Author: pwang
Date: 2011-10-27 16:19:39 -0700 (Thu, 27 Oct 2011)
New Revision: 27318
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/ui/SearchPropertyPanel.java
Log:
Refactored to work with Cy3
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/ui/SearchPropertyPanel.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/ui/SearchPropertyPanel.java
2011-10-27 22:00:34 UTC (rev 27317)
+++
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/ui/SearchPropertyPanel.java
2011-10-27 23:19:39 UTC (rev 27318)
@@ -11,8 +11,6 @@
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.awt.image.BufferedImage;
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
import java.io.File;
import java.util.Arrays;
import java.util.Set;
@@ -27,28 +25,32 @@
import org.idekerlab.PanGIAPlugin.PanGIAPlugin;
import org.idekerlab.PanGIAPlugin.SearchParameters;
import org.idekerlab.PanGIAPlugin.SearchTask;
+import org.idekerlab.PanGIAPlugin.ServicesUtil;
-import cytoscape.CyNetwork;
-import cytoscape.Cytoscape;
-import cytoscape.data.CyAttributes;
-import cytoscape.data.attr.MultiHashMapDefinition;
-import cytoscape.data.attr.MultiHashMapDefinitionListener;
-import cytoscape.task.ui.JTaskConfig;
-import cytoscape.task.util.TaskManager;
-import cytoscape.view.CyHelpBroker;
-import cytoscape.view.cytopanels.CytoPanel;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyTable;
+//import cytoscape.view.CyHelpBroker;
import org.idekerlab.PanGIAPlugin.ScalingMethodX;
import org.idekerlab.PanGIAPlugin.utilities.CyCollapsiblePanel;
-import com.lowagie.text.Font;
+//import com.lowagie.text.Font;
+import org.cytoscape.model.events.ColumnCreatedEvent;
+import org.cytoscape.model.events.ColumnCreatedListener;
+import org.cytoscape.util.swing.NetworkSelectorPanel;
+import java.util.Properties;
+import org.cytoscape.model.CyColumn;
+import java.util.Collection;
+import java.util.Iterator;
+import org.cytoscape.model.CyTableUtil;
+import org.idekerlab.PanGIAPlugin.SearchTaskFactoryImpl;
-
/**
* @author kono, ghannum
*
* 5/25/10: Removed restrictions on machine-generated sections. (Greg)
*/
-public class SearchPropertyPanel extends JPanel implements
MultiHashMapDefinitionListener, PropertyChangeListener {
+public class SearchPropertyPanel extends JPanel implements
ColumnCreatedListener,
+ ItemListener {
private static final long serialVersionUID = -3352470909434196700L;
private static final double DEF_ALPHA = 1.6;
@@ -65,7 +67,11 @@
/** Creates new form SearchPropertyPanel */
- public SearchPropertyPanel() {
+ public SearchPropertyPanel(/*NetworkSelectorPanel physicalNetworkPanel,
NetworkSelectorPanel geneticNetworkPanel*/) {
+
+ this.physicalNetworkPanel = physicalNetworkPanel;
+ this.geneticNetworkPanel = geneticNetworkPanel;
+
initComponents(); // the main panel
initComponents2(); // parameter panel
@@ -99,9 +105,6 @@
// about button is a place holder for now, hide it
this.aboutButton.setVisible(true);
-
-
Cytoscape.getNodeAttributes().getMultiHashMapDefinition().addDataDefinitionListener(this);
-
Cytoscape.getEdgeAttributes().getMultiHashMapDefinition().addDataDefinitionListener(this);
updateAttributeLists();
updateScalingMethods();
@@ -113,13 +116,17 @@
this.complexRewardTextField.setText(Double.toString(DEF_COMPLEX_REWARD));
this.degreeTextField.setText(DEF_DEGREE);
this.edgeFilterTextField.setText(Double.toString(DEF_PVALUE_THRESHOLD));
