public void test_L3_LocalParameter_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3,1);
sbmlns.addNamespaces(xmlns);
LocalParameter p = new LocalParameter(sbmlns);
assertTrue( p.getTypeCode() == libsbml.SBML_LOCAL_PARAMETER );
assertTrue( p.getMetaId() == "" );
assertTrue( p.getNotes() == null );
assertTrue( p.getAnnotation() == null );
assertTrue( p.getLevel() == 3 );
assertTrue( p.getVersion() == 1 );
assertTrue( p.getNamespaces() != null );
assertTrue( p.getNamespaces().getLength() == 2 );
assertTrue( p.getId() == "" );
assertTrue( p.getName() == "" );
assertTrue( p.getUnits() == "" );
assertEquals( true, double.IsNaN(p.getValue()) );
assertEquals( false, p.isSetId() );
assertEquals( false, p.isSetName() );
assertEquals( false, p.isSetValue() );
assertEquals( false, p.isSetUnits() );
p = null;
}
public void test_SBMLNamespaces_add_and_remove_namespaces()
{
SBMLNamespaces sbmlns = new SBMLNamespaces ( 3,1 );
assertTrue( sbmlns.getLevel() == 3 );
assertTrue( sbmlns.getVersion() == 1 );
sbmlns.addNamespace("http://www.sbml.org/sbml/level3/version1/group/version1", "group");
sbmlns.addNamespace("http://www.sbml.org/sbml/level3/version1/layout/version1", "layout");
sbmlns.addNamespace("http://www.sbml.org/sbml/level3/version1/render/version1", "render");
sbmlns.addNamespace("http://www.sbml.org/sbml/level3/version1/multi/version1", "multi");
XMLNamespaces ns = sbmlns.getNamespaces();
assertTrue( ns.getLength() == 5 );
assertTrue( ns.getURI(0) == "http://www.sbml.org/sbml/level3/version1/core" );
assertTrue( ns.getPrefix(0) == "" );
assertTrue( ns.getURI(1) == "http://www.sbml.org/sbml/level3/version1/group/version1" );
assertTrue( ns.getPrefix(1) == "group" );
assertTrue( ns.getURI(2) == "http://www.sbml.org/sbml/level3/version1/layout/version1" );
assertTrue( ns.getPrefix(2) == "layout" );
assertTrue( ns.getURI(3) == "http://www.sbml.org/sbml/level3/version1/render/version1" );
assertTrue( ns.getPrefix(3) == "render" );
assertTrue( ns.getURI(4) == "http://www.sbml.org/sbml/level3/version1/multi/version1" );
assertTrue( ns.getPrefix(4) == "multi" );
sbmlns.removeNamespace("http://www.sbml.org/sbml/level3/version1/layout/version1");
sbmlns.removeNamespace("http://www.sbml.org/sbml/level3/version1/group/version1");
sbmlns.removeNamespace("http://www.sbml.org/sbml/level3/version1/render/version1");
sbmlns.removeNamespace("http://www.sbml.org/sbml/level3/version1/multi/version1");
}
public void test_SBMLNamespaces_L1V1()
{
SBMLNamespaces sbml = new SBMLNamespaces(1,1);
assertTrue( sbml.getLevel() == 1 );
assertTrue( sbml.getVersion() == 1 );
XMLNamespaces ns = sbml.getNamespaces();
assertTrue( ns.getLength() == 1 );
assertTrue( ns.getURI(0) == "http://www.sbml.org/sbml/level1" );
assertTrue( ns.getPrefix(0) == "" );
sbml = null;
}
static void Main(string[] args)
{
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "distrib", 1);
SBMLDocument document = new SBMLDocument(sbmlns);
// set the required attribute to true
DistribSBMLDocumentPlugin docPlug = (DistribSBMLDocumentPlugin)
(document->getPlugin("distrib"));
docPlug.setRequired(true);
// create the Model
Model model = document.createModel();
// create the FunctionDefintion
FunctionDefinition fd = model.createFunctionDefinition();
fd.setId("mynormal");
ASTNode math = libsbml.parseFormula("lambda(param1, param2, 0)");
fd.setMath(math);
//
// Get a DistribFunctionDefinitionPlugin object plugged in the fd object.
