public static void main(String[] args) {
if (args.length < 1) {
System.out.println("Usage: evaluateCustomMath formula [model containing values]");
System.exit(1);
}
String formula = args[0];
String filename = args.length == 2 ? args[1] : null;
ASTNode math = libsbml.parseFormula(formula);
if (math == null) {
System.out.println("Invalid formula, aborting.");
System.exit(1);
}
SBMLDocument doc = null;
if (filename != null) {
doc = libsbml.readSBML(filename);
if (doc.getNumErrors(libsbml.LIBSBML_SEV_ERROR) > 0) {
System.out.println("The models contains errors, please correct them before continuing.");
doc.printErrors();
System.exit(1);
}
// the following maps a list of ids to their corresponding model values
// this makes it possible to evaluate expressions involving SIds.
SBMLTransforms.mapComponentValues(doc.getModel());
} else {
// create dummy document
doc = new SBMLDocument(3, 1);
}
double result = SBMLTransforms.evaluateASTNode(math, doc.getModel());
System.out.println(String.format("%s = %s", formula, result));
}
public static void main(String[] args) {
if (args.length != 2) {
println("Usage: java echoSBML input-filename output-filename");
System.exit(2);
}
SBMLReader reader = new SBMLReader();
SBMLWriter writer = new SBMLWriter();
SBMLDocument doc = reader.readSBML(args[0]);
if (doc.getNumErrors() > 0) {
doc.printErrors();
} else {
writer.writeSBML(doc, args[1]);
}
}
public static void main(String[] args) {
if (args.length != 1) {
println("Usage: java printAnnotation filename");
System.exit(1);
}
String filename = args[0];
SBMLDocument document;
SBMLReader reader = new SBMLReader();
document = reader.readSBML(filename);
long errors = document.getNumErrors();
println("\nfilename: " + filename + "\n");
if (errors > 0) {
document.printErrors();
System.exit((int) errors);
}
/* Model */
Model m = document.getModel();
printAnnotation(m);
for (int i = 0; i < m.getNumReactions(); i++) {
Reaction re = m.getReaction(i);
printAnnotation(re);
/* SpeciesReference (Reactant) */
for (int j = 0; j < re.getNumReactants(); j++) {
SpeciesReference rt = re.getReactant(j);
if (rt.isSetAnnotation()) print(" ");
printAnnotation(rt, (rt.isSetSpecies() ? rt.getSpecies() : ""));
}
/* SpeciesReference (Product) */
for (int j = 0; j < re.getNumProducts(); j++) {
SpeciesReference rt = re.getProduct(j);
if (rt.isSetAnnotation()) print(" ");
printAnnotation(rt, (rt.isSetSpecies() ? rt.getSpecies() : ""));
}
/* ModifierSpeciesReference (Modifier) */
for (int j = 0; j < re.getNumModifiers(); j++) {
ModifierSpeciesReference md = re.getModifier(j);
if (md.isSetAnnotation()) print(" ");
printAnnotation(md, (md.isSetSpecies() ? md.getSpecies() : ""));
}
/* KineticLaw */
if (re.isSetKineticLaw()) {
KineticLaw kl = re.getKineticLaw();
if (kl.isSetAnnotation()) print(" ");
printAnnotation(kl);
/* Parameter */
for (int j = 0; j < kl.getNumParameters(); j++) {
Parameter pa = kl.getParameter(j);
if (pa.isSetAnnotation()) print(" ");
printAnnotation(pa);
}
}
}
/* Species */
for (int i = 0; i < m.getNumSpecies(); i++) {
Species sp = m.getSpecies(i);
printAnnotation(sp);
}
/* Compartment */
for (int i = 0; i < m.getNumCompartments(); i++) {
Compartment sp = m.getCompartment(i);
printAnnotation(sp);
}
/* FunctionDefinition */
for (int i = 0; i < m.getNumFunctionDefinitions(); i++) {
FunctionDefinition sp = m.getFunctionDefinition(i);
printAnnotation(sp);
}
/* UnitDefinition */
for (int i = 0; i < m.getNumUnitDefinitions(); i++) {
UnitDefinition sp = m.getUnitDefinition(i);
printAnnotation(sp);
}
/* Parameter */
for (int i = 0; i < m.getNumParameters(); i++) {
Parameter sp = m.getParameter(i);
printAnnotation(sp);
}
/* Rule */
for (int i = 0; i < m.getNumRules(); i++) {
Rule sp = m.getRule(i);
printAnnotation(sp);
}
/* InitialAssignment */
for (int i = 0; i < m.getNumInitialAssignments(); i++) {
InitialAssignment sp = m.getInitialAssignment(i);
printAnnotation(sp);
}
/* Event */
for (int i = 0; i < m.getNumEvents(); i++) {
Event sp = m.getEvent(i);
printAnnotation(sp);
/* Trigger */
if (sp.isSetTrigger()) {
Trigger tg = sp.getTrigger();
if (tg.isSetAnnotation()) print(" ");
printAnnotation(tg);
}
/* Delay */
if (sp.isSetDelay()) {
Delay dl = sp.getDelay();
if (dl.isSetAnnotation()) print(" ");
printAnnotation(dl);
}
/* EventAssignment */
for (int j = 0; j < sp.getNumEventAssignments(); j++) {
EventAssignment ea = sp.getEventAssignment(j);
if (ea.isSetAnnotation()) print(" ");
printAnnotation(ea);
}
}
/* SpeciesType */
for (int i = 0; i < m.getNumSpeciesTypes(); i++) {
SpeciesType sp = m.getSpeciesType(i);
printAnnotation(sp);
}
/* Constraint */
for (int i = 0; i < m.getNumConstraints(); i++) {
Constraint sp = m.getConstraint(i);
printAnnotation(sp);
}
System.exit((int) errors);
}
public static void main(String[] args) {
System.loadLibrary("sbmlj");
if (args.length != 2) {
