Author: scooter
Date: 2011-05-20 22:13:01 -0700 (Fri, 20 May 2011)
New Revision: 25507
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodeGroupViewer.java
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/commands/MetaNodeCommandHandler.java
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/data/AttributeHandler.java
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/data/AttributeManager.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/NestedNetworkView.java
Log:
Make AttributeManager an instance class so we can independently
controll attributes aggregation for each meta node
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodeGroupViewer.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodeGroupViewer.java
2011-05-20 03:41:57 UTC (rev 25506)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/MetaNodeGroupViewer.java
2011-05-21 05:13:01 UTC (rev 25507)
@@ -257,8 +257,7 @@
public void collapse(MetaNode metaNode, CyNetworkView view) {
// Actually collapse the group
metaNode.collapse(view);
- // Handle our attributes
- AttributeManager.updateAttributes(metaNode);
+
if (haveNodeCharts) {
// Handle our node charts
NodeCharts.updateNodeCharts(metaNode, logger);
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/commands/MetaNodeCommandHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/commands/MetaNodeCommandHandler.java
2011-05-20 03:41:57 UTC (rev 25506)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/commands/MetaNodeCommandHandler.java
2011-05-21 05:13:01 UTC (rev 25507)
@@ -97,15 +97,15 @@
REMOVE("remove node",
"Remove a node from a metanode",
"metanode|node|nodelist"),
- /* MODIFYAGG("modify aggregation", // FIXME
+ MODIFYAGG("modify aggregation",
"Modify the aggregation behavior of a metanode",
-
"metanode|enabled=true|string=csv|integer=sum|double=sum|list=none|boolean=or"),
*/
+
"metanode|enabled=true|string=csv|integer=sum|double=sum|list=none|boolean=or"),
MODIFYAPP("modify appearance",
"Modify the appearance of a metanode",
-
"metanode|usenestednetworks=false|opacity=100|nodechart=none|chartattribute=none"),
- /* MODIFYAGGOVERRIDE("modify overrides", // FIXME
+
"metanode|usenestednetworks=false|opacity=100|nodechart=none|chartattribute=non"),
+ MODIFYAGGOVERRIDE("modify overrides",
"Modify aggregation overrides for specific attributes
in a metanode",
- "metanode|attribute|aggregation"), */
+ "metanode|attribute|aggregation"),
SETDEFAULTAGG("set default aggregation",
"Set the default aggregation options",
"enabled=true|string=csv|integer=sum|double=sum|list=none|boolean=or"),
@@ -485,7 +485,8 @@
// "Modify the aggregation behavior of a
metanode",
//
"metanode|enabled=true|string=csv|integer=sum|double=sum|list=none|boolean=or"),
//
- // } else if (Command.MODIFYAGG.equals(command)) {
+ } else if (Command.MODIFYAGG.equals(command)) {
+ setAggregation(result, metaNode, props, command, args);
//
// MODIFYAPP("modify appearance",
@@ -522,52 +523,30 @@
// "Modify aggregation overrides for
specific attributes in a metanode",
// "metanode|attribute|aggregation"),
//
- // } else if (Command.MODIFYAGGOVERRIDE.equals(command)) {
+ } else if (Command.MODIFYAGGOVERRIDE.equals(command)) {
+ if (!args.containsKey(ATTRIBUTE))
+ throw new RuntimeException("metanode:
"+command+" requires an attribute");
+ if (!args.containsKey(AGGREGATION))
+ throw new RuntimeException("metanode:
"+command+" requires an aggregation type");
+ if (metaNode == null)
+ throw new RuntimeException("metanode:
"+command+" requires a metanode");
+
+ String attr =
getAttribute(args.get(ATTRIBUTE).toString());
+ byte type = Cytoscape.getNodeAttributes().getType(attr);
+ String aggrType = args.get(AGGREGATION).toString();
+ AttributeHandlingType aggr = getAggregation(type,
aggrType);
+ AttributeHandler handler =
metaNode.getAttributeManager().getHandler(attr);
+ handler.setHandlerType(aggr);
+
//
// SETDEFAULTAGG("set default aggregation",
// "Set the default aggregation options",
//
"enabled=true|string=csv|integer=sum|double=sum|list=none|boolean=or"),
//
} else if (Command.SETDEFAULTAGG.equals(command)) {
- boolean attrHandling = false;
- if(args.containsKey(ENABLED))
- attrHandling = getBooleanArg(command, ENABLED,
args);
+ setAggregation(result, null, props, command, args);
- if (!attrHandling) {