//
// The type of the returned value of SBase::getPlugin() function is SBasePlugin, and
// thus the value needs to be casted for the corresponding derived class.
//
DistribFunctionDefinitionPlugin fdPlugin =
(DistribFunctionDefinitionPlugin)(fd.getPlugin("distrib"));
// create a DrawFromDistribution object
DrawFromDistribution draw = fdPlugin.createDrawFromDistribution();
// create the distribInputs
DistribInput input1 = draw.createDistribInput();
input1.setId("mu");
input1.setIndex(0);
DistribInput input2 = draw.createDistribInput();
input2.setId("sigma");
input2.setIndex(1);
// create the UncertMLNode object
UncertMLNode uncert = libsbml.createDistributionNode
("NormalDistribution", "mean, variance", "mu,sigma");
draw.setUncertML(uncert);
libsbml.writeSBMLToFile(document, "distrib_example1.xml");
}
public void test_Constraint_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,2);
sbmlns.addNamespaces(xmlns);
Constraint object1 = new Constraint(sbmlns);
assertTrue( object1.getTypeCode() == libsbml.SBML_CONSTRAINT );
assertTrue( object1.getMetaId() == "" );
assertTrue( object1.getNotes() == null );
assertTrue( object1.getAnnotation() == null );
assertTrue( object1.getLevel() == 2 );
assertTrue( object1.getVersion() == 2 );
assertTrue( object1.getNamespaces() != null );
assertTrue( object1.getNamespaces().getLength() == 2 );
object1 = null;
}
public void test_SpeciesType_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,2);
sbmlns.addNamespaces(xmlns);
SpeciesType object1 = new SpeciesType(sbmlns);
assertTrue( object1.getTypeCode() == libsbml.SBML_SPECIES_TYPE );
assertTrue( object1.getMetaId() == "" );
assertTrue( object1.getNotes() == null );
assertTrue( object1.getAnnotation() == null );
assertTrue( object1.getLevel() == 2 );
assertTrue( object1.getVersion() == 2 );
assertTrue( object1.getNamespaces() != null );
assertTrue( object1.getNamespaces().getLength() == 2 );
object1 = null;
}
public void test_Delay_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,1);
sbmlns.addNamespaces(xmlns);
Delay object1 = new Delay(sbmlns);
assertTrue( object1.getTypeCode() == libsbml.SBML_DELAY );
assertTrue( object1.getMetaId() == "" );
assertTrue( object1.getNotes() == null );
assertTrue( object1.getAnnotation() == null );
assertTrue( object1.getLevel() == 2 );
assertTrue( object1.getVersion() == 1 );
assertTrue( object1.getNamespaces() != null );
assertTrue( object1.getNamespaces().getLength() == 2 );
object1 = null;
}
public void test_StoichiometryMath_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,1);
sbmlns.addNamespaces(xmlns);
StoichiometryMath object1 = new StoichiometryMath(sbmlns);
assertTrue( object1.getTypeCode() == libsbml.SBML_STOICHIOMETRY_MATH );
assertTrue( object1.getMetaId() == "" );
assertTrue( object1.getNotes() == null );
assertTrue( object1.getAnnotation() == null );
assertTrue( object1.getLevel() == 2 );
assertTrue( object1.getVersion() == 1 );
assertTrue( object1.getNamespaces() != null );
assertTrue( object1.getNamespaces().getLength() == 2 );
object1 = null;
}
public void test_EventAssignment_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,1);
sbmlns.addNamespaces(xmlns);
EventAssignment object1 = new EventAssignment(sbmlns);
assertTrue( object1.getTypeCode() == libsbml.SBML_EVENT_ASSIGNMENT );
assertTrue( object1.getMetaId() == "" );
assertTrue( object1.getNotes() == null );
assertTrue( object1.getAnnotation() == null );
assertTrue( object1.getLevel() == 2 );
assertTrue( object1.getVersion() == 1 );
assertTrue( object1.getNamespaces() != null );
assertTrue( object1.getNamespaces().getLength() == 2 );
object1 = null;
}
public void test_ModifierSpeciesReference_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,1);
sbmlns.addNamespaces(xmlns);
SBase object1 = new ModifierSpeciesReference(sbmlns);
assertTrue( object1.getTypeCode() == libsbml.SBML_MODIFIER_SPECIES_REFERENCE );
assertTrue( object1.getMetaId() == "" );
assertTrue( object1.getNotes() == null );
assertTrue( object1.getAnnotation() == null );
assertTrue( object1.getLevel() == 2 );
