Author: scooter
Date: 2010-11-22 22:28:44 -0800 (Mon, 22 Nov 2010)
New Revision: 22991
Added:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/NodeCharts.java
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodeGroupViewer.java
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodePlugin2.java
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNodeManager.java
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/ViewUtils.java
Log:
Added NodeChart functionality. Not done, yet...
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodeGroupViewer.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodeGroupViewer.java
2010-11-23 00:23:56 UTC (rev 22990)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodeGroupViewer.java
2010-11-23 06:28:44 UTC (rev 22991)
@@ -42,6 +42,7 @@
import cytoscape.Cytoscape;
import cytoscape.view.CyNetworkView;
+import cytoscape.command.CyCommandHandler;
import cytoscape.command.CyCommandManager;
import cytoscape.command.CyCommandResult;
@@ -60,6 +61,7 @@
import metaNodePlugin2.model.MetanodeProperties;
import metaNodePlugin2.ui.MetanodeMenuListener;
import metaNodePlugin2.ui.MetanodeSettingsDialog;
+import metaNodePlugin2.view.NodeCharts;
/**
*
@@ -72,8 +74,10 @@
CyGroupViewer namedSelectionViewer = null;
MetanodeSettingsDialog settingsDialog = null;
boolean registeredWithGroupPanel = false;
+ boolean haveNodeCharts = false;
private static String NAMEDSELECTION = "namedselection";
+ private static String NODECHARTS = "nodecharts";
public MetaNodeGroupViewer (String viewerName, CyLogger logger) {
this.viewerName = viewerName;
@@ -86,9 +90,6 @@
} catch (Exception e) {
logger.error(e.getMessage(),e);
}
-
- // Tell the group panel we want to use it
- registerWithGroupPanel();
}
/**
@@ -227,16 +228,50 @@
} else if (change == CyGroupViewer.ChangeType.STATE_CHANGED) {
// Handle different representations here....
if (group.getState() == MetaNodePlugin2.COLLAPSED &&
!mn.isCollapsed()) {
+ System.out.println("Collapsing");
// Actually collapse the group
mn.collapse(Cytoscape.getCurrentNetworkView());
// Handle our attributes
AttributeManager.updateAttributes(mn);
+ if (haveNodeCharts) {
+ // Handle our node charts
+ System.out.println("Updating node
charts");
+ NodeCharts.updateNodeCharts(mn, logger);
+ }
} else if (group.getState() == MetaNodePlugin2.EXPANDED
&& mn.isCollapsed()) {
mn.expand(Cytoscape.getCurrentNetworkView());
}
}
}
+ public boolean haveNodeCharts() {
+ if (!haveNodeCharts)
+ haveNodeCharts = checkNodeCharts();
+ return haveNodeCharts;
+ }
+
+ public List<String> getChartTypes() {
+ try {
+ Map<String,Object> args = new HashMap<String,Object>();
+ CyCommandResult result =
CyCommandManager.execute(NODECHARTS, "list", args);
+ Object chartTypes = result.getResult("typeList");
+ if (chartTypes instanceof List)
+ return (List<String>)chartTypes;
+ } catch (Exception e) {
+ logger.info(e.getMessage());
+ }
+ return new ArrayList<String>();
+ }
+
+ public boolean checkNodeCharts() {
+ try {
+ CyCommandManager.getCommand(NODECHARTS, "clear");
+ } catch (RuntimeException e) {
+ return false;
+ }
+ return true;
+ }
+
private void updateGroupPanel() {
if (!registeredWithGroupPanel) {
registerWithGroupPanel();
@@ -269,10 +304,20 @@
}
public void registerWithGroupPanel() {
+ // First, see if the named selection plugin is loaded
+ CyCommandHandler handler = null;
+
+ registeredWithGroupPanel = false; // probably redundant