- setTunable(props, "enableHandling", "false");
- result.addMessage("metanode: attribute
aggregation disabled");
- } else {
- setTunable(props, "enableHandling", "true");
- result.addMessage("metanode: attribute
aggregation enabled");
-
- if (args.containsKey(STRING)) {
- setDefault(props, "stringDefaults",
CyAttributes.TYPE_STRING, args.get(STRING).toString());
- result.addMessage("metanode: set
default aggregation handling for "+STRING+" to "+args.get(STRING).toString());
- }
-
- if (args.containsKey(INTEGER)) {
- setDefault(props, "intDefaults",
CyAttributes.TYPE_INTEGER, args.get(INTEGER).toString());
- result.addMessage("metanode: set
default aggregation handling for "+INTEGER+" to "+args.get(INTEGER).toString());
- }
-
- if (args.containsKey(DOUBLE)) {
- setDefault(props, "doubleDefaults",
CyAttributes.TYPE_FLOATING, args.get(DOUBLE).toString());
- result.addMessage("metanode: set
default aggregation handling for "+DOUBLE+" to "+args.get(DOUBLE).toString());
- }
-
- if (args.containsKey(LIST)) {
- setDefault(props, "listDefaults",
CyAttributes.TYPE_SIMPLE_LIST, args.get(LIST).toString());
- result.addMessage("metanode: set
default aggregation handling for "+LIST+" to "+args.get(LIST).toString());
- }
-
- if (args.containsKey(BOOLEAN)) {
- setDefault(props, "booleanDefaults",
CyAttributes.TYPE_BOOLEAN, args.get(BOOLEAN).toString());
- result.addMessage("metanode: set
default aggregation handling for "+BOOLEAN+" to "+args.get(BOOLEAN).toString());
- }
- }
-
-
//
// SETDEFAULTAPP("set default appearance",
// "Set the default appearance options",
@@ -613,8 +592,8 @@
byte type = Cytoscape.getNodeAttributes().getType(attr);
String aggrType = args.get(AGGREGATION).toString();
AttributeHandlingType aggr = getAggregation(type,
aggrType);
- AttributeHandler handler =
AttributeManager.getHandler(attr);
- handler.setHandlerType(aggr);
+ AttributeManager manager =
MetaNodeManager.getDefaultAttributeManager();
+ manager.addHandler(attr, aggr);
result.addMessage("metanode: set attribute aggretion
for "+attr+" to "+aggr.toString());
}
@@ -709,13 +688,62 @@
throw new RuntimeException("metanode: unknown attribute
type!?!");
}
- private void setDefault(MetanodeProperties props, String tunable, byte
type, String value) {
+ private void setAggregation(CyCommandResult result, MetaNode metanode,
MetanodeProperties props,
+ String command, Map<String, Object>args) {
+ boolean attrHandling = false;
+ String messagePrefix = "metanode (default):";
+ AttributeManager attributeManager =
MetaNodeManager.getDefaultAttributeManager();
+
+ if(args.containsKey(ENABLED))
+ attrHandling = getBooleanArg(command, ENABLED, args);
+
+ if (metanode != null) {
+ messagePrefix = "metanode
("+metanode.getGroupNode().getIdentifier()+"): ";
+ attributeManager = metanode.getAttributeManager();
+ }
+
+ if (!attrHandling) {
+ setTunable(props, "enableHandling", "false");
+ attributeManager.setEnable(false);
+ result.addMessage(messagePrefix+" attribute aggregation
disabled");
+ } else {
+ setTunable(props, "enableHandling", "true");
+ attributeManager.setEnable(false);
+ result.addMessage(messagePrefix+" attribute aggregation
enabled");
+ }
+
+ if (args.containsKey(STRING)) {
+ setDefault(attributeManager, props, "stringDefaults",
CyAttributes.TYPE_STRING, args.get(STRING).toString());
+ result.addMessage(messagePrefix+" set default
aggregation handling for "+STRING+" to "+args.get(STRING).toString());
+ }
+
+ if (args.containsKey(INTEGER)) {
+ setDefault(attributeManager, props, "intDefaults",
CyAttributes.TYPE_INTEGER, args.get(INTEGER).toString());
+ result.addMessage(messagePrefix+" set default
aggregation handling for "+INTEGER+" to "+args.get(INTEGER).toString());
+ }
+
+ if (args.containsKey(DOUBLE)) {
+ setDefault(attributeManager, props, "doubleDefaults",
CyAttributes.TYPE_FLOATING, args.get(DOUBLE).toString());
+ result.addMessage(messagePrefix+" set default
aggregation handling for "+DOUBLE+" to "+args.get(DOUBLE).toString());
+ }
+
+ if (args.containsKey(LIST)) {
+ setDefault(attributeManager, props, "listDefaults",
CyAttributes.TYPE_SIMPLE_LIST, args.get(LIST).toString());
+ result.addMessage(messagePrefix+" set default
aggregation handling for "+LIST+" to "+args.get(LIST).toString());
+ }
+
+ if (args.containsKey(BOOLEAN)) {
+ setDefault(attributeManager, props, "booleanDefaults",
