Bound/Unbound option is now available and works
This commit is contained in:
LukasBuecherl
parent
b8cad2fe48
commit
927062edeb
2 changed files with 391 additions and 201 deletions
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@ -106,7 +106,6 @@ public class Converter {
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System.err.println("\t -env <SBML environment file> is the complete directory path of the environmental file to instantiate to your model. This only works when VPR model generator is used");
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System.err.println("\t-Cello This option is for dynamic modeling of Cello parts and parametrization");
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System.err.println("\t-tmID Set the ID of the top SBML model");
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System.err.println("\t-prism SBOL to PRISM converter");
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System.exit(1);
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}
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@ -140,6 +139,7 @@ public class Converter {
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boolean isValidation = false; //indicate if only validate SBOL files
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boolean topEnvir = false; // determines if there is a topEnvironment model to be instantiated
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boolean CelloModel = false; // determines if Cello-based modeling should be done
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boolean PrismUnbound = true; // determines if the prism model should be bound or unbound
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String compFileResult = ""; //-cf
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String compareFile = ""; //-e
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@ -191,6 +191,9 @@ public class Converter {
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case "-t":
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typesInURI = true;
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break;
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case "-bound":
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PrismUnbound = false;
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break;
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case "-s":
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if(index+1 >= args.length || args[index+1].equals("-"))
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{
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@ -427,7 +430,7 @@ public class Converter {
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try
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{
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inputSBMLDoc = SBMLutilities.readSBML(fullInputFileName, null, null);
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SBML2PRISM.convertSBML2PRISM(inputSBMLDoc, fullInputFileName);
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SBML2PRISM.convertSBML2PRISM(inputSBMLDoc, fullInputFileName, PrismUnbound);
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}
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catch (XMLStreamException e)
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{
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@ -68,256 +68,443 @@ import edu.utah.ece.async.ibiosim.dataModels.biomodel.util.SBMLutilities;
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import edu.utah.ece.async.ibiosim.dataModels.util.GlobalConstants;
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/**
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* Perform conversion from SBML to PRISM.
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* Perform conversion from SBML to PRISM.
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*
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* @author Lukas Buecherl
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* @author Chris Myers
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* @author <a href="http://www.async.ece.utah.edu/ibiosim#Credits"> iBioSim Contributors </a>
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* @author <a href="http://www.async.ece.utah.edu/ibiosim#Credits"> iBioSim
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* Contributors </a>
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* @version %I%
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*/
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public class SBML2PRISM {
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/*
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* Convert SBML to Prism
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* Input: SBMLDocument, File
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* Output: void
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* Convert SBML to Prism Input: SBMLDocument, File Output: void
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*
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* Function takes in a SBML document and writes the prism conversion of the file in the same directory. The function also translates the constraint into
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* a properties file that is written in the same directory in a separate file. The original filename is used for the prism and property file. The SBMML
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* file ends in .xml, the prism file in .sm, and the properties file in .props.
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* Function takes in a SBML document and writes the prism conversion of the file
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* in the same directory. The function also translates the constraint into a
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* properties file that is written in the same directory in a separate file. The
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* original filename is used for the prism and property file. The SBMML file
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* ends in .xml, the prism file in .sm, and the properties file in .props.