try {
+ handler = CyCommandManager.getCommand(NAMEDSELECTION,
"add viewer");
+ } catch (RuntimeException e) {
+ return;
+ }
+
+ try {
Map<String,Object> args = new HashMap<String,Object>();
args.put("viewer",viewerName);
- CyCommandResult result =
CyCommandManager.execute(NAMEDSELECTION, "add viewer", args);
+ CyCommandResult result = handler.execute("add viewer",
args);
if (result.getErrors() != null &&
result.getErrors().size() > 0) {
for (String error: result.getErrors())
logger.warning(error);
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodePlugin2.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodePlugin2.java
2010-11-23 00:23:56 UTC (rev 22990)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodePlugin2.java
2010-11-23 06:28:44 UTC (rev 22991)
@@ -119,11 +119,8 @@
public static final int EXPANDED = 1;
public static final int COLLAPSED = 2;
- private static boolean registeredWithGroupPanel = false;
-
private static boolean addedGraphViewChangeListener = false;
- private MetanodeSettingsDialog settingsDialog = null;
private MetaNodeGroupViewer groupViewer = null;
protected int descendents = 0;
@@ -132,6 +129,7 @@
* The main constructor
*/
public MetaNodePlugin2() {
+
logger = CyLogger.getLogger(MetaNodePlugin2.class);
// Register with CyGroup
groupViewer = new MetaNodeGroupViewer(viewerName, logger);
@@ -146,6 +144,9 @@
Cytoscape.getDesktop().getSwingPropertyChangeSupport()
.addPropertyChangeListener(
CytoscapeDesktop.NETWORK_VIEW_FOCUSED, this);
+ Cytoscape.getPropertyChangeSupport()
+ .addPropertyChangeListener(
Cytoscape.CYTOSCAPE_INITIALIZED, this);
+
// Add our context menu
Cytoscape.getCurrentNetworkView().addNodeContextMenuListener(this);
Cytoscape.getCurrentNetworkView().addGraphViewChangeListener(this);
@@ -181,6 +182,11 @@
// Load the default aggregation values for this network
groupViewer.getSettingsDialog().updateOverrides(Cytoscape.getCurrentNetwork());
//
MetaNodeManager.newView(Cytoscape.getCurrentNetworkView());
+ } else if (e.getPropertyName() ==
Cytoscape.CYTOSCAPE_INITIALIZED) {
+ // Handle interaction with other plugins
+ groupViewer.registerWithGroupPanel();
+ groupViewer.haveNodeCharts();
+ groupViewer.getSettingsDialog().updateNodeChartTypes();
}
}
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
2010-11-23 00:23:56 UTC (rev 22990)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
2010-11-23 06:28:44 UTC (rev 22991)
@@ -85,6 +85,8 @@
private boolean hideMetanode = true;
private double metanodeOpacity = 0.;
private boolean useNestedNetworks = false;
+ private String nodeChartAttribute = null;
+ private String chartType = null;
private Map<CyEdge,CyEdge> metaEdges = new HashMap<CyEdge,CyEdge>();
private Map<CyNode,CyEdge> membershipEdges = null;
@@ -340,6 +342,32 @@
}
/**
+ * Sets the attribute to use node charting
+ *
+ * @param attribute the attribute to use for node charting
+ */
+ public void setNodeChartAttribute(String nodeChartAttribute) {
+ this.nodeChartAttribute = nodeChartAttribute;
+ }
+
+ public String getNodeChartAttribute() {
+ return this.nodeChartAttribute;
+ }
+
+ /**
+ * Sets the node chart type
+ *
+ * @param chartType the chart type
+ */
+ public void setChartType(String chartType) {
+ this.chartType = chartType;
+ }
+
+ public String getChartType() {
+ return this.chartType;
+ }
+
+ /**
* Sets whether or not we hide the metnode when we expand the
* network.
