Author: scooter
Date: 2010-11-29 10:11:12 -0800 (Mon, 29 Nov 2010)
New Revision: 23032
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodeGroupViewer.java
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/NodeCharts.java
Log:
Added NodeChart functionality
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodeGroupViewer.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodeGroupViewer.java
2010-11-29 17:23:25 UTC (rev 23031)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodeGroupViewer.java
2010-11-29 18:11:12 UTC (rev 23032)
@@ -79,6 +79,12 @@
private static String NAMEDSELECTION = "namedselection";
private static String NODECHARTS = "nodecharts";
+ /**
+ * Create a new group viewer for metanodes
+ *
+ * @param viewerName the name of the viewer
+ * @param logger our current logger
+ */
public MetaNodeGroupViewer (String viewerName, CyLogger logger) {
this.viewerName = viewerName;
this.logger = logger;
@@ -104,10 +110,16 @@
return null;
}
+ /**
+ * Return the settings dialog for this group viewer
+ */
public MetanodeSettingsDialog getSettingsDialog() {
return settingsDialog;
}
+ /**
+ * Return our logger
+ */
public CyLogger getLogger() {
return this.logger;
}
@@ -228,14 +240,12 @@
} 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()) {
@@ -244,12 +254,22 @@
}
}
+ /**
+ * Returns true if the nodeChartPlugin is loaded, false otherwise
+ *
+ * @return 'true' if the nodeChartPlugin is loaded
+ */
public boolean haveNodeCharts() {
if (!haveNodeCharts)
haveNodeCharts = checkNodeCharts();
return haveNodeCharts;
}
+ /**
+ * Return the list of chart types the nodeChartPlugin supports
+ *
+ * @return a list of chart types (as Strings)
+ */
public List<String> getChartTypes() {
try {
Map<String,Object> args = new HashMap<String,Object>();
@@ -263,6 +283,9 @@
return new ArrayList<String>();
}
+ /**
+ * This routine checks to see if the nodeChartPlugin is loaded
+ */
public boolean checkNodeCharts() {
try {
CyCommandManager.getCommand(NODECHARTS, "clear");
@@ -303,6 +326,9 @@
updateGroupPanel();
}
+ /**
+ * Method to register ourselves with the group panel
+ */
public void registerWithGroupPanel() {
// First, see if the named selection plugin is loaded
CyCommandHandler handler = null;
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
2010-11-29 17:23:25 UTC (rev 23031)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
2010-11-29 18:11:12 UTC (rev 23032)
@@ -50,6 +50,7 @@
import cytoscape.CyNode;
import cytoscape.Cytoscape;
import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesUtils;
import cytoscape.groups.CyGroup;
import cytoscape.groups.CyGroupManager;
import cytoscape.groups.CyGroupViewer;
@@ -110,6 +111,11 @@
// Dialog components
JPanel tunablePanel = null;
+ /**
+ * Create a new settings dialog
+ *
+ * @param viewer the group viewer
+ */
public MetanodeSettingsDialog(MetaNodeGroupViewer viewer) {
super(Cytoscape.getDesktop(), "Metanode Settings Dialog",
false);
metanodeProperties = new MetanodeProperties("metanode");
@@ -123,6 +129,9 @@
pack();
}
+ /**
+ * Initialize the dialog
+ */
private void initialize() {
JPanel mainPanel = new JPanel();
@@ -187,6 +196,10 @@
setContentPane(mainPanel);
}
+
+ /**
+ * Create all of our properties
+ */
private void initializeProperties() {
tunableEnablers = new ArrayList<Tunable>();
nodeChartEnablers = new ArrayList<Tunable>();
@@ -395,24 +408,43 @@
}
}
+ /**
+ * Revert our settings
+ */
public void revertSettings() {
metanodeProperties.revertProperties();
AttributeManager.revertSettings();
}
+ /**
+ * Return our settings
+ *
+ * @return our properties
+ */
public MetanodeProperties getSettings() {
return metanodeProperties;
}
+ /**
+ * Update all of our attribute manager override values
+ *
+ * @param network the network we're updating our override values for
+ */
public void updateOverrides(CyNetwork network) {
AttributeManager.loadHandlerMappings(network);
}
+ /**
+ * Update the tunables that list attribute values
+ */
public void updateAttributes() {
attrList.setLowerBound(getAttributes());
nodeChartAttrList.setLowerBound(getNodeAttributes());
}
+ /**
+ * Update our list of node chart types
+ */
public void updateNodeChartTypes() {
if (groupViewer.checkNodeCharts()) {
enableNodeCharts(true);
@@ -421,6 +453,9 @@
enableNodeCharts(false);
}
+ /**
+ * Return 'true' if we're supposed to use the nested network viewer
+ */
public boolean getUseNestedNetworks() {
updateSettings(false);
String bv =
(String)metanodeProperties.getProperties().get("useNestedNetworks");
@@ -428,6 +463,11 @@
return useNestedNetworks;
}
+ /**
