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libSBML 5.18.0 |
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/**
* @file printUnits.java
* @brief Prints some unit information about the model
* @author Akira Funahashi (translated from libSBML C++ examples (using other Java examples provided by Nicolas Rodriguez))
* @author Sarah Keating
* @author Michael Hucka
*
*
*/
import org.sbml.libsbml.libsbml;
import org.sbml.libsbml.Model;
import org.sbml.libsbml.ModelCreator;
import org.sbml.libsbml.ModelHistory;
import org.sbml.libsbml.SBMLWriter;
import org.sbml.libsbml.SBMLDocument;
import org.sbml.libsbml.SBMLReader;
import org.sbml.libsbml.Species;
import org.sbml.libsbml.Compartment;
import org.sbml.libsbml.Parameter;
import org.sbml.libsbml.InitialAssignment;
import org.sbml.libsbml.Rule;
import org.sbml.libsbml.Reaction;
import org.sbml.libsbml.KineticLaw;
import org.sbml.libsbml.SpeciesReference;
import org.sbml.libsbml.Event;
import org.sbml.libsbml.EventAssignment;
import org.sbml.libsbml.UnitDefinition;
public class printUnits
{
public static void main (String[] args)
{
if (args.length != 1)
{
println("\nUsage: java printUnits filename\n");
System.exit(1);
}
String filename = args[0];
SBMLReader reader = new SBMLReader();
SBMLWriter writer = new SBMLWriter();
SBMLDocument d = reader.readSBML(filename);
if (d.getNumErrors() > 0)
{
println("Encountered the following SBML errors:");
d.printErrors();
System.exit(1);
}
Model model = d.getModel();
if (model == null)
{
println("No model present.");
System.exit(1);
}
for (int n = 0; n < model.getNumCompartments(); n++)
{
Compartment c = model.getCompartment(n);
println("Compartment #" + (n+1) + " --");
println(" id in model: " + c.getId());
printUD(c.getDerivedUnitDefinition());
}
for (int n = 0; n < model.getNumSpecies(); n++)
{
Species s = model.getSpecies(n);
println("Species #" + (n+1) + " --");
println(" id in model: " + s.getId());
printUD(s.getDerivedUnitDefinition());
}
for (int n = 0; n < model.getNumParameters(); n++)
{
Parameter p = model.getParameter(n);
println("Parameter #" + (n+1) + " --");
println(" id in model: " + p.getId());
printUD(p.getDerivedUnitDefinition());
}
for (int n = 0; n < model.getNumInitialAssignments(); n++)
{
InitialAssignment ia = model.getInitialAssignment(n);
println("InitialAssignment #" + (n+1) + " --");
println(" id in model: " + ia.getId());
printUD(ia.getDerivedUnitDefinition());
if (ia.containsUndeclaredUnits())
{
println(" undeclared parameters?: yes");
}
else
{
println(" undeclared parameters?: no");
}
print("\n");
}
for (int n = 0; n < model.getNumRules(); n++)
{
Rule r = model.getRule(n);
println("Rule #" + (n+1) + " --");
println(" id in model: " + r.getId());
printUD(r.getDerivedUnitDefinition());
if (r.containsUndeclaredUnits())
{
println(" undeclared parameters?: yes");
}
else
{
println(" undeclared parameters?: no");
}
print("\n");
}
for (int n = 0; n < model.getNumEvents(); n++)
{
Event e = model.getEvent(n);
println("Event #" + (n+1) + " --");
println(" id in model: " + e.getId());
if (e.isSetDelay())
{
println("Delay:");
printUD(e.getDelay().getDerivedUnitDefinition());
if (e.getDelay().containsUndeclaredUnits())
{
println(" undeclared parameters?: yes");
}
else
{
println(" undeclared parameters?: no");
}
print("\n");
for (int nn = 0; nn < e.getNumEventAssignments(); nn++)
{
EventAssignment ea = e.getEventAssignment(nn);
println("EventAssignment #" + (n+1) + " --");