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*
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* To run the converter use the following command:
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* java -jar conversion/target/iBioSim-conversion-3.1.0-SNAPSHOT-jar-with-dependencies.jar -l PRISM YOURSBMLFILE.xml
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* To run the converter use the following command: java -jar
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* conversion/target/iBioSim-conversion-3.1.0-SNAPSHOT-jar-with-dependencies.jar
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* -l PRISM YOURSBMLFILE.xml
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*/
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public static void convertSBML2PRISM(SBMLDocument sbmlDoc, String filename) throws IOException
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{
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public static void convertSBML2PRISM(SBMLDocument sbmlDoc, String filename, boolean unbound) throws IOException {
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if (unbound) {
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convertSBML2PRISMUnbound(sbmlDoc, filename);
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} else {
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convertSBML2PRISMbound(sbmlDoc, filename);
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}
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}
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private static void convertSBML2PRISMUnbound(SBMLDocument sbmlDoc, String filename) throws IOException {
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Model model = sbmlDoc.getModel();
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File file = new File(filename.replace(".xml", ".sm"));
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// Opening and writing preamble to the file
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FileWriter out = new FileWriter(file);
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out.write("// File generated by SBML-to-PRISM converter\n");
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out.write("// Original file: " + filename + "\n");
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out.write("// @GeneticLogicLab\n");
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out.write("\n");
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out.write("ctmc\n");
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out.write("\n");
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out.write("// const int MAX_AMOUNT = ADD VALUE \n");
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out.write("\n");
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// Identify compartments and their size
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out.write("// Compartment size\n");
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for (int i = 0; i < model.getCompartmentCount(); i++)
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{
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Compartment compartment = model.getCompartment(i);
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out.write("const double " + checkReservedKeywordPrism(compartment.getId()) + " = " + compartment.getSize() + ";\n");
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}
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out.write("\n");
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// Identify model parameters
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out.write("// Model parameters\n");
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for (int i = 0; i < model.getParameterCount(); i++)
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{
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Parameter parameter = model.getParameter(i);
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out.write("const double "+ checkReservedKeywordPrism(parameter.getId()) + " = " + parameter.getValue() +"; // " + parameter.getName() + "\n"); // if not null name
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}
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out.write("\n");
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// Identify model species
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for (int i = 0; i < model.getSpeciesCount(); i++)
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{
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// Write out syntax
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// For function checkReservedKeywordPrism see below
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Species species = model.getSpecies(i);
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out.write("// Species " + checkReservedKeywordPrism(species.getId()) + "\n");
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out.write("// const int " + checkReservedKeywordPrism(species.getId()) + "_MAX = MAX_AMOUNT;\n");
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out.write("module "+ checkReservedKeywordPrism(species.getId()) + "\n");
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out.write("\n");
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out.write(" // "+ checkReservedKeywordPrism(species.getId()) +" : " + "[0.." + checkReservedKeywordPrism(species.getId()) + "_MAX] init "+ (int) species.getInitialAmount() + ";\n");
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out.write(" "+ checkReservedKeywordPrism(species.getId()) + " : " + "int init " + (int) (species.getInitialAmount()) + ";\n");
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out.write("\n");
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// Iterate over reactions
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for (int j = 0; j < model.getReactionCount(); j++)
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{
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Reaction reaction = model.getReaction(j);
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// Identify reactants and products
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SpeciesReference reactant = reaction.getReactantForSpecies(species.getId());
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SpeciesReference product = reaction.getProductForSpecies(species.getId());
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if(reactant != null)
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{
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out.write(" // " + checkReservedKeywordPrism(reaction.getId()) + "\n");
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out.write(" [" + checkReservedKeywordPrism(reaction.getId()) + "] " + checkReservedKeywordPrism(species.getId()) + " > " + (int) (reactant.getStoichiometry() - 1) + " -> (" + checkReservedKeywordPrism(species.getId()) + "\'=" + checkReservedKeywordPrism(species.getId()) + "-" + (int) reactant.getStoichiometry() + ");\n");
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} else if (product != null)
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{
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out.write(" // " + checkReservedKeywordPrism(reaction.getId()) + "\n");
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out.write(" [" + checkReservedKeywordPrism(reaction.getId()) + "] " + checkReservedKeywordPrism(species.getId()) + " >= " + "0 -> (" + checkReservedKeywordPrism(species.getId()) + "\'=" + checkReservedKeywordPrism(species.getId()) + "+" + (int) product.getStoichiometry() + ");\n");
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}
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}
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out.write("\n");
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out.write("endmodule\n");
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out.write("\n");
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}
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// Identify reaction rate
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out.write("// Reaction rates\n");
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out.write("module reaction_rates\n");
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// Opening and writing preamble to the file
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FileWriter out = new FileWriter(file);
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out.write("// File generated by SBML-to-PRISM converter\n");
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out.write("// Original file: " + filename + "\n");
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out.write("// @GeneticLogicLab\n");
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out.write("\n");
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out.write("ctmc\n");
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out.write("\n");
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out.write("// const int MAX_AMOUNT = ADD VALUE \n");
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out.write("\n");
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// Identify compartments and their size
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out.write("// Compartment size\n");
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for (int i = 0; i < model.getCompartmentCount(); i++) {
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Compartment compartment = model.getCompartment(i);
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out.write("const double " + checkReservedKeywordPrism(compartment.getId()) + " = " + compartment.getSize()
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+ ";\n");
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}
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out.write("\n");
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// Identify model parameters
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out.write("// Model parameters\n");
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for (int i = 0; i < model.getParameterCount(); i++) {
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Parameter parameter = model.getParameter(i);
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out.write("const double " + checkReservedKeywordPrism(parameter.getId()) + " = " + parameter.getValue()
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+ "; // " + parameter.getName() + "\n"); // if not null name
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}
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out.write("\n");
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// Identify model species
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for (int i = 0; i < model.getSpeciesCount(); i++) {
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// Write out syntax
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// For function checkReservedKeywordPrism see below
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Species species = model.getSpecies(i);
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out.write("// Species " + checkReservedKeywordPrism(species.getId()) + "\n");
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out.write("// const int " + checkReservedKeywordPrism(species.getId()) + "_MAX = MAX_AMOUNT;\n");
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out.write("module " + checkReservedKeywordPrism(species.getId()) + "\n");
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out.write("\n");
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for (int i = 0; i < model.getReactionCount(); i++)
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{
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Reaction reaction = model.getReaction(i);
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// Write state transitions
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out.write(" // " + checkReservedKeywordPrism(reaction.getId()) + ": -> ");
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for(int j = 0; j < reaction.getProductCount(); j++)
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{
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out.write(checkReservedKeywordPrism(reaction.getProduct(j).getSpecies()) + " ");
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out.write(" // " + checkReservedKeywordPrism(species.getId()) + " : " + "[0.."
