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);
}