assertTrue( object1.getVersion() == 1 );
assertTrue( object1.getNamespaces() != null );
XMLNamespaces n = object1.getNamespaces();
assertTrue( n.getLength() == 2 );
object1 = null;
}
public void test_SyntaxChecker_validXHTML()
{
SBMLNamespaces NS24 = new SBMLNamespaces(2,4);
SBMLNamespaces NS31 = new SBMLNamespaces(3,1);
XMLToken toptoken;
XMLNode topnode;
XMLTriple toptriple = new XMLTriple("notes", "", "");
XMLToken token;
XMLNode node;
XMLTriple triple = new XMLTriple("p", "", "");
XMLAttributes att = new XMLAttributes();
XMLNamespaces ns = new XMLNamespaces();
ns.add( "http://www.w3.org/1999/xhtml", "");
XMLToken tt = new XMLToken("This is my text");
XMLNode n1 = new XMLNode(tt);
toptoken = new XMLToken(toptriple,att);
topnode = new XMLNode(toptoken);
token = new XMLToken(triple,att,ns);
node = new XMLNode(token);
node.addChild(n1);
topnode.addChild(node);
assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,null) == true );
assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == true );
assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == true );
triple = new XMLTriple("html", "", "");
token = new XMLToken(triple,att,ns);
node = new XMLNode(token);
node.addChild(n1);
topnode.removeChild(0);
topnode.addChild(node);
assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,null) == true );
assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == false );
assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == true );
triple = new XMLTriple("html", "", "");
ns.clear();
token = new XMLToken(triple,att,ns);
node = new XMLNode(token);
node.addChild(n1);
topnode.removeChild(0);
topnode.addChild(node);
assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,null) == false );
assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == false );
assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == false );
}
public void test_L3_Event_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3,1);
sbmlns.addNamespaces(xmlns);
Event e = new Event(sbmlns);
assertTrue( e.getTypeCode() == libsbml.SBML_EVENT );
assertTrue( e.getMetaId() == "" );
assertTrue( e.getNotes() == null );
assertTrue( e.getAnnotation() == null );
assertTrue( e.getLevel() == 3 );
assertTrue( e.getVersion() == 1 );
assertTrue( e.getNamespaces() != null );
assertTrue( e.getNamespaces().getLength() == 2 );
assertTrue( e.getId() == "" );
assertTrue( e.getName() == "" );
assertTrue( e.getUseValuesFromTriggerTime() == true );
assertEquals( false, e.isSetId() );
assertEquals( false, e.isSetName() );
assertEquals( false, e.isSetUseValuesFromTriggerTime() );
e = null;
}
static void Main(string[] args)
{
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "distrib", 1);
SBMLDocument document = new SBMLDocument(sbmlns);
// set the required attribute to true
DistribSBMLDocumentPlugin docPlug = (DistribSBMLDocumentPlugin)
(document->getPlugin("distrib"));
docPlug.setRequired(true);
// create the Model
Model model = document.createModel();
// create the Parameter
Parameter p = model.createParameter();
p.setId("V");
p.setConstant(true);
//
// Get a DistribSBasePlugin object plugged in the parameter object.
//
DistribSBasePlugin pPlugin =
(DistribSBasePlugin)(p.getPlugin("distrib"));
// create a Uncertainty object
Uncertainty uncert = pPlugin.createUncertainty();
// create the UncertMLNode object
UncertMLNode uncertML = libsbml.createDistributionNode
("Statistics", "Mean, Variance", "V_pop, V_omega");
uncert.setUncertML(uncertML);
libsbml.writeSBMLToFile(document, "distrib_example2.xml");
}
/**
* Creates a new LocalParameter object with the given SBMLNamespaces
* object @p sbmlns.
*
* *
*
* The SBMLNamespaces object encapsulates SBML Level/Version/namespaces
* information. It is used to communicate the SBML Level, Version, and (in
* Level 3) packages used in addition to SBML Level 3 Core. A
* common approach to using libSBML's SBMLNamespaces facilities is to create an
* SBMLNamespaces object somewhere in a program once, then hand that object
* as needed to object constructors that accept SBMLNamespaces as arguments.