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+ checkReservedKeywordPrism(species.getId()) + "_MAX] init " + (int) species.getInitialAmount()
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+ ";\n");
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out.write(" " + checkReservedKeywordPrism(species.getId()) + " : " + "int init "
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+ (int) (species.getInitialAmount()) + ";\n");
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out.write("\n");
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// Iterate over reactions
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for (int j = 0; j < model.getReactionCount(); j++) {
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Reaction reaction = model.getReaction(j);
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// Identify reactants and products
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SpeciesReference reactant = reaction.getReactantForSpecies(species.getId());
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SpeciesReference product = reaction.getProductForSpecies(species.getId());
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if (reactant != null) {
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out.write(" // " + checkReservedKeywordPrism(reaction.getId()) + "\n");
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out.write(" [" + checkReservedKeywordPrism(reaction.getId()) + "] "
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+ checkReservedKeywordPrism(species.getId()) + " > "
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+ (int) (reactant.getStoichiometry() - 1) + " -> ("
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+ checkReservedKeywordPrism(species.getId()) + "\'="
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+ checkReservedKeywordPrism(species.getId()) + "-" + (int) reactant.getStoichiometry()
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+ ");\n");
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} else if (product != null) {
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out.write(" // " + checkReservedKeywordPrism(reaction.getId()) + "\n");
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out.write(" [" + checkReservedKeywordPrism(reaction.getId()) + "] "
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+ checkReservedKeywordPrism(species.getId()) + " >= " + "0 -> ("
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+ checkReservedKeywordPrism(species.getId()) + "\'="
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+ checkReservedKeywordPrism(species.getId()) + "+" + (int) product.getStoichiometry()
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+ ");\n");
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}
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out.write("\n");
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// Get the math for the reaction rate
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out.write(" [" + checkReservedKeywordPrism(reaction.getId()) + "] " + checkReserveKeywordMath(SBMLutilities.convertMath2PrismProperty(reaction.getKineticLaw().getMath()), model) + " > 0 -> " + "(" + checkReserveKeywordMath(SBMLutilities.convertMath2PrismProperty(reaction.getKineticLaw().getMath()), model) + ") : true;\n");
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out.write("\n");
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}
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out.write("\n");
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out.write("endmodule\n");
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out.write("\n");
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// Identify rewards
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out.write("// Reward structures (one per species)");
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out.write("\n");
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for (int i = 0; i < model.getSpeciesCount(); i++)
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{
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Species species = model.getSpecies(i);
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out.write("// Reward " + (i+1) + ": " + checkReservedKeywordPrism(species.getId()) + "\n");
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out.write("rewards " + "\"" + checkReservedKeywordPrism(species.getId()) + "\" true : " + checkReservedKeywordPrism(species.getId()) + "; endrewards\n");
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}
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}
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out.close();
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// Write Properties File
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File property = new File(filename.replace(".xml", ".props"));
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FileWriter property_out = new FileWriter(property);
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// Property preamble
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property_out.write("// File generated by SBML-to-PRISM converter\n");
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property_out.write("// Original file: " + filename + "\n");
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property_out.write("// @GeneticLogicLab\n");
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property_out.write("\n");
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for (int i = 0; i < model.getConstraintCount(); i++)
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{
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// Get and write translation of constraint
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property_out.write(checkReserveKeywordMath(SBMLutilities.convertMath2PrismProperty(model.getConstraint(i).getMath()), model));
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// Identify reaction rate
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out.write("// Reaction rates\n");
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out.write("module reaction_rates\n");
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out.write("\n");
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for (int i = 0; i < model.getReactionCount(); i++) {
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Reaction reaction = model.getReaction(i);
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// Write state transitions
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out.write(" // " + checkReservedKeywordPrism(reaction.getId()) + ": -> ");
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for (int j = 0; j < reaction.getProductCount(); j++) {
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out.write(checkReservedKeywordPrism(reaction.getProduct(j).getSpecies()) + " ");
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}
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property_out.close();
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out.write("\n");