System.out.println(" usage: addingEvidenceCodes_2 <input-filename> <output-filename>");
System.out.println(" Adds controlled vocabulary term to a species");
System.out.println();
System.exit(2);
}
SBMLDocument d = libsbml.readSBML(args[0]);
long errors = d.getNumErrors();
if (errors > 0) {
System.out.println("Read Error(s):");
d.printErrors();
System.out.println("Correct the above and re-run.");
} else {
long n = d.getModel().getNumSpecies();
if (n <= 0) {
System.out.println("Model has no species.\n Cannot add CV terms\n");
} else {
Species s = d.getModel().getSpecies(0);
/*
* check that the species has a metaid no CVTerms will be added
* if there is no metaid to reference
*/
if (!s.isSetMetaId()) s.setMetaId("metaid_0000052");
CVTerm cv1 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv1.setBiologicalQualifierType(libsbml.BQB_OCCURS_IN);
cv1.addResource("urn:miriam:obo.go:GO%3A0005764");
s.addCVTerm(cv1);
// now create the additional annotation
// <rdf:Statement>
// <rdf:subject rdf:resource="#metaid_0000052"/>
// <rdf:predicate
// rdf:resource="http://biomodels.net/biology-qualifiers/occursIn"/>
// <rdf:object rdf:resource="urn:miriam:obo.go:GO%3A0005764"/>
// <bqbiol:isDescribedBy>
// <rdf:Bag>
// <rdf:li rdf:resource="urn:miriam:obo.eco:ECO%3A0000004"/>
// <rdf:li rdf:resource="urn:miriam:pubmed:7017716"/>
// </rdf:Bag>
// </bqbiol:isDescribedBy>
// </rdf:Statement>
/* attributes */
XMLAttributes blank_att = new XMLAttributes();
XMLAttributes resource_att = new XMLAttributes();
/* create the outer statement node */
XMLTriple statement_triple =
new XMLTriple("Statement", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
XMLToken statement_token = new XMLToken(statement_triple, blank_att);
XMLNode statement = new XMLNode(statement_token);
/* create the subject node */
XMLTriple subject_triple =
new XMLTriple("subject", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
resource_att.clear();
resource_att.add("rdf:resource", "#" + s.getMetaId());
XMLToken subject_token = new XMLToken(subject_triple, resource_att);
XMLNode subject = new XMLNode(subject_token);
/* create the predicate node */
XMLTriple predicate_triple =
new XMLTriple("predicate", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
resource_att.clear();
resource_att.add("rdf:resource", "http://biomodels.net/biology-qualifiers/occursIn");
XMLToken predicate_token = new XMLToken(predicate_triple, resource_att);
XMLNode predicate = new XMLNode(predicate_token);
/* create the object node */
XMLTriple object_triple =
new XMLTriple("object", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
resource_att.clear();
resource_att.add("rdf:resource", "urn:miriam:obo.go:GO%3A0005764");
XMLToken object_token = new XMLToken(object_triple, resource_att);
XMLNode object_ = new XMLNode(object_token);
/* create the bqbiol node */
XMLTriple bqbiol_triple =
new XMLTriple("isDescribedBy", "http://biomodels.net/biology-qualifiers/", "bqbiol");
XMLToken bqbiol_token = new XMLToken(bqbiol_triple, blank_att);
XMLNode bqbiol = new XMLNode(bqbiol_token);
/* create the bag node */
XMLTriple bag_triple =
new XMLTriple("Bag", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
XMLToken bag_token = new XMLToken(bag_triple, blank_att);
XMLNode bag = new XMLNode(bag_token);
/* create each li node and add to the bag */
XMLTriple li_triple =
new XMLTriple("li", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
resource_att.clear();
resource_att.add("rdf:resource", "urn:miriam:obo.eco:ECO%3A0000004");
XMLToken li_token = new XMLToken(li_triple, resource_att);
li_token.setEnd();
XMLNode li = new XMLNode(li_token);
bag.addChild(li);
resource_att.clear();
resource_att.add("rdf:resource", "urn:miriam:pubmed:7017716");
li_token = new XMLToken(li_triple, resource_att);
li_token.setEnd();
li = new XMLNode(li_token);
bag.addChild(li);
/* add the bag to bqbiol */
bqbiol.addChild(bag);
/* add subject, predicate, object and bqbiol to statement */
statement.addChild(subject);
statement.addChild(predicate);
statement.addChild(object_);
statement.addChild(bqbiol);
/*
* create a top-level RDF element this will ensure correct
* merging
*/
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
xmlns.add("http://purl.org/dc/elements/1.1/", "dc");
xmlns.add("http://purl.org/dc/terms/", "dcterms");
xmlns.add("http://www.w3.org/2001/vcard-rdf/3.0#", "vCard");
xmlns.add("http://biomodels.net/biology-qualifiers/", "bqbiol");
xmlns.add("http://biomodels.net/model-qualifiers/", "bqmodel");
XMLTriple RDF_triple =
new XMLTriple("RDF", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
XMLToken RDF_token = new XMLToken(RDF_triple, blank_att, xmlns);
XMLNode annotation = new XMLNode(RDF_token);
/* add the staement node to the RDF node */
annotation.addChild(statement);
s.appendAnnotation(annotation);
libsbml.writeSBML(d, args[1]);
}
}
System.exit((int) errors);
}