CyAttributes.TYPE_BOOLEAN, args.get(BOOLEAN).toString());
+ result.addMessage(messagePrefix+" set default
aggregation handling for "+BOOLEAN+" to "+args.get(BOOLEAN).toString());
+ }
+ }
+
+
+ private void setDefault(AttributeManager manager, MetanodeProperties
props, String tunable, byte type, String value) {
// First, check to see if our value is good
AttributeHandlingType aggrType = getAggregation(type, value);
+ manager.setDefault(type, aggrType);
- // Apparently it is, so set the default
- AttributeManager.setDefault(type, aggrType);
-
// Now reflect the change in our tunable
setListTunable(props, tunable, aggrType.toString());
}
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/data/AttributeHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/data/AttributeHandler.java
2011-05-20 03:41:57 UTC (rev 25506)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/data/AttributeHandler.java
2011-05-21 05:13:01 UTC (rev 25507)
@@ -65,7 +65,7 @@
*************************************************************************/
protected AttributeHandler (String attribute, AttributeHandlingType
type) {
- this.attribute = attribute.substring(5); // Skip over type
+ this.attribute = attribute;
this.type = type;
this.count = 0;
aggregateValue = null;
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/data/AttributeManager.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/data/AttributeManager.java
2011-05-20 03:41:57 UTC (rev 25506)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/data/AttributeManager.java
2011-05-21 05:13:01 UTC (rev 25507)
@@ -54,15 +54,16 @@
* themselves handle the aggregation of attributes.
*/
public class AttributeManager {
- static private Map<String, AttributeHandler>handlerMap = null;
- static private Map<String, AttributeHandler>saveHandlerMap = null;
- static private AttributeHandlingType[] defaultHandling = new
AttributeHandlingType[15];
- static private boolean aggregating = false;
- static private CyNetwork network;
static public final String OVERRIDE_ATTRIBUTE = "__MetanodeAggregation";
static public final String CHILDREN_ATTRIBUTE = "NumChildren";
static public final String DESCENDENTS_ATTRIBUTE = "NumDescendents";
+ private AttributeHandlingType[] defaultHandling = new
AttributeHandlingType[15];
+ private Map<String, AttributeHandler>handlerMap = null;
+ private Map<String, AttributeHandler>saveHandlerMap = null;
+ private boolean aggregating = false;
+ private CyNetwork network;
+
static AttributeHandlingType[] stringArray =
{AttributeHandlingType.MCV, AttributeHandlingType.CSV,
AttributeHandlingType.TSV, AttributeHandlingType.NONE};
@@ -143,6 +144,21 @@
}
}
+
/**************************************************************************
+ * Instance methods for AttributeManager
*
+
*************************************************************************/
+ public AttributeManager () {
+ }
+
+ public AttributeManager (AttributeManager source) {
+ this.handlerMap = source.handlerMap;
+ this.saveHandlerMap = source.saveHandlerMap;
+ this.aggregating = source.aggregating;
+ for (int index = 0; index < 15; index++)
+ this.defaultHandling[index] =
source.defaultHandling[index];
+ }
+
+
/**
* Add a new handler to our internal map for aggregating the designated
* attribute and handlerType
@@ -150,7 +166,7 @@
* @param attribute the attribute this handler is for
* @param handlerType the aggregation method for use by the handler
*/
- static public void addHandler(String attribute, AttributeHandlingType
handlerType) {
+ public void addHandler(String attribute, AttributeHandlingType
handlerType) {
if (handlerMap == null) handlerMap = new HashMap();
if (handlerMap.containsKey(attribute)) {
@@ -173,7 +189,7 @@
*
* @param attribute the attribute this handler is for
*/
- static public void removeHandler(String attribute) {
+ public void removeHandler(String attribute) {
if (handlerMap != null && handlerMap.containsKey(attribute)) {
handlerMap.remove(attribute);
}
@@ -182,7 +198,7 @@
/**
* Save the current attribute map
*/
- static public void saveSettings() {
+ public void saveSettings() {
if (handlerMap == null) return;
saveHandlerMap = new HashMap();
for (String attribute: handlerMap.keySet()) {
@@ -194,7 +210,7 @@
/**
* Revert the attribute map back to the saved settings.