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// Get the math for the reaction rate
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out.write(" [" + checkReservedKeywordPrism(reaction.getId()) + "] "
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+ checkReserveKeywordMath(
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SBMLutilities.convertMath2PrismProperty(reaction.getKineticLaw().getMath()), model)
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+ " > 0 -> " + "("
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+ checkReserveKeywordMath(
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SBMLutilities.convertMath2PrismProperty(reaction.getKineticLaw().getMath()), model)
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+ ") : true;\n");
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out.write("\n");
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}
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out.write("endmodule\n");
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out.write("\n");
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// Identify rewards
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out.write("// Reward structures (one per species)");
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out.write("\n");
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for (int i = 0; i < model.getSpeciesCount(); i++) {
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Species species = model.getSpecies(i);
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out.write("// Reward " + (i + 1) + ": " + checkReservedKeywordPrism(species.getId()) + "\n");
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out.write("rewards " + "\"" + checkReservedKeywordPrism(species.getId()) + "\" true : "
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+ checkReservedKeywordPrism(species.getId()) + "; endrewards\n");
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}
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out.close();
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// Write Properties File
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File property = new File(filename.replace(".xml", ".props"));
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FileWriter property_out = new FileWriter(property);
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// Property preamble
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property_out.write("// File generated by SBML-to-PRISM converter\n");
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property_out.write("// Original file: " + filename + "\n");
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property_out.write("// @GeneticLogicLab\n");
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property_out.write("\n");
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for (int i = 0; i < model.getConstraintCount(); i++) {
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// Get and write translation of constraint
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property_out.write(checkReserveKeywordMath(
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SBMLutilities.convertMath2PrismProperty(model.getConstraint(i).getMath()), model));
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}
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property_out.close();
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}
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private static void convertSBML2PRISMbound(SBMLDocument sbmlDoc, String filename) throws IOException {
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Model model = sbmlDoc.getModel();
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File file = new File(filename.replace(".xml", ".sm"));
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// Opening and writing preamble to the file
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FileWriter out = new FileWriter(file);
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out.write("// File generated by SBML-to-PRISM converter\n");
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out.write("// Original file: " + filename + "\n");
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out.write("// @GeneticLogicLab\n");
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out.write("\n");
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out.write("ctmc\n");
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out.write("\n");
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double maxAmount = 0.0;
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for (int i = 0; i < model.getSpeciesCount(); i++) {
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Species species = model.getSpecies(i);
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if (species.getInitialAmount() > maxAmount) {
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maxAmount = species.getInitialAmount();
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}
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}
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out.write(" const int MAX_AMOUNT = " + (int) maxAmount + ";\n");
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out.write("\n");
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// Identify compartments and their size
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out.write("// Compartment size\n");
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for (int i = 0; i < model.getCompartmentCount(); i++) {
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Compartment compartment = model.getCompartment(i);
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out.write("const double " + checkReservedKeywordPrism(compartment.getId()) + " = " + compartment.getSize()
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+ ";\n");
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}
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out.write("\n");
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// Identify model parameters
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out.write("// Model parameters\n");
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for (int i = 0; i < model.getParameterCount(); i++) {
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Parameter parameter = model.getParameter(i);
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out.write("const double " + checkReservedKeywordPrism(parameter.getId()) + " = " + parameter.getValue()
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+ "; // " + parameter.getName() + "\n"); // if not null name
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}
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out.write("\n");
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|
||||
// 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");
|
||||
out.write("module " + checkReservedKeywordPrism(species.getId()) + "\n");
|
||||
out.write("\n");
|
||||
out.write(" " + checkReservedKeywordPrism(species.getId()) + " : " + "[0.."