*
*
*
* It is worth emphasizing that although this constructor does not take
* an identifier argument, in SBML Level 2 and beyond, the 'id'
* (identifier) attribute of a LocalParameter is required to have a value.
* Thus, callers are cautioned to assign a value after calling this
* constructor if no identifier is provided as an argument. Setting the
* identifier can be accomplished using the method
* @if java setId(String id)@else setId()@endif.
*
* @param sbmlns an SBMLNamespaces object.
*
* @throws SBMLConstructorException
* Thrown if the given @p level and @p version combination, or this kind
* of SBML object, are either invalid or mismatched with respect to the
* parent SBMLDocument object.
*
* *
* @note Attempting to add an object to an SBMLDocument having a different
* combination of SBML Level, Version and XML namespaces than the object
* itself will result in an error at the time a caller attempts to make the
* addition. A parent object must have compatible Level, Version and XML
* namespaces. (Strictly speaking, a parent may also have more XML
* namespaces than a child, but the reverse is not permitted.) The
* restriction is necessary to ensure that an SBML model has a consistent
* overall structure. This requires callers to manage their objects
* carefully, but the benefit is increased flexibility in how models can be
* created by permitting callers to create objects bottom-up if desired. In
* situations where objects are not yet attached to parents (e.g.,
* SBMLDocument), knowledge of the intented SBML Level and Version help
* libSBML determine such things as whether it is valid to assign a
* particular value to an attribute.
*
*
*/
public LocalParameter(SBMLNamespaces sbmlns)
: this(libsbmlPINVOKE.new_LocalParameter__SWIG_1(SBMLNamespaces.getCPtr(sbmlns)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
/**
* Creates a new AlgebraicRule object using the given SBMLNamespaces object
* @p sbmlns.
*
*
*
* The SBMLNamespaces object encapsulates SBML Level/Version/namespaces
* information. It is used to communicate the SBML Level, Version, and (in
* Level 3) packages used in addition to SBML Level 3 Core. A
* common approach to using libSBML's SBMLNamespaces facilities is to create an
* SBMLNamespaces object somewhere in a program once, then hand that object
* as needed to object constructors that accept SBMLNamespaces as arguments.
*
*
*
* @param sbmlns an SBMLNamespaces object.
*
*
* @throws SBMLConstructorException
* Thrown if the given @p sbmlns is inconsistent or incompatible
* with this object.
*
*
*
*
* @note Attempting to add an object to an SBMLDocument having a different
* combination of SBML Level, Version and XML namespaces than the object
* itself will result in an error at the time a caller attempts to make the
* addition. A parent object must have compatible Level, Version and XML
* namespaces. (Strictly speaking, a parent may also have more XML
* namespaces than a child, but the reverse is not permitted.) The
* restriction is necessary to ensure that an SBML model has a consistent
* overall structure. This requires callers to manage their objects
* carefully, but the benefit is increased flexibility in how models can be
* created by permitting callers to create objects bottom-up if desired. In
* situations where objects are not yet attached to parents (e.g.,
* SBMLDocument), knowledge of the intented SBML Level and Version help
* libSBML determine such things as whether it is valid to assign a
* particular value to an attribute.
*
*
*/
public AlgebraicRule(SBMLNamespaces sbmlns)
: this(libsbmlPINVOKE.new_AlgebraicRule__SWIG_1(SBMLNamespaces.getCPtr(sbmlns)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
public void test_L3_Model_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3,1);
sbmlns.addNamespaces(xmlns);
Model m = new Model(sbmlns);
assertTrue( m.getTypeCode() == libsbml.SBML_MODEL );
assertTrue( m.getMetaId() == "" );
assertTrue( m.getNotes() == null );
assertTrue( m.getAnnotation() == null );
assertTrue( m.getLevel() == 3 );
assertTrue( m.getVersion() == 1 );
assertTrue( m.getNamespaces() != null );
assertTrue( m.getNamespaces().getLength() == 2 );
assertTrue( m.getId() == "" );
assertTrue( m.getName() == "" );
assertTrue( m.getSubstanceUnits() == "" );
assertTrue( m.getTimeUnits() == "" );
assertTrue( m.getVolumeUnits() == "" );
assertTrue( m.getAreaUnits() == "" );
assertTrue( m.getLengthUnits() == "" );
assertTrue( m.getConversionFactor() == "" );
assertEquals( false, m.isSetId() );
assertEquals( false, m.isSetName() );
assertEquals( false, m.isSetSubstanceUnits() );
assertEquals( false, m.isSetTimeUnits() );
assertEquals( false, m.isSetVolumeUnits() );
assertEquals( false, m.isSetAreaUnits() );
assertEquals( false, m.isSetLengthUnits() );
assertEquals( false, m.isSetConversionFactor() );
m = null;
}
/**
* Creates a new ListOfSpecies object.