println(" id in model: " + ea.getId());
printUD(ea.getDerivedUnitDefinition());
if (ea.containsUndeclaredUnits())
{
println(" undeclared parameters?: yes");
}
else
{
println(" undeclared parameters?: no");
}
print("\n");
}
}
}
for (int n = 0; n < model.getNumReactions(); n++)
{
Reaction rn = model.getReaction(n);
println("Reaction #" + (n+1) + " --");
println(" id in model: " + rn.getId());
if (rn.isSetKineticLaw())
{
printUD(rn.getKineticLaw().getDerivedUnitDefinition());
if (rn.getKineticLaw().containsUndeclaredUnits())
{
println(" undeclared parameters?: yes");
}
else
{
println(" undeclared parameters?: no");
}
}
print("\n");
for (int nn = 0; nn < rn.getNumReactants(); nn++)
{
SpeciesReference sr = rn.getReactant(nn);
if (sr.isSetStoichiometryMath())
{
println("Reactant #" + (n+1) + " --");
println(" id in model: " + sr.getSpecies());
printUD(sr.getStoichiometryMath().getDerivedUnitDefinition());
if (sr.getStoichiometryMath().containsUndeclaredUnits())
{
println(" undeclared parameters?: yes");
}
else
{
println(" undeclared parameters?: no");
}
print("\n");
}
}
for (int nn = 0; nn < rn.getNumProducts(); nn++)
{
SpeciesReference sr = rn.getProduct(nn);
if (sr.isSetStoichiometryMath())
{
println("Product #" + (n+1) + " --");
println(" id in model: " + sr.getSpecies());
printUD(sr.getStoichiometryMath().getDerivedUnitDefinition());
if (sr.getStoichiometryMath().containsUndeclaredUnits())
{
println(" undeclared parameters?: yes");
}
else
{
println(" undeclared parameters?: no");
}
print("\n");
}
}
}
}
static void printUD (UnitDefinition ud)
{
for (int p = 0; p < ud.getNumUnits(); p++)
{
int kind = ud.getUnit(p).getKind();
int exp = ud.getUnit(p).getExponent();
print(libsbml.UnitKind_toString(kind) + "(exponent = " + exp + ")");
if ( p + 1 < ud.getNumUnits())
{
print(", ");
}
}
print("\n\n");
}
static void print (String msg)
{
System.out.print(msg);
}
static void println (String msg)
{
System.out.println(msg);
}
/**
* Loads the SWIG-generated libSBML Java module when this class is
* loaded, or reports a sensible diagnostic message about why it failed.
*/
static
{
try
{
System.loadLibrary("sbmlj");
// For extra safety, check that the jar file is in the classpath.
Class.forName("org.sbml.libsbml.libsbml");
}
catch (UnsatisfiedLinkError e)
{
System.err.println("Error encountered while attempting to load libSBML:");
System.err.println("Please check the value of your "
+ (System.getProperty("os.name").startsWith("Mac OS")
? "DYLD_LIBRARY_PATH" : "LD_LIBRARY_PATH") +
" environment variable and/or your" +
" 'java.library.path' system property (depending on" +
" which one you are using) to make sure it list the" +
" directories needed to find the " +
System.mapLibraryName("sbmlj") + " library file and" +
" libraries it depends upon (e.g., the XML parser).");
System.exit(1);
}
catch (ClassNotFoundException e)
{
System.err.println("Error: unable to load the file 'libsbmlj.jar'." +
" It is likely that your -classpath command line " +
" setting or your CLASSPATH environment variable " +
" do not include the file 'libsbmlj.jar'.");
e.printStackTrace();
System.exit(1);
}
catch (SecurityException e)
{
System.err.println("Error encountered while attempting to load libSBML:");
e.printStackTrace();
System.err.println("Could not load the libSBML library files due to a"+
" security exception.\n");
System.exit(1);
}
}
}
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libSBML 5.18.0 |
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