Added comments to SBML2PRISM

conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/SBML2PRISM.java

@@ -135,6 +135,8 @@ public class SBML2PRISM {
 			// Identify model species
 			for (int i = 0; i < model.getSpeciesCount(); i++) 
 			{
+				// Write out syntax 
+				// For function checkReservedKeywordPrism see below
 				Species species = model.getSpecies(i);
 				out.write("// Species " + checkReservedKeywordPrism(species.getId()) + "\n");
 				out.write("// const int " + checkReservedKeywordPrism(species.getId()) + "_MAX = MAX_AMOUNT;\n");
@@ -144,10 +146,12 @@ public class SBML2PRISM {
 				out.write("  "+ checkReservedKeywordPrism(species.getId()) + "  :  " + "int init " + (int) (species.getInitialAmount()) + ";\n");
 				out.write("\n");
 				
+				// Iterate over reactions
 				for (int j = 0; j < model.getReactionCount(); j++) 
 				{
 					Reaction reaction = model.getReaction(j);
 					
+					// Identify reactants and products
 					SpeciesReference reactant = reaction.getReactantForSpecies(species.getId());
 					SpeciesReference product = reaction.getProductForSpecies(species.getId());
 					
@@ -169,8 +173,7 @@ public class SBML2PRISM {
 
 			}
 			
-			// Identify reaction rates
+			// Identify reaction rate
-			
 			out.write("// Reaction rates\n");
 			out.write("module reaction_rates\n");
 			out.write("\n");
@@ -178,6 +181,8 @@ public class SBML2PRISM {
 			for (int i = 0; i < model.getReactionCount(); i++) 
 			{
 				Reaction reaction = model.getReaction(i);
+				
+				// Write state transitions
 				out.write("		// " + checkReservedKeywordPrism(reaction.getId()) + ":  ->  ");
 				for(int j = 0; j < reaction.getProductCount(); j++)
 				{
@@ -185,6 +190,7 @@ public class SBML2PRISM {
 				}
 				out.write("\n");
 				
+				// Get the math for the reaction rate
 				out.write("		[" + checkReservedKeywordPrism(reaction.getId()) + "]  " + checkReserveKeywordMath(SBMLutilities.convertMath2PrismProperty(reaction.getKineticLaw().getMath()), model) + " > 0 -> " + "(" +  checkReserveKeywordMath(SBMLutilities.convertMath2PrismProperty(reaction.getKineticLaw().getMath()), model) + ") : true;\n");
 				out.write("\n");
 
@@ -192,11 +198,12 @@ public class SBML2PRISM {
 			out.write("endmodule\n");
 			
 			out.write("\n");
+			
+			// Identify rewards
 			out.write("// Reward structures (one per species)");
 			out.write("\n");
 
 			
-			// Identify rewards
 			for (int i = 0; i < model.getSpeciesCount(); i++) 
 			{
 				Species species = model.getSpecies(i);
@@ -212,6 +219,7 @@ public class SBML2PRISM {
 			File property = new File(filename.replace(".xml", ".props"));
 			FileWriter property_out = new FileWriter(property);
 			
+			// Property preamble
 			property_out.write("// File generated by SBML-to-PRISM converter\n");
 			property_out.write("// Original file: " + filename + "\n");
 			property_out.write("// @GeneticLogicLab\n");
@@ -219,7 +227,7 @@ public class SBML2PRISM {
 			
 			for (int i = 0; i < model.getConstraintCount(); i++) 
 			{
-				System.err.println(checkReserveKeywordMath(SBMLutilities.convertMath2PrismProperty(model.getConstraint(i).getMath()), model));
+				// Get and write translation of constraint
 				property_out.write(checkReserveKeywordMath(SBMLutilities.convertMath2PrismProperty(model.getConstraint(i).getMath()), model));
 			}
 			
@@ -228,15 +236,23 @@ public class SBML2PRISM {
 	}
 		
 	
-		
+	/*
+	 * Check for reserved keywords as species names
+	 * Input: (String) NameOfSpecies
+	 * Output: (String) _NameOfSpecies
+	 * 
+	 * Function checks if the name of a species is also a reserved keyword in the prism language. If that is the case, the species name is replaced
+	 * by the species name lead by an underscore.
+	 */
 	private static String checkReservedKeywordPrism(String speciesname)	
 	{
-		
+		// List of reserved keywords in the prism language 
 		List<String> keywords = Arrays.asList("A", "bool", "clock", "const", "ctmc", "C", "double", "dtmc", "E", "endinit", "endinvariant", "endmodule",
 				"endobservables", "endrewards", "endsystem", "false", "formula", "filter", "func", "F", "global", "G", "init", "invariant", "I", "int", "label", 
 				"max", "mdp", "min", "module", "X", "nondeterministic", "observable", "observables", "of", "Pmax", "Pmin", "P", "pomdp", "popta", "probabilistic",
 				"prob", "pta", "rate", "rewards", "Rmax", "Rmin", "R", "S", "stochastic", "system", "true", "U", "W");
 		
+		// Check if species name is in the list
 		if (keywords.contains(speciesname))
 		{
 			return "_" + speciesname;
@@ -245,15 +261,26 @@ public class SBML2PRISM {
 		}
 	}
 	
+	/*
+	 * Check for reserved keywords as species names in math properties
+	 * Input: (String) NameOfSpecies, model sbmlDoc.getModel();
+	 * Output: (String) _NameOfSpecies
+	 * 
+	 * Function checks if the name of a species in a math function is also a reserved keyword in the prism language. If that is the case, the species name in the
+	 * function is replaced by the species name lead by an underscore.
+	 */
 	private static String checkReserveKeywordMath(String math, Model model) {
 		
+		// List of reserved keywords in the prism language 
 		List<String> keywords = Arrays.asList("A", "bool", "clock", "const", "ctmc", "C", "double", "dtmc", "E", "endinit", "endinvariant", "endmodule",
 				"endobservables", "endrewards", "endsystem", "false", "formula", "filter", "func", "F", "global", "G", "init", "invariant", "I", "int", "label", 
 				"max", "mdp", "min", "module", "X", "nondeterministic", "observable", "observables", "of", "Pmax", "Pmin", "P", "pomdp", "popta", "probabilistic",
 				"prob", "pta", "rate", "rewards", "Rmax", "Rmin", "R", "S", "stochastic", "system", "true", "U", "W");
 	
+		// Declaration of new string list 
 		ArrayList<String> speciesString = new ArrayList<String>();
 		
+		// Iterating over species, if species name is a reserved keyword add it to list speciesString
 		for (int i = 0; i < model.getSpeciesCount(); i++) 
 		{
 			Species species = model.getSpecies(i);
@@ -267,14 +294,20 @@ public class SBML2PRISM {
 		
 		//System.err.println(speciesString);
 		
+		// Iterate over list and replace species name 
 		for(int i = 0; i < keywords.size(); i++) 
 		{
 			if(speciesString.contains(keywords.get(i))) 
 			{
+				// Replace species in math equations
+				// In equations species names are lead by a space
 				String Target = " " + keywords.get(i);
 				//System.err.println(Target);
 				math = math.replace(Target, "_" + keywords.get(i));
 				//System.err.println(math);
+				
+				// Replace species names in property files
+				// In property files species names are lead by a ( 
 				String TargetProperty = "(" + keywords.get(i);
 				math = math.replace(TargetProperty, "(_" + keywords.get(i));
 			}