Author: scooter
Date: 2011-11-21 16:59:13 -0800 (Mon, 21 Nov 2011)
New Revision: 27546
Modified:
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/NodeCharts.java
Log:
Added a little more support for nodecharts
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
2011-11-22 00:16:28 UTC (rev 27545)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
2011-11-22 00:59:13 UTC (rev 27546)
@@ -90,6 +90,7 @@
private boolean useNestedNetworks = false;
private String nodeChartAttribute = null;
private String chartType = null;
+ private String chartColorType = "contrasting";
private Map<CyEdge,CyEdge> metaEdges = new HashMap<CyEdge,CyEdge>();
private Map<CyNode,CyEdge> membershipEdges = null;
@@ -458,6 +459,24 @@
}
/**
+ * Sets the node chart color type
+ *
+ * @param chartColorType the chart color type
+ */
+ public void setChartColorType(String chartColorType) {
+ this.chartColorType = chartColorType;
+ }
+
+ /**
+ * Get the chart color type we're using
+ *
+ * @return chart color type
+ */
+ public String getChartColorType() {
+ return this.chartColorType;
+ }
+
+ /**
* 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
2011-11-22 00:16:28 UTC (rev 27545)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNodeManager.java
2011-11-22 00:59:13 UTC (rev 27546)
@@ -62,6 +62,7 @@
protected static boolean useNestedNetworksDefault = false;
protected static boolean dontExpandEmptyDefault = true;
protected static String chartTypeDefault = null;
+ protected static String chartColorTypeDefault = "contrasting";
protected static String nodeChartAttributeDefault = null;
protected static AttributeManager defaultAttributeManager = new
AttributeManager();
@@ -136,6 +137,7 @@
mn.setHideMetaNode(hideMetanodeDefault);
mn.setMetaNodeOpacity(metanodeOpacityDefault);
mn.setChartType(chartTypeDefault);
+ mn.setChartColorType(chartColorTypeDefault);
mn.setNodeChartAttribute(nodeChartAttributeDefault);
mn.setAttributeManager(new
AttributeManager(defaultAttributeManager));
mn.getAttributeManager().loadHandlerMappings(metaGroup.getNetwork(), mn);
@@ -348,6 +350,24 @@
}
/**
+ * Sets the chart color type to use for node charting.
+ *
+ * @param chartColorType the chart color type to use for node charts
+ */
+ static public void setChartColorTypeDefault(String chartColorType) {
+ MetaNodeManager.chartColorTypeDefault = chartColorType;
+ }
+
+ /**
+ * Gets the node chart color type.
+ *
+ * @return the node chart color type
+ */
+ static public String getChartColorTypeDefault() {
+ return MetaNodeManager.chartColorTypeDefault;
+ }
+
+ /**
* Gets the default attribute manager
*
* @return the default attribute manager object
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
2011-11-22 00:16:28 UTC (rev 27545)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
2011-11-22 00:59:13 UTC (rev 27546)
@@ -39,12 +39,13 @@
package metaNodePlugin2.ui;
import metaNodePlugin2.MetaNodeGroupViewer;
+import metaNodePlugin2.data.AttributeHandler;
+import metaNodePlugin2.data.AttributeHandlingType;
+import metaNodePlugin2.data.AttributeManager;
import metaNodePlugin2.model.MetaNode;
import metaNodePlugin2.model.MetaNodeManager;
import metaNodePlugin2.model.MetanodeProperties;
-import metaNodePlugin2.data.AttributeHandler;
-import metaNodePlugin2.data.AttributeHandlingType;
-import metaNodePlugin2.data.AttributeManager;
+import metaNodePlugin2.view.NodeCharts;
import cytoscape.CyNetwork;
import cytoscape.CyNode;
@@ -91,12 +92,14 @@
public class MetanodeSettingsDialog extends JDialog
implements ActionListener,
TunableListener, ComponentListener {
+ private static String[] colorTypes = {"contrasting", "rainbow",
"modulated", "random"};
private MetanodeProperties metanodeProperties;
private Tunable typeString = null;
private Tunable typeList = null;
private Tunable attrList = null;
private Tunable nodeChartAttrList = null;
private Tunable nodeChartTypeList = null;
+ private Tunable nodeChartColorList = null;
private String[] attributeArray = null;
private List<Tunable>tunableEnablers = null;
private List<Tunable>nodeChartEnablers = null;
@@ -106,6 +109,7 @@
private boolean useNestedNetworks = false;
private double metanodeOpacity = 100.0;
private String chartType = null;
+ private String chartColorType = null;
private String nodeChartAttribute = null;
public MetaNodeGroupViewer groupViewer = null;
private AttributeManager defaultAttributeManager = null;
@@ -284,6 +288,8 @@
}
}
+ // System.out.println("------------------------------------