*
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNodeManager.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNodeManager.java
2010-11-23 00:23:56 UTC (rev 22990)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNodeManager.java
2010-11-23 06:28:44 UTC (rev 22991)
@@ -58,6 +58,8 @@
protected static boolean hideMetanodeDefault = true;
protected static double metanodeOpacityDefault = 255.;
protected static boolean useNestedNetworksDefault = false;
+ protected static String chartTypeDefault = null;
+ protected static String nodeChartAttributeDefault = null;
public static final String X_HINT_ATTR = "__metanodeHintX";
public static final String Y_HINT_ATTR = "__metanodeHintY";
@@ -88,6 +90,8 @@
mn.setUseNestedNetworks(useNestedNetworksDefault);
mn.setHideMetaNode(hideMetanodeDefault);
mn.setMetaNodeOpacity(metanodeOpacityDefault);
+ mn.setChartType(chartTypeDefault);
+ mn.setNodeChartAttribute(nodeChartAttributeDefault);
if (metaGroup.getNetwork() == null) {
metaGroup.setNetwork(Cytoscape.getCurrentNetwork(),
false);
}
@@ -222,4 +226,40 @@
static public boolean getUseNestedNetworksDefault() {
return MetaNodeManager.useNestedNetworksDefault;
}
+
+ /**
+ * Sets the attribute to use for node charting.
+ *
+ * @param nodeChartAttribute the attribute to use for node charts
+ */
+ static public void setNodeChartAttributeDefault(String
nodeChartAttribute) {
+ MetaNodeManager.nodeChartAttributeDefault = nodeChartAttribute;
+ }
+
+ /**
+ * Gets the attribute to use for node charting.
+ *
+ * @return the attribute to use for node charts
+ */
+ static public String getNodeChartAttributeDefault() {
+ return MetaNodeManager.nodeChartAttributeDefault;
+ }
+
+ /**
+ * Sets the chart type to use for node charting.
+ *
+ * @param chartType the chart type to use for node charts
+ */
+ static public void setChartTypeDefault(String chartType) {
+ MetaNodeManager.chartTypeDefault = chartType;
+ }
+
+ /**
+ * Gets the node chart type.
+ *
+ * @return the node chart type
+ */
+ static public String getChartTypeDefault() {
+ return MetaNodeManager.chartTypeDefault;
+ }
}
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
2010-11-23 00:23:56 UTC (rev 22990)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
2010-11-23 06:28:44 UTC (rev 22991)
@@ -38,6 +38,7 @@
*/
package metaNodePlugin2.ui;
+import metaNodePlugin2.MetaNodeGroupViewer;
import metaNodePlugin2.model.MetaNode;
import metaNodePlugin2.model.MetaNodeManager;
import metaNodePlugin2.model.MetanodeProperties;
@@ -92,18 +93,24 @@
private Tunable typeString = null;
private Tunable typeList = null;
private Tunable attrList = null;
+ private Tunable nodeChartAttrList = null;
+ private Tunable nodeChartTypeList = null;
private String[] attributeArray = null;
private List<Tunable>tunableEnablers = null;
+ private List<Tunable>nodeChartEnablers = null;
private boolean hideMetaNode = true;
private boolean enableHandling = false;
private boolean useNestedNetworks = false;
private double metanodeOpacity = 255.0f;
- private CyGroupViewer groupViewer = null;
+ private String chartType = null;
+ private String nodeChartAttribute = null;
+ private MetaNodeGroupViewer groupViewer = null;
+ private static String NONETYPE = "-- None --";
// Dialog components
JPanel tunablePanel = null;
- public MetanodeSettingsDialog(CyGroupViewer viewer) {
+ public MetanodeSettingsDialog(MetaNodeGroupViewer viewer) {
super(Cytoscape.getDesktop(), "Metanode Settings Dialog",
false);
metanodeProperties = new MetanodeProperties("metanode");
this.groupViewer = viewer;
@@ -181,31 +188,34 @@
}
private void initializeProperties() {
- tunableEnablers = new ArrayList();
+ tunableEnablers = new ArrayList<Tunable>();
