Author: jm
Date: 2012-05-01 13:59:19 -0700 (Tue, 01 May 2012)
New Revision: 29063
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/SettingsAction.java
Log:
Fixes #923: Added "selected only" and attribute-based weighting options to
LayoutSettingsDialog
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
2012-05-01 20:44:51 UTC (rev 29062)
+++
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
2012-05-01 20:59:19 UTC (rev 29063)
@@ -116,6 +116,7 @@
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.view.model.events.NetworkViewChangedListener;
import org.cytoscape.view.model.events.NetworkViewDestroyedListener;
import org.cytoscape.view.presentation.RenderingEngineFactory;
import org.cytoscape.view.presentation.RenderingEngineManager;
@@ -281,6 +282,7 @@
registerService(bc, preferenceAction, CyAction.class, new
Properties());
registerService(bc, bookmarkAction, CyAction.class, new
Properties());
registerService(bc, settingsAction, CyAction.class, new
Properties());
+ registerService(bc, settingsAction,
SetCurrentNetworkViewListener.class, new Properties());
registerService(bc, cytoPanelWestAction, CyAction.class, new
Properties());
registerService(bc, cytoPanelSouthAction, CyAction.class, new
Properties());
registerService(bc, cytoPanelEastAction, CyAction.class, new
Properties());
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
===================================================================
---
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
2012-05-01 20:44:51 UTC (rev 29062)
+++
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
2012-05-01 20:59:19 UTC (rev 29063)
@@ -34,12 +34,15 @@
import java.awt.Color;
import java.awt.Component;
import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.GridLayout;
+import java.awt.Insets;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.util.Collections;
-import java.util.HashMap;
+import java.util.ArrayList;
import java.util.HashSet;
-import java.util.Map;
+import java.util.List;
import java.util.Properties;
import java.util.Set;
@@ -60,8 +63,10 @@
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.internal.task.DynamicTaskFactoryProvisioner;
+import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyTable;
import org.cytoscape.property.CyProperty;
import org.cytoscape.task.NetworkViewTaskFactory;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
@@ -70,7 +75,9 @@
import org.cytoscape.view.model.View;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
+import org.cytoscape.work.Tunable;
import org.cytoscape.work.swing.PanelTaskManager;
+import org.cytoscape.work.util.ListSingleSelection;
/**
@@ -81,7 +88,8 @@
*/
public class LayoutSettingsDialog extends JDialog implements ActionListener {
private final static long serialVersionUID = 1202339874277105L;
- private TaskFactory currentLayout = null;
+ private CyLayoutAlgorithm currentLayout;
+ private TaskFactory currentAction = null;
// Dialog components
private JLabel titleLabel; // Our title
@@ -97,6 +105,9 @@
private CyProperty cytoscapePropertiesServiceRef;
private DynamicTaskFactoryProvisioner factoryProvisioner;
private boolean initialized;
+ private LayoutAttributeTunable layoutAttributeTunable;
+ private JPanel layoutAttributePanel;
+ private final SelectedTunable selectedTunable;
/**
* Creates a new LayoutSettingsDialog object.