*
* The object is constructed such that it is valid for the SBML Level and
* Version combination determined by the SBMLNamespaces object in @p
* sbmlns.
*
* @param sbmlns an SBMLNamespaces object that is used to determine the
* characteristics of the ListOfSpecies object to be created.
*/
public ListOfSpecies(SBMLNamespaces sbmlns)
: this(libsbmlPINVOKE.new_ListOfSpecies__SWIG_1(SBMLNamespaces.getCPtr(sbmlns)), true)
{
}
/**
* Creates a new SBMLDocumentPlugin object using the given parameters.
*
*
*
* In the XML representation of an SBML document, XML namespaces are used to
* identify the origin of each XML construct used. XML namespaces are
* identified by their unique resource identifiers (URIs). The core SBML
* specifications stipulate the namespaces that must be used for core SBML
* constructs; for example, all XML elements that belong to SBML Level 3
* Version 1 Core must be placed in the XML namespace identified by the URI
* <code>'http://www.sbml.org/sbml/level3/version1/core'</code>. Individual
* SBML Level 3 packages define their own XML namespaces; for example,
* all elements belonging to the SBML Level 3 %Layout Version 1
* package must be placed in the XML namespace
* <code>'http://www.sbml.org/sbml/level3/version1/layout/version1/'</code>.
*
*
*
*
*
* The SBMLNamespaces object encapsulates SBML Level/Version/namespaces
* information. It is used to communicate the SBML Level, Version, and (in
* Level 3) packages used in addition to SBML Level 3 Core. A
* common approach to using libSBML's SBMLNamespaces facilities is to create an
* SBMLNamespaces object somewhere in a program once, then hand that object
* as needed to object constructors that accept SBMLNamespaces as arguments.
*
*
*
* @param uri the URI of the SBML Level 3 package implemented by
* this libSBML package extension.
*
* @param prefix the XML namespace prefix being used for the package.
*
* @param sbmlns the SBMLNamespaces object for the package.
*/
public SBMLDocumentPlugin(string uri, string prefix, SBMLNamespaces sbmlns)
: this(libsbmlPINVOKE.new_SBMLDocumentPlugin__SWIG_0(uri, prefix, SBMLNamespaces.getCPtr(sbmlns)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
/**
* Sets the SBML namespaces associated with this XML input stream.
*
* This allows this stream to reference the available SBML namespaces being
* read.
*
* @param sbmlns the list of namespaces to use.