+ * Return all of the node attributes as a string array
+ *
+ * @return array of node attributes
+ */
private String[] getNodeAttributes() {
CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
List<String> attributeList = new ArrayList();
@@ -438,6 +478,11 @@
return attributeArray;
}
+ /**
+ * Return all of the attributes as a string array
+ *
+ * @return array of attributes
+ */
private String[] getAttributes() {
CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
@@ -451,6 +496,11 @@
return attributeArray;
}
+ /**
+ * Return all of the chart types as a string array
+ *
+ * @return array of chart types
+ */
private String[] getChartTypes() {
String [] a = new String[1];
List<String> viewerList = groupViewer.getChartTypes();
@@ -473,6 +523,9 @@
}
}
+ /**
+ * Methods to support the ComponentListener interface
+ */
public void componentHidden(ComponentEvent e) {}
public void componentShown(ComponentEvent e) {}
public void componentMoved(ComponentEvent e) {}
@@ -481,6 +534,9 @@
pack();
}
+ /**
+ * This method is called when the user performs an action
+ */
public void actionPerformed(ActionEvent e) {
String command = e.getActionCommand();
@@ -496,6 +552,8 @@
} else if (command.equals("clear")) {
AttributeManager.clearSettings();
tunableChanged(attrList);
+
+ // Apply the current settings to the selected metanodes
} else if (command.equals("applySelected")) {
updateSettings(true);
// Get all selected nodes
@@ -507,6 +565,8 @@
}
}
setVisible(false);
+
+ // Apply the current settings to all metanodes
} else if (command.equals("applyAll")) {
updateSettings(true);
// Get the list of groups
@@ -556,52 +616,10 @@
chartType = (String)getListValue(t);
MetaNodeManager.setChartTypeDefault(chartType);
} else if (t.getName().equals("attributeList")) {
- CyAttributes attrs = null;
-
- // Get the attribute
String attributeWP = (String)getListValue(t);
-
if (attributeWP == null)
return;
-
- // Strip prefix
- String attribute = attributeWP.substring(5);
-
- if (attributeWP.startsWith("edge"))
- attrs = Cytoscape.getEdgeAttributes();
- else
- attrs = Cytoscape.getNodeAttributes();
-
- byte type = attrs.getType(attribute);
-
- // Get the list
- AttributeHandlingType[] hTypes =
AttributeManager.getHandlingOptions(type);
- AttributeHandlingType[] handlingTypes = new
AttributeHandlingType[hTypes.length+1];
-
- handlingTypes[0] = AttributeHandlingType.DEFAULT;
- for (int i = 0; i < hTypes.length; i++) {
- handlingTypes[i+1] = hTypes[i];
- }
-
- // Set the name
- typeString.setValue(attributeName(type));
-
- typeList.removeTunableValueListener(this);
- // Update the list
- typeList.setLowerBound(handlingTypes);
-
- // Do we already have a handler?
- AttributeHandler handler =
AttributeManager.getHandler(attributeWP);
- if (handler != null) {
- // Yes, show the right one to the user
- for (int i = 0; i < handlingTypes.length; i++) {
- if (handler.getHandlerType() ==
handlingTypes[i]) {
-
typeList.setValue(Integer.valueOf(i));
- break;
- }
- }
- }
- typeList.addTunableValueListener(this);
+ updateAttributeHandlers(attributeWP);
} else if (t.getName().equals("aggregationType")) {
// Get the attribute
String attributeWP = (String)getListValue(attrList);
@@ -615,25 +633,48 @@
repaint();
}
- private String attributeName(byte type) {
- switch (type) {
- case CyAttributes.TYPE_BOOLEAN:
- return "Boolean";
- case CyAttributes.TYPE_INTEGER:
- return "Integer";
- case CyAttributes.TYPE_FLOATING:
- return "Floating-point";
- case CyAttributes.TYPE_STRING:
- return "String";
- case CyAttributes.TYPE_SIMPLE_LIST:
- return "Simple List";
- case CyAttributes.TYPE_SIMPLE_MAP:
- return "Simple Map";
- case CyAttributes.TYPE_COMPLEX:
- return "Complex type (unsupported)";
- default:
- return "Undefined";
+ private void updateAttributeHandlers(String attributeWP) {
+ CyAttributes attrs = null;
+
+ // Strip prefix
+ String attribute = attributeWP.substring(5);
+
+ if (attributeWP.startsWith("edge"))
+ attrs = Cytoscape.getEdgeAttributes();
+ else
+ attrs = Cytoscape.getNodeAttributes();
+
+ byte type = attrs.getType(attribute);
+
+ // Get the list
+ AttributeHandlingType[] hTypes =
AttributeManager.getHandlingOptions(type);
+ AttributeHandlingType[] handlingTypes = new
AttributeHandlingType[hTypes.length+1];
+
+ handlingTypes[0] = AttributeHandlingType.DEFAULT;
+ for (int i = 0; i < hTypes.length; i++) {
+ handlingTypes[i+1] = hTypes[i];
}
+
+ // Set the name
+ typeString.setValue(CyAttributesUtils.toString(type));
+
+ typeList.removeTunableValueListener(this);
+ // Update the list
+ typeList.setLowerBound(handlingTypes);
+
+ // Do we already have a handler?