enableHandling = "+enableHandling);
+
{
Tunable t = new Tunable("enableHandling",
"Enable Attribute Aggregation",
@@ -334,7 +340,7 @@
// If we have nodeCharts, provide chart options for aggregated
attributes
{
Tunable t = new Tunable("nodeChartsGroup", "Node Chart
Options",
- Tunable.GROUP, new Integer(2),
+ Tunable.GROUP, new Integer(4),
new Boolean(true), null,
Tunable.COLLAPSABLE);
metanodeProperties.add(t);
t.setImmutable(true);
@@ -358,6 +364,23 @@
metanodeProperties.add(nodeChartTypeList);
nodeChartTypeList.addTunableValueListener(this);
nodeChartTypeList.setImmutable(true);
+
+ // Get the color types
+ nodeChartColorList = new
Tunable("chartColorType", "How to color chart",
+ Tunable.LIST,
new Integer(0),
+ colorTypes,
null, 0);
+ nodeChartEnablers.add(nodeChartColorList);
+ metanodeProperties.add(nodeChartColorList);
+
nodeChartColorList.addTunableValueListener(this);
+ nodeChartColorList.setImmutable(true);
+
+ // Allow the user to reset the label-color
memory
+ t = new Tunable("resetColors", "Reset colors
for this attribute",
+ Tunable.BUTTON, "Reset colors",
+ this, null, 0);
+ metanodeProperties.add(t);
+ t.setImmutable(true);
+ nodeChartEnablers.add(t);
}
}
updateSettings(true);
@@ -411,6 +434,12 @@
metanodeProperties.setProperty(t.getName(), chartType);
}
+ t = metanodeProperties.get("chartColorType");
+ if ((t != null) && (t.valueChanged() || force)) {
+ chartColorType = (String)getListValue(t);
+ metanodeProperties.setProperty(t.getName(),
chartColorType);
+ }
+
// For each default value, get the default and set it
t = metanodeProperties.get("stringDefaults");
if ((t != null) && (t.valueChanged() || force)) {
@@ -582,6 +611,7 @@
*/
public void actionPerformed(ActionEvent e) {
String command = e.getActionCommand();
+ System.out.println("actionPerformed("+e+")");
if (command.equals("done")) {
updateSettings(true);
@@ -644,6 +674,11 @@
// Update defaults
updateDefaultSettings();
setVisible(false);
+ } else if (command.equals("resetColors")) {
+ if (nodeChartAttribute != null)
+
NodeCharts.resetNodeChartLabels(nodeChartAttribute);
+ else
+ NodeCharts.resetNodeChartLabels();
}
}
@@ -656,6 +691,7 @@
this.useNestedNetworks = MetaNodeManager.getUseNestedNetworksDefault();
this.metanodeOpacity =
MetaNodeManager.getExpandedOpacityDefault();
this.chartType = MetaNodeManager.getChartTypeDefault();
+ this.chartColorType =
MetaNodeManager.getChartColorTypeDefault();
this.nodeChartAttribute =
MetaNodeManager.getNodeChartAttributeDefault();
this.myAttributeManager = new
AttributeManager(defaultAttributeManager);
this.enableHandling = myAttributeManager.getEnable();
@@ -669,7 +705,7 @@
this.dontExpandEmpty = context.getDontExpandEmpty();
this.useNestedNetworks = context.getUseNestedNetworks();
this.metanodeOpacity = context.getMetaNodeOpacity();
- this.chartType = context.getChartType();
+ this.chartColorType = context.getChartColorType();
this.nodeChartAttribute = context.getNodeChartAttribute();
this.myAttributeManager = new
AttributeManager(context.getAttributeManager());
myAttributeManager.loadHandlerMappings(Cytoscape.getCurrentNetwork(), context);
@@ -682,6 +718,7 @@
mn.setHideMetaNode(hideMetaNode);
mn.setMetaNodeOpacity(metanodeOpacity);
mn.setChartType(chartType);
+ mn.setChartColorType(chartColorType);
mn.setNodeChartAttribute(nodeChartAttribute);
mn.setAttributeManager(myAttributeManager);
myAttributeManager.updateAttributes(mn);
@@ -695,6 +732,7 @@
MetaNodeManager.setExpandedOpacityDefault(metanodeOpacity);
MetaNodeManager.setNodeChartAttributeDefault(nodeChartAttribute);
MetaNodeManager.setChartTypeDefault(chartType);
+ MetaNodeManager.setChartColorTypeDefault(chartColorType);
}
private void updateTunableSettings() {
@@ -713,6 +751,8 @@
t.setValue(nodeChartAttribute);
t = metanodeProperties.get("chartType");
t.setValue(chartType);
+ t = metanodeProperties.get("chartColorType");
+ t.setValue(chartColorType);
// Clear the tunables for overrides
}
@@ -734,6 +774,8 @@
nodeChartAttribute = (String)getListValue(t);
} else if (t.getName().equals("chartType")) {
chartType = (String)getListValue(t);
+ } else if (t.getName().equals("chartColorType")) {
+ chartColorType = (String)getListValue(t);
} else if (t.getName().equals("attributeList")) {
String attributeWP = (String)getListValue(t);
if (attributeWP == null)
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/NodeCharts.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/NodeCharts.java