*/
- static public void revertSettings() {
+ public void revertSettings() {
handlerMap = saveHandlerMap;
saveHandlerMap = null;
}
@@ -202,7 +218,7 @@
/**
* Clear the attribute handler map
*/
- static public void clearSettings() {
+ public void clearSettings() {
handlerMap = null;
saveHandlerMap = null;
}
@@ -214,7 +230,7 @@
* @return the AttributeHandler or null if there is no attribute handler
* for this attribute.
*/
- static public AttributeHandler getHandler(String attribute) {
+ public AttributeHandler getHandler(String attribute) {
if (handlerMap == null) return null;
if (handlerMap.containsKey(attribute))
return handlerMap.get(attribute);
@@ -227,9 +243,9 @@
*
* @param network the CyNetwork we're going to read our options from
*/
- static public void loadHandlerMappings(CyNetwork network) {
+ public void loadHandlerMappings(CyNetwork network) {
CyAttributes networkAttributes =
Cytoscape.getNetworkAttributes();
- AttributeManager.network = network;
+ this.network = network;
if (networkAttributes.hasAttribute(network.getIdentifier(),
OVERRIDE_ATTRIBUTE)) {
Map<String,String> attrMap =
(Map<String,String>)networkAttributes.getMapAttribute(network.getIdentifier(),
OVERRIDE_ATTRIBUTE);
for (String attr: attrMap.keySet()) {
@@ -243,7 +259,7 @@
*
* @param enable if 'true' enable aggregation otherwise, disable
aggregation
*/
- static public void setEnable(boolean enable) {
+ public void setEnable(boolean enable) {
aggregating = enable;
}
@@ -252,16 +268,16 @@
*
* @return 'true' if attribute aggregation is enabled otherwise, 'false'
*/
- static public boolean getEnable() {
+ public boolean getEnable() {
return aggregating;
}
- static public void setDefault(byte attributeType, AttributeHandlingType
type) {
+ public void setDefault(byte attributeType, AttributeHandlingType type) {
if (attributeType < 0) attributeType += 10;
defaultHandling[attributeType] = type;
}
- static public AttributeHandler getDefaultHandler(byte attributeType,
String attribute) {
+ public AttributeHandler getDefaultHandler(byte attributeType, String
attribute) {
AttributeHandlingType t;
if (attributeType < 0) attributeType += 10;
t = defaultHandling[attributeType];
@@ -276,7 +292,7 @@
}
- static public AttributeHandlingType stringToType(String str) {
+ public AttributeHandlingType stringToType(String str) {
for (AttributeHandlingType type:
AttributeHandlingType.values()) {
if (str.equals(type.toString()))
return type;
@@ -291,7 +307,7 @@
*
* @param mNode the metanode we're agregating over
*/
- static public void updateAttributes(MetaNode mNode) {
+ public void updateAttributes(MetaNode mNode) {
CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
CyGroup metaGroup = mNode.getCyGroup();
@@ -311,16 +327,16 @@
// Yes, do it
if (MetaNodeManager.getMetaNode(node) != null) {
// This is a metanode -- some algorithm
(e.g. median) require recursion...
