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Added comments to SBML2PRISM

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This commit is contained in:
LukasBuecherl 2022-07-14 13:15:28 -06:00
parent 5453e5031d
commit b8cad2fe48
1 changed files with 41 additions and 8 deletions
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49
conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/SBML2PRISM.java
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@ -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));
}
@ -227,16 +235,24 @@ 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;
@ -244,16 +260,27 @@ public class SBML2PRISM {
return speciesname;
}
}
/*
* 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));
}