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SBML-to-PRISM updates: maxAmount tidy up, listOfParameters bugfix, support for product stoichiometries. 

git-svn-id: https://www.prismmodelchecker.org/svn/prism/prism/trunk@370 bbc10eb1-c90d-0410-af57-cb519fbb1720
master
Dave Parker 19 years ago
parent
e52675b838
commit
21bfd39f10
1 changed files with 76 additions and 35 deletions
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  1. 111
      prism/src/prism/SBML2Prism.java

111
prism/src/prism/SBML2Prism.java
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@ -44,19 +44,21 @@ public class SBML2Prism implements EntityResolver
private ArrayList<Species> speciesList;
private ArrayList<Parameter> parameterList;
private ArrayList<Reaction> reactionList;
private int scaleFactor;
private int maxAmount;
// Calling point: e.g. java -cp classes prism.SBML2Prism myfile.sbml 100
// (100 denotes (integer) scale factor used to compute population sizes from (real-valued) concentrations, default is 10)
//
// (100 denotes (integer) maximum for species population sizes, default is 100)
// (also used to compute amounts from (real-valued) concentrations)
public static void main(String args[])
{
try {
if (args.length < 1) {
System.err.println("Usage: java -cp classes prism.SBML2Prism <sbml_file> [scale_factor]");
System.err.println("Usage: java -cp classes prism.SBML2Prism <sbml_file> [max_amount]");
System.exit(1);
}
new SBML2Prism().load(new File(args[0]), (args.length>1)?args[1]:"10");
new SBML2Prism().load(new File(args[0]), (args.length>1)?args[1]:"100");
}
catch (PrismException e) {
System.err.println("Error: "+e.getMessage());
@ -66,7 +68,7 @@ public class SBML2Prism implements EntityResolver
// Main method: load SBML file, process and sent resulting PRISM file to stdout
public void load(File f, String scaleFactor) throws PrismException
public void load(File f, String maxAmount) throws PrismException
{
try {
// obtain exclusive acces to the prism parser
@ -75,8 +77,8 @@ public class SBML2Prism implements EntityResolver
// translate
try {
try { this.scaleFactor = Integer.parseInt(scaleFactor); }
catch (NumberFormatException e) { throw new PrismException("Invalid scale factor \""+scaleFactor+"\""); }
try { this.maxAmount = Integer.parseInt(maxAmount); }
catch (NumberFormatException e) { throw new PrismException("Invalid max amount \""+maxAmount+"\""); }
Document doc = parseSBML(f);
extractModelFromSBML(doc);
//printModel(System.err);
@ -158,12 +160,14 @@ public class SBML2Prism implements EntityResolver
{
Element e, e_model, e_list, e_species, e_parameter, e_reaction, e_kinetics, e_mathml, e_params;
NodeList nodes, nodes2;
Node node = null;
Species species;
Parameter parameter;
Reaction reaction;
int i, j, n, m;
int i, j, k, n, m;
double d;
String s;
String s, s2;
boolean found;
// Get "model" element of SBML file
nodes = doc.getDocumentElement().getElementsByTagName("model");
@ -183,8 +187,16 @@ public class SBML2Prism implements EntityResolver
// Process list of parameters (if present)
parameterList = new ArrayList<Parameter>();
e_list = (Element)e_model.getElementsByTagName("listOfParameters").item(0);
if (e_list != null) {
// Look at direct children only (there might be listOfParameters nodes lower in the tree)
nodes = e_model.getChildNodes();
n = nodes.getLength();
found = false;
for (i = 0; i < n; i++) {
node = nodes.item(i);
if ("listOfParameters".equals(node.getNodeName())) { found = true; break; }
}
if (found) {
e_list = (Element)node;
nodes = e_list.getElementsByTagName("parameter");
n = nodes.getLength();
for (i = 0; i < n; i++) {
@ -224,8 +236,15 @@ public class SBML2Prism implements EntityResolver
m = nodes2.getLength();
for (j = 0; j < m; j++) {
e = (Element)nodes2.item(j);
// Get species name of product
s = e.getAttribute("species");
reaction.addProduct(s);
// Get stoichiometry if present
s2 = e.getAttribute("stoichiometry");
k = 1;
if (s2.length() > 0) try { k = Integer.parseInt(s2); }
catch (NumberFormatException ex) { throw new PrismException("Invalid stoichiometry value \""+s2+"\""); }
// Add product to reaction
reaction.addProduct(s, k);
}
}
@ -276,6 +295,14 @@ public class SBML2Prism implements EntityResolver
Parameter parameter;
HashSet<String> modulesNames;
HashSet<String> prismIdents;
// Look at initial amounts for all species
// If any exceed MAX_AMOUNT, increase it accordingly
n = speciesList.size();
for (i = 0; i < n; i++) {
species = speciesList.get(i);
if (species.init > maxAmount) maxAmount = (int)species.init;
}
// Generate unique and valid PRISM identifier (module and variable name) for each species
modulesNames = new HashSet<String>();
@ -337,7 +364,7 @@ public class SBML2Prism implements EntityResolver