*/
public void setSBMLNamespaces(SBMLNamespaces sbmlns)
{
libsbmlPINVOKE.XMLInputStream_setSBMLNamespaces(swigCPtr, SBMLNamespaces.getCPtr(sbmlns));
}
void loadASTPlugins(SBMLNamespaces sbmlns)
{
libsbmlPINVOKE.ASTBase_loadASTPlugins(swigCPtr, SBMLNamespaces.getCPtr(sbmlns));
}
ConversionProperties(SBMLNamespaces targetNS) : this(libsbmlPINVOKE.new_ConversionProperties__SWIG_0(SBMLNamespaces.getCPtr(targetNS)), true)
{
}
void setTargetNamespaces(SBMLNamespaces targetNS)
{
libsbmlPINVOKE.ConversionProperties_setTargetNamespaces(swigCPtr, SBMLNamespaces.getCPtr(targetNS));
}
ListOfCompartmentTypes(SBMLNamespaces sbmlns) : this(libsbmlPINVOKE.new_ListOfCompartmentTypes__SWIG_1(SBMLNamespaces.getCPtr(sbmlns)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
SpeciesType(SBMLNamespaces sbmlns) : this(libsbmlPINVOKE.new_SpeciesType__SWIG_1(SBMLNamespaces.getCPtr(sbmlns)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
ListOfInitialAssignments(SBMLNamespaces sbmlns) : this(libsbmlPINVOKE.new_ListOfInitialAssignments__SWIG_1(SBMLNamespaces.getCPtr(sbmlns)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
LocalParameter(SBMLNamespaces sbmlns) : this(libsbmlPINVOKE.new_LocalParameter__SWIG_1(SBMLNamespaces.getCPtr(sbmlns)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
internal static HandleRef getCPtr(SBMLNamespaces obj)
{
return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
}
UnitDefinition(SBMLNamespaces sbmlns) : this(libsbmlPINVOKE.new_UnitDefinition__SWIG_1(SBMLNamespaces.getCPtr(sbmlns)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
static bool hasExpectedXHTMLSyntax(XMLNode xhtml, SBMLNamespaces sbmlns)
{
bool ret = libsbmlPINVOKE.SyntaxChecker_hasExpectedXHTMLSyntax__SWIG_0(XMLNode.getCPtr(xhtml), SBMLNamespaces.getCPtr(sbmlns));
return(ret);
}
void setSBMLNamespaces(SBMLNamespaces sbmlns)
{
libsbmlPINVOKE.XMLInputStream_setSBMLNamespaces(swigCPtr, SBMLNamespaces.getCPtr(sbmlns));
}
/**
* Creates a new InitialAssignment using the given SBMLNamespaces object
* @p sbmlns.
*
* *
*
* The SBMLNamespaces object encapsulates SBML Level/Version/namespaces
* information. It is used to communicate the SBML Level, Version, and (in
* Level 3) packages used in addition to SBML Level 3 Core. A
* common approach to using libSBML's SBMLNamespaces facilities is to create an
* SBMLNamespaces object somewhere in a program once, then hand that object
* as needed to object constructors that accept SBMLNamespaces as arguments.
*
*
*
* @param sbmlns an SBMLNamespaces object.
*
* @throws @if python ValueError @else SBMLConstructorException @endif
* Thrown if the given @p level and @p version combination, or this kind
* of SBML object, are either invalid or mismatched with respect to the
* parent SBMLDocument object.
*
* *
* @note Upon the addition of a InitialAssignment object to an SBMLDocument
* (e.g., using Model::addInitialAssignment(@if java InitialAssignment
* ia@endif)), the SBML Level, SBML Version and XML namespace of the document
* @em override the values used when creating the InitialAssignment object
* via this constructor. This is necessary to ensure that an SBML document
* is a consistent structure. Nevertheless, the ability to supply the values
* at the time of creation of a InitialAssignment is an important aid to
* producing valid SBML. Knowledge of the intented SBML Level and Version
* determine whether it is valid to assign a particular value to an
* attribute, or whether it is valid to add an object to an existing
* SBMLDocument.
*
*/
public InitialAssignment(SBMLNamespaces sbmlns)
: this(libsbmlPINVOKE.new_InitialAssignment__SWIG_1(SBMLNamespaces.getCPtr(sbmlns)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
/**
* Creates a new ListOfSpeciesReferences object.
*
* The object is constructed such that it is valid for the SBML Level and
* Version combination determined by the SBMLNamespaces object in @p
* sbmlns.
*
* @param sbmlns an SBMLNamespaces object that is used to determine the
* characteristics of the ListOfSpeciesReferences object to be created.
*/
public ListOfSpeciesReferences(SBMLNamespaces sbmlns)
: this(libsbmlPINVOKE.new_ListOfSpeciesReferences__SWIG_1(SBMLNamespaces.getCPtr(sbmlns)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
/**
* Creates a new SpeciesType using the given SBMLNamespaces object
* @p sbmlns.
*
*
*
* The SBMLNamespaces object encapsulates SBML Level/Version/namespaces
* information. It is used to communicate the SBML Level, Version, and (in
* Level 3) packages used in addition to SBML Level 3 Core. A
* common approach to using libSBML's SBMLNamespaces facilities is to create an
* SBMLNamespaces object somewhere in a program once, then hand that object
* as needed to object constructors that accept SBMLNamespaces as arguments.