- aggregateAttributes(nodeAttributes,
"node", node.getIdentifier(),
+ aggregateAttributes(nodeAttributes,
node.getIdentifier(),
MetaNodeManager.getMetaNode(node));
} else {
- aggregateAttributes(nodeAttributes,
"node", node.getIdentifier(), null);
+ aggregateAttributes(nodeAttributes,
node.getIdentifier(), null);
}
}
}
if (getEnable()) {
// Update all of the node attributes
- assignAttributes(nodeAttributes, "node", metaNodeName);
+ assignAttributes(nodeAttributes, metaNodeName);
}
// Update our special attributes
@@ -338,9 +354,8 @@
* @param source the source (node or edge ID) for the attributes
* @param recurse a metanode if we are supposed to recurse (only done
for MEDIAN)
*/
- private static void aggregateAttributes(CyAttributes attrMap,
- String attrType,
- String source, MetaNode
recurse) {
+ private void aggregateAttributes(CyAttributes attrMap,
+ String source, MetaNode recurse) {
String [] attributes = attrMap.getAttributeNames();
for (int i = 0; i < attributes.length; i++) {
String attr = attributes[i];
@@ -353,12 +368,13 @@
}
// Do we have a specific handler (override)?
- AttributeHandler handler =
getHandler(attrType+"."+attr);
+ // AttributeHandler handler =
getHandler(attrType+"."+attr);
+ AttributeHandler handler = getHandler(attr);
if (handler == null) {
// No, create a basic handler
- handler =
getDefaultHandler(attrMap.getType(attr), attrType+"."+attr);
- }
- if (handler != null) {
+ handler =
getDefaultHandler(attrMap.getType(attr), attr);
+ aggregateAttribute(attrMap, handler, source,
recurse);
+ } else {
// Aggregate
aggregateAttribute(attrMap, handler, source,
recurse);
}
@@ -373,10 +389,10 @@
* @param source the source (node or edge ID) for the attributes
* @param recurse a metanode if we are supposed to recurse (only done
for MEDIAN)
*/
- private static void aggregateAttribute(CyAttributes attrMap,
- AttributeHandler handler,
- String source,
- MetaNode recurse) {
+ private void aggregateAttribute(CyAttributes attrMap,
+ AttributeHandler handler,
+ String source,
+ MetaNode recurse) {
if (recurse == null) {
Object value = handler.aggregateAttribute(attrMap,
source, 1);
@@ -408,15 +424,15 @@
* @param attrType "edge" or "node"
* @param target the name of the object
*/
- private static void assignAttributes(CyAttributes attrMap,
- String attrType,
- String target) {
+ private void assignAttributes(CyAttributes attrMap,
+ String target) {
String [] attributes = attrMap.getAttributeNames();
for (int i = 0; i < attributes.length; i++) {
String attr = attributes[i];
// Get our handler
- AttributeHandler handler =
getHandler(attrType+"."+attr);
+ // AttributeHandler handler =
getHandler(attrType+"."+attr);
+ AttributeHandler handler = getHandler(attr);
if (handler != null)
handler.assignAttribute(attrMap, target);
}
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
2011-05-20 03:41:57 UTC (rev 25506)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNode.java
2011-05-21 05:13:01 UTC (rev 25507)
@@ -62,6 +62,7 @@
// our imports
import metaNodePlugin2.MetaNodePlugin2;
+import metaNodePlugin2.data.AttributeManager;
import metaNodePlugin2.view.ViewUtils;
// import csplugins.layout.Profile;
@@ -81,7 +82,7 @@
private CyLogger logger = null;
private CyGroup metaGroup = null;
- private boolean aggregateAttributes = false;
+ private AttributeManager attributeManager = null;
private boolean hideMetanode = true;
private double metanodeOpacity = 0.;
private boolean useNestedNetworks = false;
@@ -112,6 +113,8 @@
public CyGroup getCyGroup() { return metaGroup; }
+ public CyNode getGroupNode() { return metaGroup.getGroupNode(); }
+
/**
* Add a node to this metaNode. It will already have been added to the
* group, but we need to update our internal data structures and
(possibly)
@@ -197,6 +200,10 @@
// Restore our meta-edges
ViewUtils.restoreEdges(metaGroup, metaEdges.values(), view);
+ // Update our attributes (if we're aggregating)
+ if (attributeManager != null)
+ attributeManager.updateAttributes(this);
+
collapsed = true;
}
@@ -373,6 +380,11 @@
this.nodeChartAttribute = nodeChartAttribute;
}
+ /**
+ * Gets the attribute to use node charting
+ *
+ * @return the attribute to use for node charting
+ */
public String getNodeChartAttribute() {
return this.nodeChartAttribute;
}
@@ -386,6 +398,11 @@
this.chartType = chartType;
}
+ /**
+ * Get the chart type we're using
+ *
+ * @return chart type
+ */
public String getChartType() {
return this.chartType;
}
@@ -401,20 +418,26 @@
}
/**
- * Controls whether this metanode is aggregating attributes
+ * Set the attribute manager (for attribute aggregation) that
+ * we're supposed to use.