+ nodeChartEnablers = new ArrayList<Tunable>();
metanodeProperties.add(new Tunable("appearanceGroup", "Metanode
Appearance",
Tunable.GROUP, new
Integer(2),
new Boolean(true), null,
Tunable.COLLAPSABLE));
{
- Tunable t = new Tunable("useNestedNetworks",
- "Create a nested network for
collapsed metanodes",
- Tunable.BOOLEAN, new
Boolean(false), 0);
- t.addTunableValueListener(this);
- metanodeProperties.add(t);
- }
+ {
+ Tunable t = new Tunable("useNestedNetworks",
+ "Create a nested
network for collapsed metanodes",
+ Tunable.BOOLEAN, new
Boolean(false), 0);
+ t.addTunableValueListener(this);
+ metanodeProperties.add(t);
+ }
- // Sliders always look better when grouped
- metanodeProperties.add(new Tunable("opacityGroup", "Metanode
Opacity",
- Tunable.GROUP, new
Integer(1),
- null, null, 0));
+ // Sliders always look better when grouped
+ metanodeProperties.add(new Tunable("opacityGroup",
"Metanode Opacity",
+ Tunable.GROUP, new
Integer(1),
+ null, null, 0));
- {
- Tunable t = new Tunable("metanodeOpacity",
- "Percent opacity of collapsed
metanodes",
- Tunable.DOUBLE, new Double(0),
new Double(0), new Double(100), Tunable.USESLIDER);
- t.addTunableValueListener(this);
- metanodeProperties.add(t);
+ {
+ Tunable t = new Tunable("metanodeOpacity",
+ "Percent opacity of
collapsed metanodes",
+ Tunable.DOUBLE, new
Double(0), new Double(0), new Double(100), Tunable.USESLIDER);
+ t.addTunableValueListener(this);
+ metanodeProperties.add(t);
+ }
}
{
@@ -216,6 +226,32 @@
metanodeProperties.add(t);
}
+ // If we have nodeCharts, provide chart options for aggregated
attributes
+ {
+ Tunable t = new Tunable("nodeChartsGroup", "Node Chart
Options",
+ Tunable.GROUP, new Integer(2),
+ new Boolean(true), null,
Tunable.COLLAPSABLE);
+ metanodeProperties.add(t);
+
+ {
+ // Get the attribute to map
+ nodeChartAttrList = new
Tunable("nodeChartAttribute", "Attribute to use for node chart",
+ Tunable.LIST,
new Integer(0),
+
getNodeAttributes(), null, 0);
+ nodeChartEnablers.add(nodeChartAttrList);
+ metanodeProperties.add(nodeChartAttrList);
+ nodeChartAttrList.addTunableValueListener(this);
+
+ // Get the chart type (might change depending
on the chart type)
+ nodeChartTypeList = new Tunable("chartType",
"Chart type",
+ Tunable.LIST,
new Integer(0),
+
getChartTypes(), null, 0);
+ nodeChartEnablers.add(nodeChartTypeList);
+ metanodeProperties.add(nodeChartTypeList);
+ nodeChartTypeList.addTunableValueListener(this);
+ }
+ }
+
metanodeProperties.add(new Tunable("defaultsGroup", "Defaults",
Tunable.GROUP, new
Integer(5),
new Boolean(true), null,
Tunable.COLLAPSABLE));
@@ -316,7 +352,21 @@
metanodeProperties.setProperty(t.getName(),
t.getValue().toString());
}
+ t = metanodeProperties.get("nodeChartAttribute");
+ if ((t != null) && (t.valueChanged() || force)) {
+ nodeChartAttribute = (String)getListValue(t);
+
MetaNodeManager.setNodeChartAttributeDefault(nodeChartAttribute);
+ metanodeProperties.setProperty(t.getName(),
t.getValue().toString());
+ }
+ t = metanodeProperties.get("chartType");
+ if ((t != null) && (t.valueChanged() || force)) {
+ chartType = (String)getListValue(t);
+ MetaNodeManager.setChartTypeDefault(chartType);
+ metanodeProperties.setProperty(t.getName(),
t.getValue().toString());
+ }
+
+
// For each default value, get the default and set it
t = metanodeProperties.get("stringDefaults");
if ((t != null) && (t.valueChanged() || force)) {
@@ -360,8 +410,17 @@
public void updateAttributes() {
attrList.setLowerBound(getAttributes());
+ nodeChartAttrList.setLowerBound(getNodeAttributes());
}
+ public void updateNodeChartTypes() {
+ if (groupViewer.checkNodeCharts()) {
+ enableNodeCharts(true);
+ nodeChartTypeList.setLowerBound(getChartTypes());