-
-
Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(Cytoscape.ATTRIBUTES_CHANGED,
this);
+
+
ServicesUtil.cyServiceRegistrarServiceRef.registerAllServices(this.physicalNetworkPanel,
new Properties());
+
ServicesUtil.cyServiceRegistrarServiceRef.registerAllServices(this.geneticNetworkPanel,
new Properties());
+
+ this.physicalNetworkPanel.getJCombobox().addItemListener(this);
+ this.geneticNetworkPanel.getJCombobox().addItemListener(this);
+
}
- public void propertyChange(PropertyChangeEvent e) {
- if
(e.getPropertyName().equalsIgnoreCase(Cytoscape.ATTRIBUTES_CHANGED))
- this.updateAttributeLists();
+ public void itemStateChanged(ItemEvent itemEvent){
+ updateAttributeLists();
}
public SearchParameters getParameters() {
@@ -164,7 +171,7 @@
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
topPane.add(lbPhysicalNetwork, gridBagConstraints);
- physicalNetworkPanel.setComboBoxToolTip("Choose a network which
contains edges representing physical interactions.");
+ physicalNetworkPanel.getJCombobox().setToolTipText("Choose a network
which contains edges representing physical interactions.");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridy = 0;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
@@ -233,7 +240,7 @@
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
edgeAttributePanel.add(lbGeneticNetwork, gridBagConstraints);
- geneticNetworkPanel.setComboBoxToolTip("Choose a network which
contains edges representing genetic interactions.");
+ geneticNetworkPanel.getJCombobox().setToolTipText("Choose a network
which contains edges representing genetic interactions.");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 0;
@@ -307,7 +314,7 @@
parameterErrorTextArea.setWrapStyleWord(true);
parameterErrorTextArea.setEditable(false);
parameterErrorTextArea.setForeground(Color.blue);
-
parameterErrorTextArea.setFont(parameterErrorTextArea.getFont().deriveFont(Font.BOLD));
+//
parameterErrorTextArea.setFont(parameterErrorTextArea.getFont().deriveFont(Font.BOLD));
parameterErrorTextArea.setToolTipText("This issue must be addressed
before a search can be performed.");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridy = 5;
@@ -902,31 +909,26 @@
}
private void searchButtonActionPerformed(java.awt.event.ActionEvent
evt) {
- physicalNetworkPanel.establishSelected();
- geneticNetworkPanel.establishSelected();
+// physicalNetworkPanel.establishSelected();
+// geneticNetworkPanel.establishSelected();
// Build parameter object
if (buildSearchParameters() == false)
return;
// Run search algorithm
- JTaskConfig jTaskConfig = new JTaskConfig();
- jTaskConfig.displayCancelButton(true);
- jTaskConfig.displayCloseButton(true);
- jTaskConfig.displayStatus(true);
- jTaskConfig.displayTimeElapsed(true);
- jTaskConfig.displayTimeRemaining(false);
- jTaskConfig.setAutoDispose(false);
- jTaskConfig.setModal(false);
- jTaskConfig.setOwner(Cytoscape.getDesktop());
- TaskManager.executeTask(new SearchTask(parameters),
jTaskConfig);
+ SearchTask task = new SearchTask(parameters);
+ SearchTaskFactoryImpl factory = new SearchTaskFactoryImpl(task);
+ ServicesUtil.taskManagerServiceRef.execute(factory);
}
private void closeButtonActionPerformed(java.awt.event.ActionEvent evt)
{
+
+ System.out.println("Entering
SearchPropertyPanel.closeButtonActionPerformed()....");
