WIP

the XMLproducer for springsalad (springsalad-specific reaction rule spec params)
virtualcell · Sep 13, 2023 · 5f3a9e1 · 5f3a9e1
1 parent f58ea33
commit 5f3a9e1
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Showing 3 changed files with 27 additions and 6 deletions.
diff --git a/vcell-core/src/main/java/cbit/vcell/xml/XMLTags.java b/vcell-core/src/main/java/cbit/vcell/xml/XMLTags.java
@@ -862,11 +862,15 @@ public class XMLTags {
 	public final static String SiteCoordXAttrTag = "SiteCoordX";
 	public final static String SiteCoordYAttrTag = "SiteCoordY";
 	public final static String SiteCoordZAttrTag = "SiteCoordZ";
-	public final static String BondLengthAttrTag = "BondLength";
 
 	public final static String InternalLinkSpecTag = "InternalLinkSpec";
 	public final static String SiteOneRefAttrTag = "SiteOneRef";
 	public final static String SiteTwoRefAttrTag = "SiteTwoRef";
 
+	public final static String BondLengthAttrTag = "BondLength";
+	public final static String SubTypeAttrTag = "SubType";
+	public final static String TransitionConditionAttrTag = "TransitionCondition";
+
+
 
 }
diff --git a/vcell-core/src/main/java/cbit/vcell/xml/Xmlproducer.java b/vcell-core/src/main/java/cbit/vcell/xml/Xmlproducer.java
@@ -19,6 +19,7 @@
 import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.Iterator;
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Locale;
 import java.util.Map;
@@ -128,6 +129,7 @@
 import cbit.vcell.mapping.MolecularInternalLinkSpec;
 import cbit.vcell.mapping.ParameterContext.LocalParameter;
 import cbit.vcell.mapping.ParameterContext.ParameterRoleEnum;
+import cbit.vcell.mapping.ReactionRuleSpec.TransitionCondition;
 import cbit.vcell.mapping.RateRule;
 import cbit.vcell.mapping.ReactionContext;
 import cbit.vcell.mapping.ReactionRuleSpec;
@@ -1498,8 +1500,8 @@ private Element getXML(ReactionContext param) {
 	}
 	//Add ReactionRuleSpecs
 	ReactionRuleSpec[] reactionRuleArray = param.getReactionRuleSpecs();
-	if (reactionRuleArray.length>0){
-		reactioncontext.addContent( getXML(reactionRuleArray) );
+	if (reactionRuleArray.length>0) {
+		reactioncontext.addContent( getXML(reactionRuleArray, param.getSimulationContext()) );
 	}
 
 	return reactioncontext;
@@ -1523,13 +1525,28 @@ private Element getXML(ReactionSpec param) {
 }
 
 //For rateRules in SimulationContext
-public Element getXML(ReactionRuleSpec[] reactionRuleSpecs) {
+public Element getXML(ReactionRuleSpec[] reactionRuleSpecs, SimulationContext simContext) {
 	Element reactionRuleSpecsElement = new Element(XMLTags.ReactionRuleSpecsTag);
 	for (ReactionRuleSpec reactionRuleSpec : reactionRuleSpecs){
 		Element reactionRuleSpecElement = new Element(XMLTags.ReactionRuleSpecTag);
 		reactionRuleSpecElement.setAttribute(XMLTags.ReactionRuleRefAttrTag, mangle(reactionRuleSpec.getReactionRule().getName()));
 		reactionRuleSpecElement.setAttribute(XMLTags.ReactionRuleMappingAttrTag, mangle(reactionRuleSpec.getReactionRuleMapping().getDatabaseName()));
-
+		if(Application.SPRINGSALAD == simContext.getApplicationType()) {
+			reactionRuleSpecElement.setAttribute(XMLTags.BondLengthAttrTag, Double.toString(reactionRuleSpec.getFieldBondLength()));
+			//
+			// the next 2 attributes are sent only for debugging purposes, they are derived attributes and should be calculated at needed
+			//
+			Map<String, Object> analysisResults = new LinkedHashMap<> ();
+			reactionRuleSpec.analizeReaction(analysisResults);
+			ReactionRuleSpec.Subtype st = reactionRuleSpec.getSubtype(analysisResults);
+			reactionRuleSpecElement.setAttribute(XMLTags.SubTypeAttrTag, st.columnName);
+			if(ReactionRuleSpec.Subtype.TRANSITION == st) {
+				TransitionCondition tc = reactionRuleSpec.getTransitionCondition(analysisResults);
+				if(tc != null) {
+					reactionRuleSpecElement.setAttribute(XMLTags.TransitionConditionAttrTag, tc.vcellName);
+				}
+			}
+		}
 		reactionRuleSpecsElement.addContent(reactionRuleSpecElement);
 	}
 

diff --git a/vcell-server/src/main/java/cbit/vcell/modeldb/SimContextTable.java b/vcell-server/src/main/java/cbit/vcell/modeldb/SimContextTable.java
@@ -315,7 +315,7 @@ public static String getAppComponentsForDatabase(SimulationContext simContext) {
 	// ReactionRuleSpecs
 	ReactionRuleSpec[] reactionRuleSpecs = simContext.getReactionContext().getReactionRuleSpecs();
 	if (reactionRuleSpecs != null && reactionRuleSpecs.length > 0){
-		Element reactionRuleSpecsElement = xmlProducer.getXML(reactionRuleSpecs);
+		Element reactionRuleSpecsElement = xmlProducer.getXML(reactionRuleSpecs, simContext);
 		appComponentsElement.addContent(reactionRuleSpecsElement);
 	}