModules Help");
helpDialog.setDefaultCloseOperation(JDialog.HIDE_ON_CLOSE);
try {
- JEditorPane helpPane = new
JEditorPane(pluginMainClass.getClass()
- .getResource("/help.html"));
+
+ JEditorPane helpPane = new
JEditorPane(getClass().getResource("/help/help.html"));
helpPane.setEditable(false);
JScrollPane scrollPane = new JScrollPane(helpPane);
helpDialog.setContentPane(scrollPane);
@@ -1668,9 +1690,9 @@
public void actionPerformed(ActionEvent e) {
// listener.cancelActivePathsFinding ();
- CytoPanel cytoPanel =
Cytoscape.getDesktop().getCytoPanel(
- SwingConstants.WEST);
- cytoPanel.remove(ActivePathsParameterPanel.this);
+ //CytoPanel cytoPanel =
Cytoscape.getDesktop().getCytoPanel(
+ // SwingConstants.WEST);
+ //cytoPanel.remove(ActivePathsParameterPanel.this);
}
} // DismissAction
@@ -1714,5 +1736,21 @@
// do nothing
}
}
+
+ public void handlePanelSelected(){
+ }
+
+ public void setPluginMainClass(ActiveModulesUI ui){
+ pluginMainClass = ui;
+ }
+
+ public void itemStateChanged(ItemEvent e) {
+ updateAttributePanel();
+ }
+
+ private void updateAttributePanel(){
+ System.out.println("Entering
ActivePathParameterpanel.updateAttributePanel()...");
+ }
+
} // class ActivePathsParametersPopupDialog
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