@@ -120,6 +131,8 @@
this.cytoscapePropertiesServiceRef =
cytoscapePropertiesServiceRef;
this.factoryProvisioner = new
DynamicTaskFactoryProvisioner(appMgr);
+ selectedTunable = new SelectedTunable();
+
Properties props =
(Properties)this.cytoscapePropertiesServiceRef.getProperties();
//
@@ -141,7 +154,7 @@
if (command.equals("done"))
setVisible(false);
else if (command.equals("execute")) {
- taskManager.execute(currentLayout.createTaskIterator());
+ taskManager.execute(currentAction.createTaskIterator());
} else {
// OK, initialize and display
if (isVisible()) {
@@ -152,6 +165,7 @@
setLocationRelativeTo(desktop.getJFrame());
pack();
}
+ setNetworkView(appMgr.getCurrentNetworkView());
setVisible(true);
initialized = true;
}
@@ -326,8 +340,9 @@
mainPanel.add(algorithmSelectorPanel);
// Create a panel for algorithm's content
- this.algorithmPanel = new JPanel(new BorderLayout(10, 10));
+ this.algorithmPanel = new JPanel();
algorithmPanel.setAutoscrolls(true);
+ algorithmPanel.setLayout(new GridBagLayout());
mainPanel.add(algorithmPanel);
// Create a panel for our button box
@@ -375,41 +390,126 @@
Object o = algorithmSelector.getSelectedItem();
// if it's a string, that means it's the instructions
if (!(o instanceof String)) {
- final CyLayoutAlgorithm newLayout =
(CyLayoutAlgorithm)o;
+ currentLayout = (CyLayoutAlgorithm)o;
//Checking if the context has already been
charged, if so there is no need to do it again
- Object context =
newLayout.getDefaultLayoutContext();
+ Object context =
currentLayout.getDefaultLayoutContext();
- TaskFactory provisioner =
factoryProvisioner.createFor(wrapWithContext(newLayout, context));
+ TaskFactory provisioner =
factoryProvisioner.createFor(wrapWithContext(currentLayout, context));
if (!provisioner.isReady()) {
throw new
IllegalArgumentException("Layout is not fully configured");
}
JPanel tunablePanel =
taskManager.getConfiguration(provisioner, context);
+ int row = 0;
if (tunablePanel == null){
-
JOptionPane.showMessageDialog(LayoutSettingsDialog.this, "Can not change
setting for this algorithm, because tunable info is not avialable!", "Warning",
JOptionPane.WARNING_MESSAGE);
+
JOptionPane.showMessageDialog(LayoutSettingsDialog.this, "Can not change
setting for this algorithm, because tunable info is not available!", "Warning",
JOptionPane.WARNING_MESSAGE);
algorithmPanel.removeAll();
}
else {
algorithmPanel.removeAll();
- algorithmPanel.add(tunablePanel);
+ algorithmPanel.add(tunablePanel, new
GridBagConstraints(0, row++, 1, 1, 1, 1, GridBagConstraints.PAGE_START,
GridBagConstraints.HORIZONTAL, new Insets(0, 0, 0, 0), 0, 0));
}
- currentLayout = provisioner;
+
+ layoutAttributePanel = new JPanel();
+ layoutAttributePanel.setLayout(new
GridLayout());
+ algorithmPanel.add(layoutAttributePanel, new
GridBagConstraints(0, row++, 1, 1, 1, 1, GridBagConstraints.PAGE_START,
GridBagConstraints.HORIZONTAL, new Insets(0, 0, 0, 0), 0, 0));
+
+ CyNetworkView view =
appMgr.getCurrentNetworkView();
+ setNetworkView(view);
+
+ if (currentLayout.getSupportsSelectedOnly()) {
+ selectedTunable.selectedNodesOnly =
hasSelectedNodes(view);
+ JPanel panel =
taskManager.getConfiguration(null, selectedTunable);
+ algorithmPanel.add(panel, new
GridBagConstraints(0, row++, 1, 1, 1, 1, GridBagConstraints.PAGE_START,
GridBagConstraints.HORIZONTAL, new Insets(0, 0, 0, 0), 0, 0));
+ }
+ currentAction = provisioner;
LayoutSettingsDialog.this.pack();
}
}
}
+ void setNetworkView(CyNetworkView view) {
+ if (layoutAttributePanel == null) {
+ return;
+ }
+ layoutAttributePanel.removeAll();
+ layoutAttributeTunable = new LayoutAttributeTunable();
+ if (view != null) {
+ List<String> attributeList =
getAttributeList(view.getModel(),
currentLayout.getSupportedNodeAttributeTypes(),
currentLayout.getSupportedEdgeAttributeTypes());
+ if (attributeList.size() > 0) {
+ layoutAttributeTunable.layoutAttribute = new
ListSingleSelection<String>(attributeList);
+
layoutAttributeTunable.layoutAttribute.setSelectedValue(attributeList.get(0));
+ JPanel panel =
taskManager.getConfiguration(null, layoutAttributeTunable);
+ layoutAttributePanel.add(panel);