*
- * @param aggregate if 'true' aggregate
+ * @param attributeManager the attribute manager to use
*/
- public void setAggregateAttributes(boolean aggregate) {
- if (!this.aggregateAttributes && aggregate) {
- this.aggregateAttributes = aggregate;
- // updateAttributes();
- } else {
- this.aggregateAttributes = aggregate;
- }
+ public void setAttributeManager(AttributeManager attributeManager) {
+ this.attributeManager = attributeManager;
}
/**
+ * Get the attribute manager (for attribute aggregation) that
+ * we're using.
+ *
+ * @return the attribute manager we're using
+ */
+ public AttributeManager getAttributeManager() {
+ return attributeManager;
+ }
+
+ /**
* Returns 'true' if we hide the metnode when we expand the
* network.
*
@@ -475,6 +498,7 @@
* add a meta-edge to the parter
* if the partner is a group and the group is in our
network:
* add ourselves to the group's outer edges list
(recursively)
+ * add ourselves to the partner's meta edge list
* if the partner is in a group:
* add ourselves to the group's meta edge list
*/
@@ -494,7 +518,7 @@
CyEdge metaEdge = createMetaEdge(edge.getIdentifier(),
metaGroup.getGroupNode(), node);
MetaNode metaPartner =
MetaNodeManager.getMetaNode(node);
- if (metaPartner != null) {
+ if (metaPartner != null &&
metaPartner.metaGroup.getNetwork().equals(metaGroup.getNetwork())) {
// Recursively add links to the appropriate
children
addPartnerEdges(metaPartner);
metaPartner.addMetaEdge(metaEdge);
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNodeManager.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNodeManager.java
2011-05-20 03:41:57 UTC (rev 25506)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/model/MetaNodeManager.java
2011-05-21 05:13:01 UTC (rev 25507)
@@ -44,6 +44,7 @@
import cytoscape.view.CyNetworkView;
import metaNodePlugin2.MetaNodePlugin2;
+import metaNodePlugin2.data.AttributeManager;
/**
@@ -60,6 +61,7 @@
protected static boolean useNestedNetworksDefault = false;
protected static String chartTypeDefault = null;
protected static String nodeChartAttributeDefault = null;
+ protected static AttributeManager defaultAttributeManager = new
AttributeManager();
public static final String X_HINT_ATTR = "__metanodeHintX";
public static final String Y_HINT_ATTR = "__metanodeHintY";
@@ -92,6 +94,7 @@
mn.setMetaNodeOpacity(metanodeOpacityDefault);
mn.setChartType(chartTypeDefault);
mn.setNodeChartAttribute(nodeChartAttributeDefault);
+ mn.setAttributeManager(new
AttributeManager(defaultAttributeManager));
if (metaGroup.getNetwork() == null) {
metaGroup.setNetwork(Cytoscape.getCurrentNetwork(),
false);
}
@@ -282,4 +285,13 @@
static public String getChartTypeDefault() {
return MetaNodeManager.chartTypeDefault;
}
+
+ /**
+ * Gets the default attribute manager
+ *
+ * @return the default attribute manager object
+ */
+ static public AttributeManager getDefaultAttributeManager () {
+ return MetaNodeManager.defaultAttributeManager;
+ }
}
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
2011-05-20 03:41:57 UTC (rev 25506)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/ui/MetanodeSettingsDialog.java
2011-05-21 05:13:01 UTC (rev 25507)
@@ -106,6 +106,7 @@
private String chartType = null;
private String nodeChartAttribute = null;
private MetaNodeGroupViewer groupViewer = null;
+ private AttributeManager defaultAttributeManager = null;
// Dialog components
JPanel tunablePanel = null;
@@ -120,9 +121,11 @@
metanodeProperties = new MetanodeProperties("metanode");
this.groupViewer = viewer;
+ defaultAttributeManager =
MetaNodeManager.getDefaultAttributeManager();
+
initializeProperties();
- AttributeManager.saveSettings();
+ defaultAttributeManager.saveSettings();
initialize();
pack();
@@ -248,7 +251,7 @@
nodeChartEnablers.add(t);
{
- // Get the attribute to map
+ // Get the attribute to map (This should be a
list! -- FIXME)
nodeChartAttrList = new
Tunable("nodeChartAttribute", "Attribute to use for node chart",
Tunable.LIST,
new Integer(0),
getNodeAttributes(), null, 0);
@@ -343,7 +346,7 @@
Tunable t = metanodeProperties.get("enableHandling");
if ((t != null) && (t.valueChanged() || force)) {
enableHandling = ((Boolean) t.getValue()).booleanValue();
- AttributeManager.setEnable(enableHandling);
+ defaultAttributeManager.setEnable(enableHandling);
metanodeProperties.setProperty(t.getName(),
t.getValue().toString());
enableTunables(enableHandling);
}
@@ -387,27 +390,27 @@
// For each default value, get the default and set it
t = metanodeProperties.get("stringDefaults");
if ((t != null) && (t.valueChanged() || force)) {
- AttributeManager.setDefault(CyAttributes.TYPE_STRING,
(AttributeHandlingType)getListValue(t));
+
defaultAttributeManager.setDefault(CyAttributes.TYPE_STRING,
(AttributeHandlingType)getListValue(t));
metanodeProperties.setProperty(t.getName(),
t.getValue().toString());
}
t = metanodeProperties.get("intDefaults");
if ((t != null) && (t.valueChanged() || force)) {
- AttributeManager.setDefault(CyAttributes.TYPE_INTEGER,
(AttributeHandlingType)getListValue(t));
+
defaultAttributeManager.setDefault(CyAttributes.TYPE_INTEGER,
(AttributeHandlingType)getListValue(t));
metanodeProperties.setProperty(t.getName(),
t.getValue().toString());
}
t = metanodeProperties.get("doubleDefaults");
if ((t != null) && (t.valueChanged() || force)) {
- AttributeManager.setDefault(CyAttributes.TYPE_FLOATING,
(AttributeHandlingType)getListValue(t));
+
defaultAttributeManager.setDefault(CyAttributes.TYPE_FLOATING,
(AttributeHandlingType)getListValue(t));
metanodeProperties.setProperty(t.getName(),
t.getValue().toString());
}
t = metanodeProperties.get("listDefaults");
if ((t != null) && (t.valueChanged() || force)) {
-
AttributeManager.setDefault(CyAttributes.TYPE_SIMPLE_LIST,
(AttributeHandlingType)getListValue(t));
+
defaultAttributeManager.setDefault(CyAttributes.TYPE_SIMPLE_LIST,
(AttributeHandlingType)getListValue(t));
metanodeProperties.setProperty(t.getName(),
t.getValue().toString());
}
t = metanodeProperties.get("booleanDefaults");
if ((t != null) && (t.valueChanged() || force)) {
- AttributeManager.setDefault(CyAttributes.TYPE_BOOLEAN,
(AttributeHandlingType)getListValue(t));
+
defaultAttributeManager.setDefault(CyAttributes.TYPE_BOOLEAN,
(AttributeHandlingType)getListValue(t));
metanodeProperties.setProperty(t.getName(),
t.getValue().toString());
}
}
@@ -417,7 +420,7 @@
*/
public void revertSettings() {
metanodeProperties.revertProperties();
- AttributeManager.revertSettings();
+ defaultAttributeManager.revertSettings();
}
/**
@@ -435,7 +438,7 @@
* @param network the network we're updating our override values for
*/
public void updateOverrides(CyNetwork network) {
- AttributeManager.loadHandlerMappings(network);
+ defaultAttributeManager.loadHandlerMappings(network);
}
/**
@@ -489,11 +492,12 @@
*/
private String[] getAttributes() {
CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
- CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+ // CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