+ } else
+ enableNodeCharts(false);
+ }
+
public boolean getUseNestedNetworks() {
updateSettings(false);
String bv =
(String)metanodeProperties.getProperties().get("useNestedNetworks");
@@ -369,6 +428,16 @@
return useNestedNetworks;
}
+ private String[] getNodeAttributes() {
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ List<String> attributeList = new ArrayList();
+ makeAttributes(null, nodeAttributes, attributeList);
+ String [] a = new String[1];
+ attributeArray = attributeList.toArray(a);
+ Arrays.sort(attributeArray);
+ return attributeArray;
+ }
+
private String[] getAttributes() {
CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
@@ -382,13 +451,25 @@
return attributeArray;
}
+ private String[] getChartTypes() {
+ String [] a = new String[1];
+ List<String> viewerList = groupViewer.getChartTypes();
+ viewerList.add(NONETYPE);
+ String [] viewerArray = viewerList.toArray(a);
+ Arrays.sort(viewerArray);
+ return viewerArray;
+ }
+
private void makeAttributes(String prefix, CyAttributes attrs,
List<String>list) {
// Build a list
String[] names = attrs.getAttributeNames();
for (int i = 0; i < names.length; i++) {
if (!attrs.getUserVisible(names[i]))
continue;
- list.add(prefix+"."+names[i]);
+ if (prefix != null)
+ list.add(prefix+"."+names[i]);
+ else
+ list.add(names[i]);
}
}
@@ -422,12 +503,7 @@
for (CyNode node: nodeList) {
MetaNode mn = MetaNodeManager.getMetaNode(node);
if (mn != null) {
-
mn.setUseNestedNetworks(useNestedNetworks);
- //
mn.setSizeToBoundingBox(sizeToBoundingBox);
- mn.setHideMetaNode(hideMetaNode);
-
mn.setAggregateAttributes(enableHandling);
- // System.out.println("setting opacity
for "+mn+" to "+metanodeOpacity);
- mn.setMetaNodeOpacity(metanodeOpacity);
+ updateMetaNodeSettings(mn);
}
}
setVisible(false);
@@ -440,12 +516,7 @@
for (CyGroup group: groupList) {
MetaNode mn =
MetaNodeManager.getMetaNode(group);
if (mn != null) {
-
mn.setUseNestedNetworks(useNestedNetworks);
- //
mn.setSizeToBoundingBox(sizeToBoundingBox);
-
mn.setHideMetaNode(hideMetaNode);
-
mn.setAggregateAttributes(enableHandling);
- // System.out.println("setting
opacity for "+mn+" to "+metanodeOpacity);
-
mn.setMetaNodeOpacity(metanodeOpacity);
+ updateMetaNodeSettings(mn);
}
}
}
@@ -453,6 +524,17 @@
}
}
+ private void updateMetaNodeSettings(MetaNode mn) {
+ mn.setUseNestedNetworks(useNestedNetworks);
+ // mn.setSizeToBoundingBox(sizeToBoundingBox);
+ mn.setHideMetaNode(hideMetaNode);
+ mn.setAggregateAttributes(enableHandling);
+ // System.out.println("setting opacity for "+mn+" to
"+metanodeOpacity);
+ mn.setMetaNodeOpacity(metanodeOpacity);
+ mn.setChartType(chartType);
+ mn.setNodeChartAttribute(nodeChartAttribute);
+ }
+
public void tunableChanged(Tunable t) {
if (t.getName().equals("hideMetanodes")) {
hideMetaNode = ((Boolean) t.getValue()).booleanValue();
@@ -467,6 +549,12 @@
enableHandling = ((Boolean) t.getValue()).booleanValue();
AttributeManager.setEnable(enableHandling);
enableTunables(enableHandling);
+ } else if (t.getName().equals("nodeChartAttribute")) {
+ nodeChartAttribute = (String)getListValue(t);
+
MetaNodeManager.setNodeChartAttributeDefault(nodeChartAttribute);
+ } else if (t.getName().equals("chartType")) {
+ chartType = (String)getListValue(t);
+ MetaNodeManager.setChartTypeDefault(chartType);
} else if (t.getName().equals("attributeList")) {
CyAttributes attrs = null;
@@ -569,6 +657,15 @@
pack();
}
+ private void enableNodeCharts(boolean enableHandling) {
+ for (Tunable t: nodeChartEnablers) {
+ // System.out.println("Setting immutable for "+t+" to
"+(!enableHandling));
+ t.setImmutable(!enableHandling);
+ }
+ doLayout();
+ pack();
+ }
+
private void modifyVizMap() {
