public void setUp()
{
NS = new XMLNamespaces();
if (NS == null);
{
}
}
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_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_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_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_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_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_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;
}
public void test_L3_Unit_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3,1);
sbmlns.addNamespaces(xmlns);
Unit u = new Unit(sbmlns);
assertTrue( u.getTypeCode() == libsbml.SBML_UNIT );
assertTrue( u.getMetaId() == "" );
assertTrue( u.getNotes() == null );
assertTrue( u.getAnnotation() == null );
assertTrue( u.getLevel() == 3 );
assertTrue( u.getVersion() == 1 );
assertTrue( u.getNamespaces() != null );
assertTrue( u.getNamespaces().getLength() == 2 );
assertTrue( u.getKind() == libsbml.UNIT_KIND_INVALID );
assertEquals( true, isnan(u.getExponentAsDouble()) );
assertEquals( true, isnan(u.getMultiplier()) );
assertEquals( false, u.isSetKind() );
assertEquals( false, u.isSetExponent() );
assertEquals( false, u.isSetMultiplier() );
assertEquals( false, u.isSetScale() );
u = null;
}
/**
* Adds SBML Level 2 namespaces to the namespace list.
*
* @if clike
* This will call all overridden
* <code>SBMLExtension::addL2Namespaces()</code> methods.
* @endif
*
* @param xmlns an XMLNamespaces object providing one or more namespaces to
* be added.
*/
public void addL2Namespaces(XMLNamespaces xmlns)
{
libsbmlPINVOKE.SBMLExtensionRegistry_addL2Namespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));
}
XMLNode(XMLTriple triple, XMLAttributes attributes, XMLNamespaces namespaces) : this(libsbmlPINVOKE.new_XMLNode__SWIG_4(XMLTriple.getCPtr(triple), XMLAttributes.getCPtr(attributes), XMLNamespaces.getCPtr(namespaces)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
public static int Main(string[] args)
{
if (args.Length != 2)
{
Console.WriteLine(" usage: addingEvidenceCodes_2 <input-filename> <output-filename>");
Console.WriteLine(" Adds controlled vocabulary term to a species");
Console.WriteLine();
return 2;
}
SBMLDocument d = libsbml.readSBML(args[0]);
long errors = d.getNumErrors();
if (errors > 0)
{
Console.WriteLine("Read Error(s):");
d.printErrors();
Console.WriteLine("Correct the above and re-run.");
}
else
{
long n = d.getModel().getNumSpecies();
if (n <= 0)
{
Console.WriteLine("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]);
}
}
return (int)errors;
}
XMLNamespaces(XMLNamespaces orig) : this(libsbmlPINVOKE.new_XMLNamespaces__SWIG_1(XMLNamespaces.getCPtr(orig)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
/**
* Sets the namespaces relevant of this SBML object.
*
* The content of @p xmlns is copied, and this object's existing
* namespace content is deleted.
*
* 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.
*
* @param xmlns the namespaces to set
*
* @return integer value indicating success/failure of the
* function. The possible values returned by this function are:
* @li @link libsbmlcs.libsbml.LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
*/
public int setNamespaces(XMLNamespaces xmlns)
{
int ret = libsbmlPINVOKE.SBase_setNamespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));
return ret;
}
internal static HandleRef getCPtr(XMLNamespaces obj)
{
return((obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr);
}
int addPkgNamespaces(XMLNamespaces xmlns)
{
int ret = libsbmlPINVOKE.SBMLNamespaces_addPkgNamespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));
return(ret);
}
/**
* Copy constructor; creates a copy of this XMLNamespaces list.
*
* @param orig the XMLNamespaces object to copy
*/
public XMLNamespaces(XMLNamespaces orig)
: this(libsbmlPINVOKE.new_XMLNamespaces__SWIG_1(XMLNamespaces.getCPtr(orig)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
internal static HandleRef getCPtr(XMLNamespaces obj)
{
return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
}
static XMLNode convertStringToXMLNode(string xmlstr, XMLNamespaces xmlns)
{
IntPtr cPtr = libsbmlPINVOKE.XMLNode_convertStringToXMLNode__SWIG_0(xmlstr, XMLNamespaces.getCPtr(xmlns));
XMLNode ret = (cPtr == IntPtr.Zero) ? null : new XMLNode(cPtr, true);
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
return(ret);
}
internal static HandleRef getCPtrAndDisown(XMLNamespaces obj)
{
HandleRef ptr = new HandleRef(null, IntPtr.Zero);
if (obj != null)
{
ptr = obj.swigCPtr;
obj.swigCMemOwn = false;
}
return ptr;
}
/**
* Creates a start element XMLToken with the given set of attributes and
* namespace declarations.
*
* @param triple XMLTriple.