|
||||
+ checkReservedKeywordPrism(species.getId()) + "_MAX] init " + (int) species.getInitialAmount()
|
||||
+ ";\n");
|
||||
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());
|
||||
|
||||
if (reactant != null) {
|
||||
out.write(" // " + checkReservedKeywordPrism(reaction.getId()) + "\n");
|
||||
out.write(" [" + checkReservedKeywordPrism(reaction.getId()) + "] "
|
||||
+ checkReservedKeywordPrism(species.getId()) + " > "
|
||||
+ (int) (reactant.getStoichiometry() - 1) + " -> ("
|
||||
+ checkReservedKeywordPrism(species.getId()) + "\'="
|
||||
+ checkReservedKeywordPrism(species.getId()) + "-" + (int) reactant.getStoichiometry()
|
||||
+ ");\n");
|
||||
} else if (product != null) {
|
||||
out.write(" // " + checkReservedKeywordPrism(reaction.getId()) + "\n");
|
||||
out.write(" [" + checkReservedKeywordPrism(reaction.getId()) + "] "
|
||||
+ checkReservedKeywordPrism(species.getId()) + " <= " + checkReservedKeywordPrism(species.getId()) + "_MAX-"
|
||||
+ (int) product.getStoichiometry() + " -> ("
|
||||
+ checkReservedKeywordPrism(species.getId()) + "\'="
|
||||
+ checkReservedKeywordPrism(species.getId()) + "+" + (int) product.getStoichiometry()
|
||||
+ ");\n");
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
out.write("\n");
|
||||
out.write("endmodule\n");
|
||||
out.write("\n");
|
||||
}
|
||||
|
||||
// Identify reaction rate
|
||||
out.write("// Reaction rates\n");
|
||||
out.write("module reaction_rates\n");
|
||||
out.write("\n");
|
||||
|
||||
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++) {
|
||||
out.write(checkReservedKeywordPrism(reaction.getProduct(j).getSpecies()) + " ");
|
||||
}
|
||||
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");
|
||||
|
||||
}
|
||||
out.write("endmodule\n");
|
||||
|
||||
out.write("\n");
|
||||
|
||||
// Identify rewards
|
||||
out.write("// Reward structures (one per species)");
|
||||
out.write("\n");
|
||||
|
||||
for (int i = 0; i < model.getSpeciesCount(); i++) {
|
||||
Species species = model.getSpecies(i);
|
||||
|
||||
out.write("// Reward " + (i + 1) + ": " + checkReservedKeywordPrism(species.getId()) + "\n");
|
||||
out.write("rewards " + "\"" + checkReservedKeywordPrism(species.getId()) + "\" true : "
|
||||
+ checkReservedKeywordPrism(species.getId()) + "; endrewards\n");
|
||||
|
||||
}
|
||||
|
||||
out.close();
|
||||
|
||||
// Write Properties File
|
||||
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");
|
||||
property_out.write("\n");
|
||||
|
||||
for (int i = 0; i < model.getConstraintCount(); i++) {
|
||||
// Get and write translation of constraint
|
||||
property_out.write(checkReserveKeywordMath(
|
||||
SBMLutilities.convertMath2PrismProperty(model.getConstraint(i).getMath()), model));
|
||||
}
|
||||
|
||||
property_out.close();
|
||||
|
||||
}
|
||||
|
||||
/*
|
||||
* Check for reserved keywords as species names
|
||||
* Input: (String) NameOfSpecies
|
||||
* 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.
|
||||
* 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");
|
||||
|
||||
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))
|
||||
{
|
||||
if (keywords.contains(speciesname)) {
|
||||
return "_" + speciesname;
|
||||
}else {
|
||||
} else {
|
||||
return speciesname;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/*
|
||||
* Check for reserved keywords as species names in math properties
|
||||
* Input: (String) NameOfSpecies, model sbmlDoc.getModel();
|
||||
* Output: (String) _NameOfSpecies
|
||||
* 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.
|
||||
* 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
|
||||
|
||||
// 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++)
|
||||
{
|
||||
|
||||
// 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);
|
||||
|
||||
if(keywords.contains(species.getId()))
|
||||
{
|
||||
|
||||
if (keywords.contains(species.getId())) {
|
||||
speciesString.add(species.getId());
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
//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)))
|
||||
{
|
||||
|
||||
// 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);
|
||||
// System.err.println(Target);
|
||||
math = math.replace(Target, "_" + keywords.get(i));
|
||||
//System.err.println(math);
|
||||
|
||||
// System.err.println(math);
|
||||
|
||||
// Replace species names in property files
|
||||
// In property files species names are lead by a (
|
||||
// In property files species names are lead by a (
|
||||
String TargetProperty = "(" + keywords.get(i);
|
||||
math = math.replace(TargetProperty, "(_" + keywords.get(i));
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
return math;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
/*
|
||||
BioModel bioModel = BioModel.createBioModel(properties.getDirectory(), this);
|
||||
bioModel.load(filename);
|
||||
if (bioModel.flattenModel(true) != null) {}
|
||||
bioModel.getSBMLDocument()
|
||||
*/
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue