/// <summary>
/// Converts the current binary model to an SBML 3.1 Qual document.
/// </summary>
/// <returns>A new SBML Qual document based on curent binary model</returns>
public SBMLDocument ToSbmlQualDocument(BinaryModel model)
{
var sbmlns = new SBMLNamespaces(3, 1, "qual", 1);
var document = new SBMLDocument(sbmlns);
document.setPackageRequired("qual", true);
var sbmlModel = document.createModel();
var qualModel = (QualModelPlugin)sbmlModel.getPlugin("qual");
var compartment = sbmlModel.createCompartment();
compartment.setConstant(false);
compartment.setId("Default");
compartment.setName("Default");
foreach (var binaryNode in model.Nodes)
{
var qualitativeSpecies = qualModel.createQualitativeSpecies();
qualitativeSpecies.setConstant(false);
qualitativeSpecies.setId(binaryNode.Id);
qualitativeSpecies.setName(binaryNode.Name);
qualitativeSpecies.setCompartment("Default");
}
foreach (var binaryEdge in model.Edges)
{
var transition = qualModel.createTransition();
var input = transition.createInput();
input.setQualitativeSpecies(binaryEdge.Input.Id);
input.setTransitionEffect(libsbml.INPUT_TRANSITION_EFFECT_NONE);
input.setSign(binaryEdge.IsPositive() ? libsbml.INPUT_SIGN_POSITIVE : libsbml.INPUT_SIGN_NEGATIVE);
var output = transition.createOutput();
output.setQualitativeSpecies(binaryEdge.Output.Id);
output.setTransitionEffect(libsbml.OUTPUT_TRANSITION_EFFECT_PRODUCTION);
output.setOutputLevel(1);
var defaultTrem = transition.createDefaultTerm();
defaultTrem.setResultLevel(1);
}
return(document);
}
public static int Main(string[] args)
{
// Creates an SBMLNamespaces object with the given SBML level, version
// package name, package version.
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "qual", 1);
// create the document
SBMLDocument document = new SBMLDocument(sbmlns);
// mark qual as required
document.setPackageRequired("qual", true);
// create the Model
Model model = document.createModel();
// create the Compartment
Compartment compartment = model.createCompartment();
compartment.setId("c");
compartment.setConstant(true);
// Get a QualModelPlugin object plugged in the model object.
QualModelPlugin mplugin = (QualModelPlugin)(model.getPlugin("qual"));
// create the QualitativeSpecies
QualitativeSpecies qs = mplugin.createQualitativeSpecies();
qs.setId("s1");
qs.setCompartment("c");
qs.setConstant(false);
qs.setInitialLevel(1);
qs.setMaxLevel(4);
qs.setName("sss");
// create the Transition
Transition t = mplugin.createTransition();
t.setId("d");
t.setSBOTerm(1);
Input i = t.createInput();
i.setId("RD");
i.setQualitativeSpecies("s1");
i.setTransitionEffect(libsbml.INPUT_TRANSITION_EFFECT_NONE);
i.setSign(libsbml.INPUT_SIGN_NEGATIVE);
i.setThresholdLevel(2);
i.setName("aa");
Output o = t.createOutput();
o.setId("wd");
o.setQualitativeSpecies("s1");
o.setTransitionEffect(libsbml.OUTPUT_TRANSITION_EFFECT_PRODUCTION);
o.setOutputLevel(2);
o.setName("aa");
FunctionTerm ft = t.createFunctionTerm();
ASTNode math = libsbml.parseL3Formula("geq(s1, 2)");
ft.setResultLevel(1);
ft.setMath(math);
DefaultTerm dt = t.createDefaultTerm();
dt.setResultLevel(2);
int result = libsbml.writeSBML(document, "qual_example1.xml");
if (result == 1)
{
Console.WriteLine("Wrote file");
return(0);
}
else
{
Console.WriteLine("Failed to write");
return(1);
}
}
public static void Main(string[] args)
{
ArraysPkgNamespaces arraysNs = new ArraysPkgNamespaces();
SBMLDocument doc = new SBMLDocument(arraysNs);
doc.setPackageRequired("arrays", true);
Model model = doc.createModel();
// create parameters