private void printPRISMModel(File f) throws PrismException
{
int i, i2, n, n2;
int i, i2, n, n2, before, after;
Species species;
Reaction reaction;
Parameter parameter;
@ -349,9 +376,7 @@ public class SBML2Prism implements EntityResolver
s += "// File generated by automatic SBML-to-PRISM conversion\n";
s += "// Original SBML file: " + f.getPath() + "\n\n";
s += "ctmc\n";
//
s += "\nconst int SCALE_FACTOR = " + scaleFactor + ";\n";
s += "\nconst int MAX_AMOUNT = " + maxAmount + ";\n";
// Generate constant definition for each (model and reaction) parameter
n = parameterList.size();
@ -380,35 +405,34 @@ public class SBML2Prism implements EntityResolver
for (i = 0; i < n; i++) {
species = speciesList.get(i);
s += "\n// Species " + species + "\n";
s += "const int "+species.prismName+"_MAX = MAX_AMOUNT;\n";
s += "module " + species.prismName + "\n";
// Generate variable representing the amount of this species
s += "\t\n\t" + species.prismName + " : [0.." + scaleFactor + "]";
s += " init " + (int)Math.round(scaleFactor*species.init) + "; // Initial amount " + species.init + "\n\t\n";
s += "\t\n\t" + species.prismName + " : [0.."+species.prismName+"_MAX]";
s += " init " + (int)species.init + "; // Initial amount " + (int)species.init + "\n\t\n";
// s += " init " + (int)Math.round(scaleFactor*species.init) + "; // Initial amount " + species.init + "\n\t\n";
// Generate a command for each reaction that involves this species as a reactant
// Generate a command for each reaction that involves this species
n2 = reactionList.size();
for (i2 = 0; i2 < n2; i2++) {
reaction = reactionList.get(i2);
if (reaction.reactants.contains(species.id)) {
if (reaction.isSpeciesInvolved(species.id)) {
s += "\t// " + reaction.id;
if (reaction.name.length() > 0) s += " (" + reaction.name + ")";
s += "\n";
s += "\t[" + reaction.id + "] " ;
s += species.prismName + " > 0 -> (" + species.prismName + "'=" + species.prismName + "-1);\n";
}
}
// Generate a command for each reaction that involves this species as a product
n2 = reactionList.size();
for (i2 = 0; i2 < n2; i2++) {
reaction = reactionList.get(i2);
if (reaction.products.contains(species.id)) {
s += "\t// " + reaction.id;
if (reaction.name.length() > 0) s += " (" + reaction.name + ")";
s += "\n";
s += "\t[" + reaction.id + "] " ;
s += species.prismName + " < " + scaleFactor + " -> (" + species.prismName + "'=" + species.prismName + "+1);\n";
before = reaction.before(species.id);
after = reaction.after(species.id);
if (before > 0) s += species.prismName + " > "+(before-1);
if (after-before > 0) {
if (before > 0) s += " &";
s += " " + species.prismName + " <= "+species.prismName + "_MAX-" + (after-before);
}
s += " -> (" + species.prismName + "'=" + species.prismName;
if (after-before > 0) s += "+" + (after-before);
if (after-before < 0) s += (after-before);
s += ");\n";
}
}
@ -511,6 +535,7 @@ public class SBML2Prism implements EntityResolver
public String name;
public ArrayList<String> reactants;
public ArrayList<String> products;
public ArrayList<Integer> productStoichs;
public Element kineticLaw;
public ArrayList<Parameter> parameters;
public Reaction(String id, String name)
@ -519,13 +544,28 @@ public class SBML2Prism implements EntityResolver
this.name = name;
reactants = new ArrayList<String>();
products = new ArrayList<String>();
productStoichs = new ArrayList<Integer>();
kineticLaw = null;
parameters = new ArrayList<Parameter>();
}
public void addReactant(String reactant) { reactants.add(reactant); }
public void addProduct(String product) { products.add(product); }
public void addProduct(String product) { addProduct(product, 1); }
public void addProduct(String product, int stoich) { products.add(product); productStoichs.add(stoich); }
public void setKineticLaw(Element kineticLaw) { this.kineticLaw = kineticLaw; }
public void addParameter(String name, String value) { parameters.add(new Parameter(name, value)); }
public boolean isSpeciesInvolved(String species) { return reactants.contains(species) || products.contains(species); }
public int before(String species)
{
int i = reactants.indexOf(species);
if (i == -1) return 0;
return 1;
}
public int after(String species)
{
int i = products.indexOf(species);
if (i == -1) return 0;
return productStoichs.get(i);
}
public String toString()
{
String s = "";
@ -534,6 +574,7 @@ public class SBML2Prism implements EntityResolver
s += ":\n";
s += " Reactants: " + reactants+"\n";
s += " Products: " + products+"\n";
s += " Products stoichiometry: " + productStoichs+"\n";
s += " Kinetic law: " + kineticLaw+"\n";
s += " Parameters: " + parameters+"\n";
return s;

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