List<String> attributeList = new ArrayList();
- makeAttributes("node", nodeAttributes, attributeList);
- makeAttributes("edge", edgeAttributes, attributeList);
+ makeAttributes(null, nodeAttributes, attributeList);
+ // makeAttributes("node", nodeAttributes, attributeList);
+ // makeAttributes("edge", edgeAttributes, attributeList);
String [] a = new String[1];
attributeArray = attributeList.toArray(a);
Arrays.sort(attributeArray);
@@ -554,7 +558,7 @@
revertSettings();
setVisible(false);
} else if (command.equals("clear")) {
- AttributeManager.clearSettings();
+ defaultAttributeManager.clearSettings();
tunableChanged(attrList);
// Apply the current settings to the selected metanodes
@@ -592,11 +596,11 @@
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);
+ mn.setAttributeManager(defaultAttributeManager);
}
public void tunableChanged(Tunable t) {
@@ -611,7 +615,7 @@
MetaNodeManager.setExpandedOpacityDefault(metanodeOpacity);
} else if (t.getName().equals("enableHandling")) {
enableHandling = ((Boolean) t.getValue()).booleanValue();
- AttributeManager.setEnable(enableHandling);
+ defaultAttributeManager.setEnable(enableHandling);
enableTunables(enableHandling);
} else if (t.getName().equals("nodeChartAttribute")) {
nodeChartAttribute = (String)getListValue(t);
@@ -632,7 +636,7 @@
AttributeHandlingType handlerType =
(AttributeHandlingType)getListValue(t);
// Create the handler
- AttributeManager.addHandler(attributeWP, handlerType);
+
defaultAttributeManager.addHandler(attributeWP.substring(5), handlerType);
}
repaint();
}
@@ -640,16 +644,10 @@
private void updateAttributeHandlers(String attributeWP) {
CyAttributes attrs = null;
- // Strip prefix
- String attribute = attributeWP.substring(5);
+ attrs = Cytoscape.getNodeAttributes();
- if (attributeWP.startsWith("edge"))
- attrs = Cytoscape.getEdgeAttributes();
- else
- attrs = Cytoscape.getNodeAttributes();
+ byte type = attrs.getType(attributeWP);
- byte type = attrs.getType(attribute);
-
// Get the list
AttributeHandlingType[] hTypes =
AttributeManager.getHandlingOptions(type);
AttributeHandlingType[] handlingTypes = new
AttributeHandlingType[hTypes.length+1];
@@ -667,7 +665,7 @@
typeList.setLowerBound(handlingTypes);
// Do we already have a handler?
- AttributeHandler handler =
AttributeManager.getHandler(attributeWP);
+ AttributeHandler handler =
defaultAttributeManager.getHandler(attributeWP);
if (handler != null) {
// Yes, show the right one to the user
for (int i = 0; i < handlingTypes.length; i++) {
Modified:
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/NestedNetworkView.java
===================================================================
---
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/NestedNetworkView.java
2011-05-20 03:41:57 UTC (rev 25506)
+++
csplugins/trunk/ucsf/scooter/metaNodePlugin2/src/metaNodePlugin2/view/NestedNetworkView.java
2011-05-21 05:13:01 UTC (rev 25507)
@@ -60,7 +60,7 @@
// Move the nodes around
Dimension boundingBox = ViewUtils.restoreNodes(group, nn,
nnView, position, Cytoscape.getNodeAttributes(), null);
- System.out.println("Bounding box for "+group.toString()+" is
"+boundingBox.getWidth()+"x"+boundingBox.getHeight());
+ // System.out.println("Bounding box for "+group.toString()+" is
"+boundingBox.getWidth()+"x"+boundingBox.getHeight());
// Add it to the network map as a child of the group's network
CyNetwork network = group.getNetwork();
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