// Close parent tab
- final CytoPanel cytoPanel =
Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST);
- cytoPanel.remove(this.getParent().getParent());
+// final CytoPanel cytoPanel =
Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST);
+// cytoPanel.remove(this.getParent().getParent());
}
private void aboutButtonActionPerformed(java.awt.event.ActionEvent evt)
{
@@ -1186,8 +1188,8 @@
// End of variables declaration
- private NetworkSelectorPanelX physicalNetworkPanel = new
NetworkSelectorPanelX();
- private NetworkSelectorPanelX geneticNetworkPanel = new
NetworkSelectorPanelX();
+ private NetworkSelectorPanel physicalNetworkPanel = new
NetworkSelectorPanel(ServicesUtil.cyApplicationManagerServiceRef,
ServicesUtil.cyNetworkManagerServiceRef);
+ private NetworkSelectorPanel geneticNetworkPanel = new
NetworkSelectorPanel(ServicesUtil.cyApplicationManagerServiceRef,
ServicesUtil.cyNetworkManagerServiceRef);
public void updateAttributeLists() {
// Save current selection
@@ -1203,73 +1205,134 @@
annotationAttribComboBox.removeAllItems();
nodeAttrComboBox.addItem("canonicalName");
- physicalEdgeAttribComboBox.addItem(DEFAULT_ATTRIBUTE);
- geneticEdgeAttribComboBox.addItem(DEFAULT_ATTRIBUTE);
-
+ physicalEdgeAttribComboBox.addItem(DEFAULT_ATTRIBUTE); // none
+ geneticEdgeAttribComboBox.addItem(DEFAULT_ATTRIBUTE); // none
+
//Populate the node boxes
- final CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
- final Set<String> nodeAttrNames = new
TreeSet<String>(Arrays.asList(nodeAttr.getAttributeNames()));
+ CyTable nodeAttr_phy = null;
+ Set<String> nodeAttrNames_phy = null;
+ if (this.physicalNetworkPanel.getSelectedNetwork() != null){
+ nodeAttr_phy =
this.physicalNetworkPanel.getSelectedNetwork().getDefaultNodeTable();
+ nodeAttrNames_phy =
CyTableUtil.getColumnNames(nodeAttr_phy);
+ }
+ CyTable nodeAttr_gen = null;
+ Set<String> nodeAttrNames_gen = null;
+ if (this.geneticNetworkPanel.getSelectedNetwork() != null){
+ nodeAttr_gen =
this.geneticNetworkPanel.getSelectedNetwork().getDefaultNodeTable();
+ nodeAttrNames_gen =
CyTableUtil.getColumnNames(nodeAttr_gen);
+ }
+
+ // Find common nodeAttr names for both network
+ Set<String> nodeAttrNames = null;
+ if (nodeAttrNames_phy != null){
+ nodeAttrNames = new TreeSet<String>();
+ Iterator<String> it = nodeAttrNames_phy.iterator();
+ while (it.hasNext()){
+ String name = it.next();
+ if (nodeAttrNames_gen.contains(name)){
+ nodeAttrNames.add(name);
+ }
+ }
+ }
+
boolean isNodeSelectedExist = false;
- for (String name : nodeAttrNames)
- {
- // Use only double or int attributes
- final byte attribType =
nodeAttr.getMultiHashMapDefinition().getAttributeValueType(name);
-
- if (attribType == MultiHashMapDefinition.TYPE_STRING &&
nodeAttr.getUserVisible(name) && !name.equals("canonicalName"))
+ if (nodeAttrNames != null){
+ for (String name : nodeAttrNames)
{
- nodeAttrComboBox.addItem(name);
+ // Use only double or int attributes
+ Class<?> attribType_phy =
nodeAttr_phy.getColumn(name).getType();
+ Class<?> attribType_gen =
nodeAttr_gen.getColumn(name).getType();
+ if (attribType_phy != attribType_gen){
+ continue;
+ }
- if (name.equals(nodeSelected))
isNodeSelectedExist = true;
+ if (name.equals("canonicalName")){
+ continue;
+ }
+
+ //final byte attribType =
nodeAttr.getMultiHashMapDefinition().getAttributeValueType(name);
+ //if (attribType ==
MultiHashMapDefinition.TYPE_STRING && nodeAttr.getUserVisible(name) &&
!name.equals("canonicalName"))
+
+ if (attribType_phy == Double.class ||
attribType_phy == Float.class || attribType_phy == Integer.class)
+ {
+ nodeAttrComboBox.addItem(name);
+ if (name.equals(nodeSelected))
isNodeSelectedExist = true;
+ }
}
+
+ if (isNodeSelectedExist)
nodeAttrComboBox.setSelectedItem(nodeSelected);
}
- if (isNodeSelectedExist)
nodeAttrComboBox.setSelectedItem(nodeSelected);
+ //Populate the edge box -- physical
+ CyTable edgeAttr_phy = null;
+ Set<String> edgeAttrNames_phy = null;
+ if (this.physicalNetworkPanel.getSelectedNetwork() != null){
+ edgeAttr_phy =
this.physicalNetworkPanel.getSelectedNetwork().getDefaultEdgeTable();
+ edgeAttrNames_phy =
CyTableUtil.getColumnNames(edgeAttr_phy);
+ }
+
-
- //Populate the edge boxes
- final CyAttributes edgeAttr = Cytoscape.getEdgeAttributes();
- final Set<String> edgeAttrNames = new
TreeSet<String>(Arrays.asList(edgeAttr.getAttributeNames()));
-
- boolean isGeneticEdgeSelectedExist = false;
boolean isPhysicalEdgeSelectedExist = false;
- for (String name : edgeAttrNames)
- {
- // Use only double or int attributes
- final byte attribType =
edgeAttr.getMultiHashMapDefinition().getAttributeValueType(name);
-
- if ((attribType ==
MultiHashMapDefinition.TYPE_FLOATING_POINT || attribType ==
MultiHashMapDefinition.TYPE_INTEGER) && edgeAttr.getUserVisible(name))
+ if (edgeAttrNames_phy != null){
+ for (String name : edgeAttrNames_phy)
{
- geneticEdgeAttribComboBox.addItem(name);
- physicalEdgeAttribComboBox.addItem(name);
-
- if (name.equals(geneticEdgeSelected))
isGeneticEdgeSelectedExist = true;
- if (name.equals(physicalEdgeSelected))
isPhysicalEdgeSelectedExist = true;
+ // Use only double or int attributes
+ if (edgeAttr_phy.getColumn(name).getType() ==
Double.class || edgeAttr_phy.getColumn(name).getType() == Float.class
+
||edgeAttr_phy.getColumn(name).getType() == Integer.class)
+ {
+
physicalEdgeAttribComboBox.addItem(name);
+ if (name.equals(physicalEdgeSelected))
isPhysicalEdgeSelectedExist = true;
+ }
}
+ if (isPhysicalEdgeSelectedExist)
physicalEdgeAttribComboBox.setSelectedItem(physicalEdgeSelected);
}
+
+ //Populate the edge box -- genetic
+ CyTable edgeAttr_gen = null;
+ Set<String> edgeAttrNames_gen = null;
- if (isGeneticEdgeSelectedExist)
geneticEdgeAttribComboBox.setSelectedItem(geneticEdgeSelected);
- if (isPhysicalEdgeSelectedExist)
physicalEdgeAttribComboBox.setSelectedItem(physicalEdgeSelected);
+ if (this.geneticNetworkPanel.getSelectedNetwork() != null){
+ edgeAttr_gen =
this.geneticNetworkPanel.getSelectedNetwork().getDefaultEdgeTable();
+ edgeAttrNames_gen =
CyTableUtil.getColumnNames(edgeAttr_gen);
+ }
+ boolean isGeneticEdgeSelectedExist = false;
+ if (edgeAttrNames_gen != null){
+ for (String name : edgeAttrNames_gen)
+ {
+ // Use only double or int attributes
+ if (edgeAttr_gen.getColumn(name).getType() ==
Double.class || edgeAttr_gen.getColumn(name).getType() == Float.class
+
||edgeAttr_gen.getColumn(name).getType() == Integer.class)
+ {
+ geneticEdgeAttribComboBox.addItem(name);
+
+ if (name.equals(geneticEdgeSelected))
isGeneticEdgeSelectedExist = true;
+ }
+ }
+ if (isGeneticEdgeSelectedExist)
geneticEdgeAttribComboBox.setSelectedItem(geneticEdgeSelected);
+ }
+
+
//Populate the annotation box