Parameter param = model.createParameter();
param.setId("n");
param.setValue(10);
param.setConstant(true);
param = model.createParameter();
param.setId("m");
param.setValue(10);
param.setConstant(true);
param = model.createParameter();
param.setId("x");
param.setValue(5.7);
param.setConstant(true);
ArraysSBasePlugin paramPlugin = (ArraysSBasePlugin)param.getPlugin("arrays");
Dimension dim = paramPlugin.createDimension();
dim.setId("i");
dim.setSize("n");
param = model.createParameter();
param.setId("y");
param.setConstant(false);
paramPlugin = (ArraysSBasePlugin)param.getPlugin("arrays");
dim = paramPlugin.createDimension();
dim.setId("i");
dim.setSize("n");
param = model.createParameter();
param.setId("z");
param.setConstant(false);
paramPlugin = (ArraysSBasePlugin)param.getPlugin("arrays");
dim = paramPlugin.createDimension();
dim.setId("i");
dim.setSize("n");
// create initial assignments
InitialAssignment assignment = model.createInitialAssignment();
assignment.setSymbol("y");
ASTNode ast = new ASTNode(libsbml.AST_REAL);
ast.setValue(3.2);
assignment.setMath(ast);
assignment = model.createInitialAssignment();
assignment.setSymbol("z");
ast = new ASTNode(libsbml.AST_REAL);
ast.setValue(5.7);
assignment.setMath(ast);
ArraysSBasePlugin assignmentPlugin = (ArraysSBasePlugin)assignment.getPlugin("arrays");
dim = assignmentPlugin.createDimension();
dim.setId("i");
dim.setSize("m");
Index index = assignmentPlugin.createIndex();
ASTNode newAst = new ASTNode(libsbml.AST_FUNCTION);
newAst.setName("selector");
ASTNode ci = new ASTNode(libsbml.AST_NAME);
ci.setName("z");
newAst.addChild(ci);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("i");
newAst.addChild(ci);
index.setMath(newAst);
assignment = model.createInitialAssignment();
assignment.setSymbol("z");
ast = new ASTNode(libsbml.AST_REAL);
ast.setValue(3.2);
assignment.setMath(ast);
assignmentPlugin = (ArraysSBasePlugin)assignment.getPlugin("arrays");
dim = assignmentPlugin.createDimension();
dim.setId("i");
dim.setSize("m");
index = assignmentPlugin.createIndex();
newAst = new ASTNode(libsbml.AST_LINEAR_ALGEBRA_SELECTOR);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("z");
newAst.addChild(ci);
ASTNode plus = new ASTNode(libsbml.AST_PLUS);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("i");
plus.addChild(ci);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("m");
plus.addChild(ci);
newAst.addChild(plus);
index.setMath(newAst);
libsbml.writeSBMLToFile(doc, "arrays2.xml");
}
public static void Main(string[] args)
{
ArraysPkgNamespaces arraysNs = new ArraysPkgNamespaces();
SBMLDocument doc = new SBMLDocument(arraysNs);
doc.setPackageRequired("arrays", true);
Model model = doc.createModel();
// create compartment
Compartment comp = model.createCompartment();
comp.setMetaId("dd");
comp.setId("s");
comp.setConstant(true);
// set dimensions
ArraysSBasePlugin compPlugin = (ArraysSBasePlugin)comp.getPlugin("arrays");
Dimension dim = compPlugin.createDimension();
dim.setId("i");
dim.setSize("n");
// create species
Species species = model.createSpecies();
species.setId("A");
species.setCompartment("s");
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species.setConstant(false);
ArraysSBasePlugin splugin = (ArraysSBasePlugin)species.getPlugin("arrays");
dim = splugin.createDimension();
dim.setId("i");
dim.setSize("n");
species = model.createSpecies();
species.setId("B");
species.setCompartment("s");
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species.setConstant(false);
splugin = (ArraysSBasePlugin)species.getPlugin("arrays");