// Get the current Visual Style
VisualStyle currentStyle =
Cytoscape.getCurrentNetworkView().getVisualStyle();
Added:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/NodeCharts.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/NodeCharts.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/NodeCharts.java
2010-11-23 06:28:44 UTC (rev 22991)
@@ -0,0 +1,205 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2007 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package metaNodePlugin2.view;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+// giny imports
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+// Cytoscape imports
+import cytoscape.Cytoscape;
+import cytoscape.CyNode;
+import cytoscape.CyNetwork;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandResult;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+import cytoscape.data.CyAttributes;
+
+import cytoscape.groups.CyGroup;
+
+// Metanode imports
+import metaNodePlugin2.model.MetaNode;
+
+
+/**
+ * The NodeCharts class provides several static methods that
+ * manage the interface to the nodechart plugin
+ *
+ * It would be nice to reuse the AttributeHandler implementations, but
+ * we interpret things differently for nodeCharts than we do for aggregated
+ * attributes...
+ *
+ * At this point, this handles the following types:
+ * TYPE_INTEGER: labels are the names of the nodes and the values are the
values
+ * TYPE_FLOATING: labels are the names of the nodes and the values are the
values
+ * TYPE_STRING: labels are the names of the strings and the values are the
number of times that string occurs
+ * TYPE_BOOLEAN: labels are either "True" or "False" and the values are
the number of times that condition occurs
+ * TYPE_SIMPLE_LIST: results depend on type:
+ * String: labels are the names of the strings and the values are
the number of times that string occurs
+ * Integer: ??
+ * Double: ??
+ */
+public class NodeCharts {
+
+ private static String VALUELIST = "valuelist";
+ private static String LABELLIST = "labellist";
+
+ public static void updateNodeCharts(MetaNode mn, CyLogger logger) {
+ // Get the attribute we're using
+ String nodeChartAttribute = mn.getNodeChartAttribute();
+
+ // Get the chart type
+ String chartType = mn.getChartType();
+
+ if (nodeChartAttribute == null || chartType == null) return;
+
+ // Get the values from all of our children
+ CyGroup group = mn.getCyGroup();
+ List<CyNode> nodeList = group.getNodes();
+ if (nodeList == null) return;
+
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+
+ // Make sure this is a type that makes sense for us
+ byte attributeType = nodeAttributes.getType(nodeChartAttribute);
+ if (attributeType == CyAttributes.TYPE_UNDEFINED ||
attributeType == CyAttributes.TYPE_SIMPLE_MAP ||
+ attributeType == CyAttributes.TYPE_COMPLEX || attributeType
== CyAttributes.TYPE_BOOLEAN)
+ return;
+
+ Map<String, Object> args = new HashMap<String, Object>();
+ args.put("node", group.getGroupNode().getIdentifier());
+ System.out.println("Node:
"+group.getGroupNode().getIdentifier());
+ args.put("colorlist", "contrasting");
+ switch (attributeType) {
+ case CyAttributes.TYPE_SIMPLE_LIST:
+ getHistogramLabelsAndValues(args, group,
nodeAttributes, nodeChartAttribute, chartType);
+ break;
+ case CyAttributes.TYPE_INTEGER:
+ case CyAttributes.TYPE_FLOATING:
+ getNumericLabelsAndValues(args, group,
nodeAttributes, nodeChartAttribute, chartType);
+ break;
+ case CyAttributes.TYPE_BOOLEAN:
+ case CyAttributes.TYPE_STRING:
+ getStringLabelsAndValues(args, group,
nodeAttributes, nodeChartAttribute, chartType);
+ break;
+ default:
+ }
+
+ try {
+ CyCommandResult result =