+ panel.invalidate();
+ }
+ }
+ }
+
+ private boolean hasSelectedNodes(CyNetworkView view) {
+ CyNetwork network = view.getModel();
+ for (CyNode node : network.getNodeList()) {
+ if (network.getRow(node).get(CyNetwork.SELECTED,
Boolean.class)) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ private List<String> getAttributeList(CyNetwork network, Set<Class<?>>
allowedNodeAttributeTypes, Set<Class<?>> allowedEdgeAttributeTypes) {
+ List<String> attributes = new ArrayList<String>();
+ Set<Class<?>> allowedTypes;
+ CyTable table;
+ if (allowedNodeAttributeTypes.size() > 0) {
+ allowedTypes = allowedNodeAttributeTypes;
+ table = network.getDefaultNodeTable();
+ } else if (allowedEdgeAttributeTypes.size() > 0) {
+ allowedTypes = allowedEdgeAttributeTypes;
+ table = network.getDefaultEdgeTable();
+ } else {
+ return attributes;
+ }
+
+ for (final CyColumn column : table.getColumns()) {
+ if (allowedTypes.contains(column.getType())) {
+ attributes.add(column.getName());
+ }
+ }
+ return attributes;
+ }
+
+ private String getLayoutAttribute() {
+ if (layoutAttributeTunable == null ||
layoutAttributeTunable.layoutAttribute == null) {
+ return null;
+ }
+ return
layoutAttributeTunable.layoutAttribute.getSelectedValue();
+ }
+
+ private Set<View<CyNode>> getLayoutNodes(CyLayoutAlgorithm layout,
CyNetworkView networkView) {
+ if (layout.getSupportsSelectedOnly() &&
selectedTunable.selectedNodesOnly) {
+ Set<View<CyNode>> nodeViews = new
HashSet<View<CyNode>>();
+ CyNetwork network = networkView.getModel();
+ for (View<CyNode> view : networkView.getNodeViews()) {
+ if
(network.getRow(view.getModel()).get(CyNetwork.SELECTED, Boolean.class)) {
+ nodeViews.add(view);
+ }
+ }
+ return nodeViews;
+ }
+ return CyLayoutAlgorithm.ALL_NODE_VIEWS;
+ }
+
private NetworkViewTaskFactory wrapWithContext(final CyLayoutAlgorithm
layout, final Object tunableContext) {
return new NetworkViewTaskFactory() {
@Override
public boolean isReady(CyNetworkView networkView) {
- return layout.isReady(networkView,
tunableContext, CyLayoutAlgorithm.ALL_NODE_VIEWS,"");
+ return layout.isReady(networkView,
tunableContext, getLayoutNodes(layout, networkView), getLayoutAttribute());
}
@Override
public TaskIterator createTaskIterator(CyNetworkView
networkView) {
- return layout.createTaskIterator(networkView,
tunableContext, CyLayoutAlgorithm.ALL_NODE_VIEWS,"");
+ return layout.createTaskIterator(networkView,
tunableContext, getLayoutNodes(layout, networkView), getLayoutAttribute());
}
};
}
@@ -448,4 +548,14 @@
return this;
}
}
+
+ public static class SelectedTunable {
+ @Tunable(description="Layout only selected nodes")
+ public boolean selectedNodesOnly;
+ }
+
+ public static class LayoutAttributeTunable {
+ @Tunable(description="Weight using")
+ public ListSingleSelection<String> layoutAttribute;
+ }
}
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/SettingsAction.java
===================================================================
---
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/SettingsAction.java
2012-05-01 20:44:51 UTC (rev 29062)
+++
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/SettingsAction.java
2012-05-01 20:59:19 UTC (rev 29063)
@@ -31,6 +31,8 @@
import org.cytoscape.application.CyApplicationManager;
+import org.cytoscape.application.events.SetCurrentNetworkViewEvent;
+import org.cytoscape.application.events.SetCurrentNetworkViewListener;
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.application.swing.AbstractCyAction;
import org.cytoscape.property.CyProperty;
@@ -41,7 +43,7 @@
import java.awt.event.ActionEvent;
-public class SettingsAction extends AbstractCyAction {
+public class SettingsAction extends AbstractCyAction implements
SetCurrentNetworkViewListener {
private final static long serialVersionUID = 1202339874289357L;
private CyLayoutAlgorithmManager cyl;
@@ -70,4 +72,9 @@
public void actionPerformed(ActionEvent e) {
settingsDialog.actionPerformed(e);
}
+
+ @Override
+ public void handleEvent(SetCurrentNetworkViewEvent e) {
+ settingsDialog.setNetworkView(e.getNetworkView());
+ }
}
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