2011-11-22 00:16:28 UTC (rev 27545)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/NodeCharts.java
2011-11-22 00:59:13 UTC (rev 27546)
@@ -81,6 +81,8 @@
private static String VALUELIST = "valuelist";
private static String LABELLIST = "labellist";
+
+ private static Map<String, List<String>> attrLabelListMap = null;
/**
* This method calculates the values and labels and draws the
@@ -98,6 +100,12 @@
if (nodeChartAttribute == null || chartType == null ||
chartType.equals(MetaNodeGroupViewer.NONODECHART)) return;
+ if (attrLabelListMap == null)
+ attrLabelListMap = new HashMap<String, List<String>>();
+
+ if (!attrLabelListMap.containsKey(nodeChartAttribute))
+ attrLabelListMap.put(nodeChartAttribute, new
ArrayList<String>());
+
// Get the values from all of our children
CyGroup group = mn.getCyGroup();
List<CyNode> nodeList = group.getNodes();
@@ -114,7 +122,7 @@
// Create our argument map
Map<String, Object> args = new HashMap<String, Object>();
args.put("node", group.getGroupNode().getIdentifier());
- args.put("colorlist", "contrasting");
+ args.put("colorlist", mn.getChartColorType());
// Depending on the attribute type -- do the right thing
switch (attributeType) {
@@ -132,6 +140,10 @@
default:
}
+ // System.out.println("Nodechart args: ");
+ // for (String arg: args.keySet()) {
+ // System.out.println(" "+arg+"="+args.get(arg));
+ // }
try {
// First, make sure we don't have any nodechart on the
node
CyCommandResult result =
CyCommandManager.execute("nodecharts", "clear", args);
@@ -142,6 +154,15 @@
}
}
+ public static void resetNodeChartLabels() {
+ attrLabelListMap = new HashMap<String, List<String>>();
+ }
+
+ public static void resetNodeChartLabels(String attr) {
+ if (attrLabelListMap != null)
+ attrLabelListMap.put(attr, new ArrayList<String>());
+ }
+
/**
* This method is used to handle numeric attribute types
*/
@@ -162,49 +183,64 @@
/**
* 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>();
+ private static void getStringLabelsAndValues(Map<String,Object>args,
CyGroup group,
+ CyAttributes
nodeAttributes,
+ String nodeChartAttribute,
String chartType) {
+ Map<String, Integer> valueMap =
initializeHistogram(nodeChartAttribute);
for (CyNode node: group.getNodes()) {
if (nodeAttributes.hasAttribute(node.getIdentifier(),
nodeChartAttribute)) {
String v =
nodeAttributes.getAttribute(node.getIdentifier(),
nodeChartAttribute).toString();
- incrementHistogram(valueMap, v);
+ incrementHistogram(nodeChartAttribute,
valueMap, v);
}
}
- addHistoArgs(valueMap, args);
+ addHistoArgs(nodeChartAttribute, 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) {
- Map<String, Integer> valueMap = new HashMap<String, Integer>();
+ private static void getHistogramLabelsAndValues(Map<String,Object>args,
+ CyGroup group,
CyAttributes nodeAttributes,
+ String
nodeChartAttribute, String chartType) {
+ Map<String, Integer> valueMap =
initializeHistogram(nodeChartAttribute);
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();
- incrementHistogram(valueMap, label);
+ incrementHistogram(nodeChartAttribute,
valueMap, label);
}
}
}
- addHistoArgs(valueMap, args);
+ addHistoArgs(nodeChartAttribute, valueMap, args);
}
- private static void incrementHistogram(Map<String, Integer> map, String
value) {
- if (!map.containsKey(value))
+ private static Map<String, Integer> initializeHistogram(String
nodeChartAttribute) {
+ Map<String, Integer> histo = new HashMap<String, Integer>();
+ for (String s: attrLabelListMap.get(nodeChartAttribute)) {
+ // System.out.println("Initializing value for "+s+" to
0");
+ histo.put(s, 0);
+ }
+ return histo;
+ }
+
+ private static void incrementHistogram(String nodeChartAttribute,
+ Map<String, Integer> map, String
value) {
+ if (!map.containsKey(value)) {
map.put(value, new Integer(1));
- else {
+ // System.out.println("Adding "+value+" to value map");
+ attrLabelListMap.get(nodeChartAttribute).add(value);
+ } else {
Integer count = map.get(value);
map.put(value, count+1);
}
}
- private static void addHistoArgs(Map<String, Integer> map, Map<String,
Object> args) {
+ private static void addHistoArgs(String nodeChartAttribute,
+ Map<String, Integer> map, Map<String,
Object> args) {
// Now, we've got the histogram, create the appropriate arrays
- List<String>labels = new ArrayList<String>(map.keySet());
+ List<String>labels = attrLabelListMap.get(nodeChartAttribute);
List<Integer>values = new ArrayList<Integer>();
for (String label: labels) {
values.add(map.get(label));
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