Merge pull request #531 from ckmadsen/operatorSiteFix

Operator site fix

Author: cjmyers

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/network/AbstractionEngine.java

@@ -240,9 +240,8 @@ public String abstractOperatorSite(Promoter promoter) {
 				Kao = KaoArray[0];
 			}
 			if (sbmlMode) {
-				promRate += "(np__" + promoter.getId() + "*ng__" + promoter.getId() + ")*((kb__" + promoter.getId() + "*Ko__"
+				promRate += "(ng__" + promoter.getId() + ")*((kb__" + promoter.getId() + "*Ko__"
 						+ promoter.getId() + "*RNAP)";
-				Utility.Parameter(kl,"np__" + promoter.getId(), np, GeneticNetwork.getMoleParameter(2));
 				Utility.Parameter(kl,"ng__" + promoter.getId(), ng, GeneticNetwork.getMoleParameter(2));
 				Utility.Parameter(kl,"kb__" + promoter.getId(), kb, GeneticNetwork.getMoleTimeParameter(1));
 				Utility.Parameter(kl,"Ko__" + promoter.getId(), Ko, GeneticNetwork.getMoleParameter(2));
@@ -358,10 +357,9 @@ else if (sbmlMode) {
 				Ko = KoArray[0];
 			}
 			if (sbmlMode) {
-				promRate += "(np__" + promoter.getId() + "*ko__" + promoter.getId() + "*ng__" + promoter.getId()
+				promRate += "(ko__" + promoter.getId() + "*ng__" + promoter.getId()
 				+ ")*((Ko__" + promoter.getId() + "*RNAP))/((1+(Ko__"
 				+ promoter.getId() + "*RNAP))";
-				Utility.Parameter(kl,"np__" + promoter.getId(), np, GeneticNetwork.getMoleParameter(2));
 				Utility.Parameter(kl,"ng__" + promoter.getId(), ng, GeneticNetwork.getMoleParameter(2));
 				Utility.Parameter(kl,"Ko__" + promoter.getId(), Ko, GeneticNetwork.getMoleParameter(2));
 				Utility.Parameter(kl,"ko__" + promoter.getId(), ko, GeneticNetwork.getMoleTimeParameter(1));

verification/src/main/java/edu/utah/ece/async/lema/verification/lpn/LPN.java

@@ -345,10 +345,10 @@ public static LPN convertToLHPN(ArrayList<String> specs, ArrayList<Object[]> con
 						}
 						if (!rate.equals("") || !reactionProductions.equals("")) {
 							if (rate.equals("")) {
-								rate = "(" + reactionProductions + ")";
+								rate = "(" + np + "*(" + reactionProductions + "))";
 							}
 							else if (!reactionProductions.equals("")) {
-								rate = "(" + rate + "+" + reactionProductions + ")";
+								rate = "(" + rate + "+" + np + "*(" + reactionProductions + "))";
 							}
 							LHPN.addTransition(specs.get(i) + "_trans" + transNum);
 							LHPN.addMovement(previousPlaceName, specs.get(i) + "_trans" + transNum);