dim = splugin.createDimension();
dim.setId("i");
dim.setSize("n");
species = model.createSpecies();
species.setId("C");
species.setCompartment("s");
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species.setConstant(false);
splugin = (ArraysSBasePlugin)species.getPlugin("arrays");
dim = splugin.createDimension();
dim.setId("i");
dim.setSize("n");
// create parameter
Parameter param = model.createParameter();
param.setId("n");
param.setValue(100);
param.setConstant(true);
// create reaction
Reaction reaction = model.createReaction();
reaction.setId("reaction1");
reaction.setReversible(false);
reaction.setFast(false);
ArraysSBasePlugin reactionPlugin = (ArraysSBasePlugin)reaction.getPlugin("arrays");
dim = reactionPlugin.createDimension();
dim.setId("i");
dim.setSize("n");
SpeciesReference speciesRef = reaction.createReactant();
speciesRef.setSpecies("A");
speciesRef.setConstant(false);
ArraysSBasePlugin refPlugin = (ArraysSBasePlugin)speciesRef.getPlugin("arrays");
Index index = refPlugin.createIndex();
ASTNode ast = new ASTNode(libsbml.AST_LINEAR_ALGEBRA_SELECTOR);
ASTNode ci = new ASTNode(libsbml.AST_NAME);
ci.setName("A");
ast.addChild(ci);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("i");
ast.addChild(ci);
index.setMath(ast);
speciesRef = reaction.createProduct();
speciesRef.setSpecies("C");
speciesRef.setConstant(false);
refPlugin = (ArraysSBasePlugin)speciesRef.getPlugin("arrays");
index = refPlugin.createIndex();
ast = new ASTNode(libsbml.AST_LINEAR_ALGEBRA_SELECTOR);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("C");
ast.addChild(ci);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("i");
ast.addChild(ci);
index.setMath(ast);
libsbml.writeSBMLToFile(doc, "arrays1.xml");
}
public static int Main(string[] args)
{
if (args.Length != 2)
{
Console.WriteLine(" Usage: addRenderInformation <input file> <output file> \n" +
" Adds a render information object to the input file");
return(1);
}
string inputFile = args[0];
string outputFile = args[1];
SBMLDocument doc = libsbml.readSBMLFromFile(inputFile);
long numErrors = doc.getNumErrors(libsbml.LIBSBML_SEV_ERROR);
if (numErrors > 0)
{
Console.WriteLine("Encountered errors while reading the file. ");
Console.WriteLine("Please correct the following errors and try again.");
doc.printErrors();
return(2);
}
Model model = doc.getModel();
LayoutModelPlugin plugin = (LayoutModelPlugin)model.getPlugin("layout");
if (plugin == null || plugin.getNumLayouts() == 0)
{
Console.WriteLine("The loaded model contains no layout information, please add these first.");
return(3);
}
RenderListOfLayoutsPlugin lolPlugin = (RenderListOfLayoutsPlugin)plugin.getListOfLayouts().getPlugin("render");
if (lolPlugin != null && lolPlugin.getNumGlobalRenderInformationObjects() > 0)
{
Console.WriteLine("The loaded model contains global Render information. ");
}
// add render information to the first layout
Layout layout = plugin.getLayout(0);
RenderLayoutPlugin rPlugin = (RenderLayoutPlugin)layout.getPlugin("render");
if (rPlugin != null && rPlugin.getNumLocalRenderInformationObjects() > 0)
{
Console.WriteLine("The loaded model contains local Render information. ");
}
else
{
string uri = doc.getLevel() == 2 ? RenderExtension.getXmlnsL2() : RenderExtension.getXmlnsL3V1V1();
// enable render package
doc.enablePackage(uri, "render", true);
doc.setPackageRequired("render", false);
rPlugin = (RenderLayoutPlugin)layout.getPlugin("render");
addRenderInformation(rPlugin);
libsbml.writeSBMLToFile(doc, outputFile);
}
return(0);
}