Author: pwang
Date: 2011-10-20 15:46:50 -0700 (Thu, 20 Oct 2011)
New Revision: 27255
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/data/ActivePathFinderParameters.java
Log:
Refactored to work with Cy3
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/data/ActivePathFinderParameters.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/data/ActivePathFinderParameters.java
2011-10-20 22:45:10 UTC (rev 27254)
+++
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/data/ActivePathFinderParameters.java
2011-10-20 22:46:50 UTC (rev 27255)
@@ -16,15 +16,21 @@
import java.util.Properties;
import java.util.Enumeration;
-import cytoscape.Cytoscape;
-import cytoscape.CyNode;
-import cytoscape.data.CyAttributes;
-import cytoscape.data.CyAttributesUtils;
-import cytoscape.logger.CyLogger;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.property.CyProperty;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyTable;
+import org.cytoscape.model.CyColumn;
+import csplugins.jActiveModules.util.SelectUtil;
+import org.cytoscape.model.CyTableUtil;
//---------------------------------------------------------------------------------------
public class ActivePathFinderParameters {
+ private static final Logger logger =
LoggerFactory.getLogger(ActivePathFinderParameters.class);
+
double initialTemperature = 1.0;
double finalTemperature = 0.01;
double hubAdjustment = 0;
@@ -59,9 +65,11 @@
List<Boolean> switchSigs = new ArrayList<Boolean>();
List<String> scalingMethods = new ArrayList<String>();
+ private CyNetwork network;
//
---------------------------------------------------------------------------------------
- public ActivePathFinderParameters(Properties properties){
+ public ActivePathFinderParameters(CyProperty<?>
cytoscapePropertiesServiceRef){
+ Properties properties = (Properties)
cytoscapePropertiesServiceRef.getProperties();
for (Enumeration e = properties.propertyNames() ; e.hasMoreElements()
;) {
String name = (String)e.nextElement();
if(name.startsWith("AP")){
@@ -142,7 +150,7 @@
overlapThreshold = Double.valueOf(property);
}
else{
-
CyLogger.getLogger(ActivePathFinderParameters.class).warn("Unrecognized option
"+name);
+ logger.warn("Unrecognized option "+name);
}
}
@@ -413,25 +421,30 @@
possibleExpressionAttrs.clear();
+ if (this.network == null){
+ return;
+ }
// find all of the double type parameters
- CyAttributes nodeAttrs = Cytoscape.getNodeAttributes();
- String[] names = nodeAttrs.getAttributeNames();
- for ( String name : names ) {
- if ( nodeAttrs.getType(name) ==
CyAttributes.TYPE_FLOATING ) {
- Map attrMap =
CyAttributesUtils.getAttribute(name,nodeAttrs);
+ CyTable nodeAttrs = this.network.getDefaultNodeTable();
+ String[] names =
(String[])CyTableUtil.getColumnNames(nodeAttrs).toArray();
- if ( attrMap == null )
+ for ( String name : names ) {
+ if ( nodeAttrs.getColumn(name).getType() == Float.class
||nodeAttrs.getColumn(name).getType() == Double.class) {
+
+ List<Float> values
=nodeAttrs.getColumn(name).getValues(Float.class);
+
+ if ( values == null )
continue; // no values have been
defined for the attr yet
boolean isPValue = true;
- for ( Object value : attrMap.values() ) {
+ for ( Object value : values ) {
double d =
((Double)value).doubleValue();
if ( d < 0 || d > 1 ) {
isPValue = false;
break;
}
}
-
+
if ( isPValue )
possibleExpressionAttrs.add(name);
}
@@ -506,5 +519,8 @@
} // toString
+ public void setNetwork(CyNetwork network){
+ this.network = network;
+ }
} // class ActivePathFinderParameters
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