+ AttributeHandler handler =
AttributeManager.getHandler(attributeWP);
+ if (handler != null) {
+ // Yes, show the right one to the user
+ for (int i = 0; i < handlingTypes.length; i++) {
+ if (handler.getHandlerType() ==
handlingTypes[i]) {
+ typeList.setValue(Integer.valueOf(i));
+ break;
+ }
+ }
+ }
+ typeList.addTunableValueListener(this);
+ return;
}
private Object getListValue(Tunable t) {
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/NodeCharts.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/NodeCharts.java
2010-11-29 17:23:25 UTC (rev 23031)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/NodeCharts.java
2010-11-29 18:11:12 UTC (rev 23032)
@@ -81,6 +81,13 @@
private static String VALUELIST = "valuelist";
private static String LABELLIST = "labellist";
+ /**
+ * This method calculates the values and labels and draws the
+ * node chart on a metanode.
+ *
+ * @param mn the metanode we're drawing on
+ * @param logger the CyLogger we're using
+ */
public static void updateNodeCharts(MetaNode mn, CyLogger logger) {
// Get the attribute we're using
String nodeChartAttribute = mn.getNodeChartAttribute();
@@ -103,10 +110,12 @@
attributeType == CyAttributes.TYPE_COMPLEX || attributeType
== CyAttributes.TYPE_BOOLEAN)
return;
+ // Create our argument map
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");
+
+ // Depending on the attribute type -- do the right thing
switch (attributeType) {
case CyAttributes.TYPE_SIMPLE_LIST:
getHistogramLabelsAndValues(args, group,
nodeAttributes, nodeChartAttribute, chartType);
@@ -123,14 +132,18 @@
}
try {
+ // First, make sure we don't have any nodechart on the
node
CyCommandResult result =
CyCommandManager.execute("nodecharts", "clear", args);
+ // Now, add the node chart
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());
}
}
+ /**
+ * This method is used to handle numeric attribute types
+ */
private static void getNumericLabelsAndValues(Map<String,Object>args,
CyGroup group, CyAttributes nodeAttributes,
String
nodeChartAttribute, String chartType) {
List<String> labels = new ArrayList<String>();
@@ -145,60 +158,57 @@
args.put(LABELLIST, labels);
}
+ /**
+ * This method is used to handle string attribute types
+ */
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);
- }
+ incrementHistogram(valueMap, v);
}
}
- // 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);
+ addHistoArgs(valueMap, args);
}
+ /**
+ * This method is used to handle list attribute types
+ */
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);
- }
+ incrementHistogram(valueMap, label);
}
}
}
+ addHistoArgs(valueMap, args);
+ }
+ private static void incrementHistogram(Map<String, Integer> map, String
value) {
+ if (!map.containsKey(value))
+ map.put(value, new Integer(1));
+ else {
+ Integer count = map.get(value);
+ map.put(value, count+1);
+ }
+ }
+
+ private static void addHistoArgs(Map<String, Integer> map, Map<String,
Object> args) {
// Now, we've got the histogram, create the appropriate arrays
- List<String>labels = new ArrayList<String>(valueMap.keySet());
+ List<String>labels = new ArrayList<String>(map.keySet());
List<Integer>values = new ArrayList<Integer>();
for (String label: labels) {
- values.add(valueMap.get(label));
+ values.add(map.get(label));
}
- System.out.println("Values: "+values);
args.put(VALUELIST, values);
- System.out.println("Labels: "+labels);
args.put(LABELLIST, labels);
}
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