CyCommandManager.execute("nodecharts", "clear", args);
+ result = CyCommandManager.execute("nodecharts",
chartType, args);
+ } catch (CyCommandException cce) {
+ logger.warning("node chart command failed:
"+cce.getMessage());
+ System.out.println("node chart command failed:
"+cce.getMessage());
+ }
+ }
+
+ private static void getNumericLabelsAndValues(Map<String,Object>args,
CyGroup group, CyAttributes nodeAttributes,
+ String
nodeChartAttribute, String chartType) {
+ List<String> labels = new ArrayList<String>();
+ List<String> values = new ArrayList<String>();
+ for (CyNode node: group.getNodes()) {
+ if (nodeAttributes.hasAttribute(node.getIdentifier(),
nodeChartAttribute)) {
+ labels.add(node.getIdentifier());
+
values.add(nodeAttributes.getAttribute(node.getIdentifier(),
nodeChartAttribute).toString());
+ }
+ }
+ args.put(VALUELIST, values);
+ args.put(LABELLIST, labels);
+ }
+
+ private static void getStringLabelsAndValues(Map<String,Object>args,
CyGroup group, CyAttributes nodeAttributes,
+ String
nodeChartAttribute, String chartType) {
+ Map<String, Integer> valueMap = new HashMap<String, Integer>();
+ for (CyNode node: group.getNodes()) {
+ if (nodeAttributes.hasAttribute(node.getIdentifier(),
nodeChartAttribute)) {
+ String v =
nodeAttributes.getAttribute(node.getIdentifier(),
nodeChartAttribute).toString();
+
+ if (!valueMap.containsKey(v))
+ valueMap.put(v, new Integer(1));
+ else {
+ Integer count = valueMap.get(v);
+ valueMap.put(v, count+1);
+ }
+ }
+ }
+
+ // Now, we've got the histogram, create the appropriate arrays
+ List<String>labels = new ArrayList<String>(valueMap.keySet());
+ List<Integer>values = new ArrayList<Integer>();
+ for (String label: labels) {
+ values.add(valueMap.get(label));
+ }
+ args.put(VALUELIST, values);
+ args.put(LABELLIST, labels);
+ }
+
+ private static void getHistogramLabelsAndValues(Map<String,Object>args,
CyGroup group, CyAttributes nodeAttributes,
+ String
nodeChartAttribute, String chartType) {
+ System.out.println("Getting histogram labels and values");
+ Map<String, Integer> valueMap = new HashMap<String, Integer>();
+ for (CyNode node: group.getNodes()) {
+ if (nodeAttributes.hasAttribute(node.getIdentifier(),
nodeChartAttribute)) {
+ List l =
nodeAttributes.getListAttribute(node.getIdentifier(), nodeChartAttribute);
+ for (Object v: l) {
+ String label = v.toString();
+ if (!valueMap.containsKey(label))
+ valueMap.put(label, new
Integer(1));
+ else {
+ Integer count =
valueMap.get(label);
+ valueMap.put(label, count+1);
+ }
+ }
+ }
+ }
+
+ // Now, we've got the histogram, create the appropriate arrays
+ List<String>labels = new ArrayList<String>(valueMap.keySet());
+ List<Integer>values = new ArrayList<Integer>();
+ for (String label: labels) {
+ values.add(valueMap.get(label));
+ }
+ System.out.println("Values: "+values);
+ args.put(VALUELIST, values);
+ System.out.println("Labels: "+labels);
+ args.put(LABELLIST, labels);
+ }
+
+}
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/ViewUtils.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/ViewUtils.java
2010-11-23 00:23:56 UTC (rev 22990)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/ViewUtils.java
2010-11-23 06:28:44 UTC (rev 22991)
@@ -206,7 +206,7 @@
Dimension offset = getAttributes(node, nodeAttributes);
// offset might be null if we've just added the node
if (offset != null) {
- System.out.println("Offset for
"+node.toString()+" is "+offset.getWidth()+"x"+offset.getHeight());
+ // System.out.println("Offset for
"+node.toString()+" is "+offset.getWidth()+"x"+offset.getHeight());
net.restoreNode(node);
NodeView nView = view.getNodeView(node);
double nodeWidth = 0.0;
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