*
*
*
* It is worth emphasizing that although this constructor does not take
* an identifier argument, in SBML Level 2 and beyond, the 'id'
* (identifier) attribute of a SpeciesType object is required to have a value.
* Thus, callers are cautioned to assign a value after calling this
* constructor. Setting the identifier can be accomplished using the
* method SBase::setId(@if java String@endif).
*
* @param sbmlns an SBMLNamespaces object.
*
*
* @throws SBMLConstructorException
* Thrown if the given @p sbmlns is inconsistent or incompatible
* with this object.
*
*
*
*
* @note Attempting to add an object to an SBMLDocument having a different
* combination of SBML Level, Version and XML namespaces than the object
* itself will result in an error at the time a caller attempts to make the
* addition. A parent object must have compatible Level, Version and XML
* namespaces. (Strictly speaking, a parent may also have more XML
* namespaces than a child, but the reverse is not permitted.) The
* restriction is necessary to ensure that an SBML model has a consistent
* overall structure. This requires callers to manage their objects
* carefully, but the benefit is increased flexibility in how models can be
* created by permitting callers to create objects bottom-up if desired. In
* situations where objects are not yet attached to parents (e.g.,
* SBMLDocument), knowledge of the intented SBML Level and Version help
* libSBML determine such things as whether it is valid to assign a
* particular value to an attribute.
*
*
*/
public SpeciesType(SBMLNamespaces sbmlns)
: this(libsbmlPINVOKE.new_SpeciesType__SWIG_1(SBMLNamespaces.getCPtr(sbmlns)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
void setPlugins(SBMLNamespaces sbmlns)
{
libsbmlPINVOKE.L3ParserSettings_setPlugins(swigCPtr, SBMLNamespaces.getCPtr(sbmlns));
}
/**
* Creates a new KineticLaw using the given SBMLNamespaces object
* @p sbmlns.
*
* *
*
* The SBMLNamespaces object encapsulates SBML Level/Version/namespaces
* information. It is used to communicate the SBML Level, Version, and (in
* Level 3) packages used in addition to SBML Level 3 Core. A
* common approach to using libSBML's SBMLNamespaces facilities is to create an
* SBMLNamespaces object somewhere in a program once, then hand that object
* as needed to object constructors that accept SBMLNamespaces as arguments.
*
*
*
* @param sbmlns an SBMLNamespaces object.
*
* @throws SBMLConstructorException
* Thrown if the given @p level and @p version combination, or this kind
* of SBML object, are either invalid or mismatched with respect to the
* parent SBMLDocument object.
*
* *
* @note Attempting to add an object to an SBMLDocument having a different
* combination of SBML Level, Version and XML namespaces than the object
* itself will result in an error at the time a caller attempts to make the
* addition. A parent object must have compatible Level, Version and XML
* namespaces. (Strictly speaking, a parent may also have more XML
* namespaces than a child, but the reverse is not permitted.) The
* restriction is necessary to ensure that an SBML model has a consistent
* overall structure. This requires callers to manage their objects
* carefully, but the benefit is increased flexibility in how models can be
* created by permitting callers to create objects bottom-up if desired. In
* situations where objects are not yet attached to parents (e.g.,
* SBMLDocument), knowledge of the intented SBML Level and Version help
* libSBML determine such things as whether it is valid to assign a
* particular value to an attribute.
*
*
*/
public KineticLaw(SBMLNamespaces sbmlns)
: this(libsbmlPINVOKE.new_KineticLaw__SWIG_1(SBMLNamespaces.getCPtr(sbmlns)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
ListOfSpeciesReferences(SBMLNamespaces sbmlns) : this(libsbmlPINVOKE.new_ListOfSpeciesReferences__SWIG_1(SBMLNamespaces.getCPtr(sbmlns)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
public void test_SBMLNamespaces_constructor()
{
SBMLNamespaces s;
try
{
s = new SBMLNamespaces(3,1);
}
catch (SBMLConstructorException e)
{
s = null;
}
assertTrue(s != null);
}
bool hasCorrectNamespace(SBMLNamespaces namespaces)
{
bool ret = libsbmlPINVOKE.L3v2extendedmathASTPlugin_hasCorrectNamespace(swigCPtr, SBMLNamespaces.getCPtr(namespaces));
return(ret);
}
/**
* Creates a new ListOfEventAssignments object.