boolean isAnnotSelectedExist = false;
- for (String name : nodeAttrNames)
- {
- // Use only string attributes
- final byte attribType =
nodeAttr.getMultiHashMapDefinition().getAttributeValueType(name);
- if (attribType == MultiHashMapDefinition.TYPE_STRING &&
nodeAttr.getUserVisible(name) && !name.equals("canonicalName"))
+ if (nodeAttrNames != null){
+ for (String name : nodeAttrNames)
{
- annotationAttribComboBox.addItem(name);
-
- if (name.equals(geneticEdgeSelected))
isAnnotSelectedExist = true;
+ // Use only string attributes
+ Class<?> attribType =
nodeAttr_phy.getColumn(name).getType();
+ if (attribType == String.class &&
!name.equals("canonicalName")){
+ annotationAttribComboBox.addItem(name);
+ if (name.equals(geneticEdgeSelected))
isAnnotSelectedExist = true;
+ }
}
+
+ if (isAnnotSelectedExist)
+
annotationAttribComboBox.setSelectedItem(annotSelected);
}
- if (isAnnotSelectedExist)
- annotationAttribComboBox.setSelectedItem(annotSelected);
-
updateSearchButtonState();
}
@@ -1460,8 +1523,10 @@
String physicalSelected =
physicalEdgeAttribComboBox.getSelectedItem().toString();
- if
(!physicalSelected.trim().equalsIgnoreCase(DEFAULT_ATTRIBUTE) &&
(Cytoscape.getEdgeAttributes().getType(physicalSelected) !=
CyAttributes.TYPE_INTEGER &&
-
Cytoscape.getEdgeAttributes().getType(physicalSelected) !=
CyAttributes.TYPE_FLOATING))
+ Class<?> attrType =
this.physicalNetworkPanel.getSelectedNetwork().getDefaultEdgeTable().getColumn(physicalSelected).getType();
+
+ if
(!physicalSelected.trim().equalsIgnoreCase(DEFAULT_ATTRIBUTE) && (attrType !=
Integer.class &&
+ attrType != Double.class))
{
searchButton.setEnabled(false);
parameterErrorTextArea.setText("Please choose physical
edge scores of type integer or float.");
@@ -1469,12 +1534,18 @@
}
String geneticSelected =
geneticEdgeAttribComboBox.getSelectedItem().toString();
- if (!geneticSelected.trim().equalsIgnoreCase(DEFAULT_ATTRIBUTE)
&& (Cytoscape.getEdgeAttributes().getType(geneticSelected) !=
CyAttributes.TYPE_INTEGER &&
-
Cytoscape.getEdgeAttributes().getType(geneticSelected) !=
CyAttributes.TYPE_FLOATING))
- {
- searchButton.setEnabled(false);
- parameterErrorTextArea.setText("Please choose genetic
edge scores of type integer or float.");
- return;
+ if (this.geneticNetworkPanel.getSelectedNetwork() != null &&
+
this.geneticNetworkPanel.getSelectedNetwork().getDefaultEdgeTable().getColumn(geneticSelected)
!= null){
+
+ Class<?> attrType2 =
this.geneticNetworkPanel.getSelectedNetwork().getDefaultEdgeTable().getColumn(geneticSelected).getType();
+
+ if
(!geneticSelected.trim().equalsIgnoreCase(DEFAULT_ATTRIBUTE) && (attrType2 !=
Integer.class &&
+ attrType2 != Double.class))
+ {
+ searchButton.setEnabled(false);
+ parameterErrorTextArea.setText("Please choose
genetic edge scores of type integer or float.");
+ return;
+ }
}
if ((annotationCheckBox.isSelected() ||
trainingCheckBox.isSelected()) && annotationAttribComboBox.getSelectedIndex()<0)
@@ -1482,7 +1553,7 @@
searchButton.setEnabled(false);
parameterErrorTextArea.setText("To use annotation,
please choose an annotation node attribute.");
return;
- }
+ }
//TextField validity
@@ -1612,4 +1683,8 @@
parameterErrorTextArea.setText("");
searchButton.setEnabled(true);
}
+
+ public void handleEvent(ColumnCreatedEvent e){
+ updateAttributeLists();
+ }
}
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