*
* The object is constructed such that it is valid for the SBML Level and
* Version combination determined by the SBMLNamespaces object in @p
* sbmlns.
*
* @param sbmlns an SBMLNamespaces object that is used to determine the
* characteristics of the ListOfEventAssignments object to be created.
*/
public ListOfEventAssignments(SBMLNamespaces sbmlns)
: this(libsbmlPINVOKE.new_ListOfEventAssignments__SWIG_1(SBMLNamespaces.getCPtr(sbmlns)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
SBMLConstructorException(string elementName, SBMLNamespaces xmlns) : this(libsbmlPINVOKE.new_SBMLConstructorException__SWIG_2(elementName, SBMLNamespaces.getCPtr(xmlns)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
/** */
/* libsbml-internal */
public void setSBMLNamespacesAndOwn(SBMLNamespaces sbmlns)
{
libsbmlPINVOKE.SBase_setSBMLNamespacesAndOwn(swigCPtr, SBMLNamespaces.getCPtr(sbmlns));
}
SBMLDocumentPlugin(string uri, string prefix, SBMLNamespaces sbmlns) : this(libsbmlPINVOKE.new_SBMLDocumentPlugin__SWIG_0(uri, prefix, SBMLNamespaces.getCPtr(sbmlns)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
/**
* Copy constructor; creates a copy of a SBMLNamespaces.
*
* @param orig the SBMLNamespaces instance to copy.
*
* @throws SBMLConstructorException
* Thrown if the argument @p orig is @c null.
*/
public SBMLNamespaces(SBMLNamespaces orig)
: this(libsbmlPINVOKE.new_SBMLNamespaces__SWIG_5(SBMLNamespaces.getCPtr(orig)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
public void prepend(SBMLNamespaces item)
{
libsbmlPINVOKE.SBMLNamespacesList_prepend(swigCPtr, SBMLNamespaces.getCPtr(item));
}
internal static HandleRef getCPtrAndDisown(SBMLNamespaces obj)
{
HandleRef ptr = new HandleRef(null, IntPtr.Zero);
if (obj != null)
{
ptr = obj.swigCPtr;
obj.swigCMemOwn = false;
}
return ptr;
}
private IntPtr SwigDirectorgetTargetNamespaces()
{
return(SBMLNamespaces.getCPtr(getTargetNamespaces()).Handle);
}
/**
* Creates a new ListOfFunctionDefinitions object.
*
* The object is constructed such that it is valid for the SBML Level and
* Version combination determined by the SBMLNamespaces object in @p
* sbmlns.
*
* @param sbmlns an SBMLNamespaces object that is used to determine the
* characteristics of the ListOfFunctionDefinitions object to be created.
*
*
* @throws SBMLConstructorException
* Thrown if the given @p sbmlns is inconsistent or incompatible
* with this object.
*
*
*
*
* @note Attempting to add an object to an SBMLDocument having a different
* combination of SBML Level, Version and XML namespaces than the object
* itself will result in an error at the time a caller attempts to make the
* addition. A parent object must have compatible Level, Version and XML
* namespaces. (Strictly speaking, a parent may also have more XML
* namespaces than a child, but the reverse is not permitted.) The
* restriction is necessary to ensure that an SBML model has a consistent
* overall structure. This requires callers to manage their objects
* carefully, but the benefit is increased flexibility in how models can be
* created by permitting callers to create objects bottom-up if desired. In
* situations where objects are not yet attached to parents (e.g.,
* SBMLDocument), knowledge of the intented SBML Level and Version help
* libSBML determine such things as whether it is valid to assign a
* particular value to an attribute.
*
*
*/
public ListOfFunctionDefinitions(SBMLNamespaces sbmlns)
: this(libsbmlPINVOKE.new_ListOfFunctionDefinitions__SWIG_1(SBMLNamespaces.getCPtr(sbmlns)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
L3ParserSettings(Model model, int parselog, bool collapseminus, bool parseunits, bool avocsymbol, bool caseSensitive, SBMLNamespaces sbmlns) : this(libsbmlPINVOKE.new_L3ParserSettings__SWIG_1(Model.getCPtr(model), parselog, collapseminus, parseunits, avocsymbol, caseSensitive, SBMLNamespaces.getCPtr(sbmlns)), true)
{
}