* @param attributes XMLAttributes, the attributes to set.
* @param namespaces XMLNamespaces, the namespaces to set.
* @param line a long integer, the line number (default = 0).
* @param column a long integer, the column number (default = 0).
*
* @ifnot hasDefaultArgs @htmlinclude warn-default-args-in-docs.html @endif
*/
public XMLToken(XMLTriple triple, XMLAttributes attributes, XMLNamespaces namespaces, long line, long column)
: this(libsbmlPINVOKE.new_XMLToken__SWIG_1(XMLTriple.getCPtr(triple), XMLAttributes.getCPtr(attributes), XMLNamespaces.getCPtr(namespaces), line, column), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
public void test_L3_SpeciesReference_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3,1);
sbmlns.addNamespaces(xmlns);
SpeciesReference sr = new SpeciesReference(sbmlns);
assertTrue( sr.getTypeCode() == libsbml.SBML_SPECIES_REFERENCE );
assertTrue( sr.getMetaId() == "" );
assertTrue( sr.getNotes() == null );
assertTrue( sr.getAnnotation() == null );
assertTrue( sr.getLevel() == 3 );
assertTrue( sr.getVersion() == 1 );
assertTrue( sr.getNamespaces() != null );
assertTrue( sr.getNamespaces().getLength() == 2 );
assertTrue( sr.getId() == "" );
assertTrue( sr.getName() == "" );
assertTrue( sr.getSpecies() == "" );
assertEquals( true, isnan(sr.getStoichiometry()) );
assertTrue( sr.getConstant() == false );
assertEquals( false, sr.isSetId() );
assertEquals( false, sr.isSetName() );
assertEquals( false, sr.isSetSpecies() );
assertEquals( false, sr.isSetStoichiometry() );
assertEquals( false, sr.isSetConstant() );
sr = null;
}
public void test_Compartment_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,1);
sbmlns.addNamespaces(xmlns);
Compartment c = new Compartment(sbmlns);
assertTrue( c.getTypeCode() == libsbml.SBML_COMPARTMENT );
assertTrue( c.getMetaId() == "" );
assertTrue( c.getNotes() == null );
assertTrue( c.getAnnotation() == null );
assertTrue( c.getLevel() == 2 );
assertTrue( c.getVersion() == 1 );
assertTrue( c.getNamespaces() != null );
assertTrue( c.getNamespaces().getLength() == 2 );
assertTrue( c.getName() == "" );
assertTrue( c.getSpatialDimensions() == 3 );
assertTrue( c.getConstant() == true );
c = null;
}
/**
* Removes the L2 Namespaces.
*
* This method should be overridden by all extensions that want to serialize
* to an L2 annotation.
*/
public new void removeL2Namespaces(XMLNamespaces xmlns)
{
libsbmlPINVOKE.SBMLExtension_removeL2Namespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));
}
/**
* Creates a new start element XMLNode with the given set of attributes and
* namespace declarations.
*
* @param triple XMLTriple.
* @param attributes XMLAttributes, the attributes to set.
* @param namespaces XMLNamespaces, the namespaces to set.
* @param line a long integer, the line number (default = 0).
* @param column a long integer, the column number (default = 0).
*
* @ifnot hasDefaultArgs @htmlinclude warn-default-args-in-docs.html @endif
*/
public XMLNode(XMLTriple triple, XMLAttributes attributes, XMLNamespaces namespaces)
: this(libsbmlPINVOKE.new_XMLNode__SWIG_4(XMLTriple.getCPtr(triple), XMLAttributes.getCPtr(attributes), XMLNamespaces.getCPtr(namespaces)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
/**
* Sets an XMLnamespaces to this XML element.
* Nothing will be done if this XMLToken is not a start element.
*
* @param namespaces XMLNamespaces to be set to this XMLToken.
*
* @return integer value indicating success/failure of the
* function. The possible values
* returned by this function are:
* @li @link libsbmlcs#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@endlink
* @li @link libsbmlcs#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED@endlink
* @li @link libsbmlcs#LIBSBML_INVALID_XML_OPERATION LIBSBML_INVALID_XML_OPERATION@endlink
* @li @link libsbmlcs#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT@endlink
*
* @note This function replaces the existing XMLNamespaces with the new one.
*/
public int setNamespaces(XMLNamespaces namespaces)
{
int ret = libsbmlPINVOKE.XMLToken_setNamespaces(swigCPtr, XMLNamespaces.getCPtr(namespaces));
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
return ret;
}
void addL2Namespaces(XMLNamespaces xmlns)
{
libsbmlPINVOKE.SBMLExtensionRegistry_addL2Namespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));
}
/**
* Returns the XML namespace declarations for this XML element.
*
* @return the XML namespace declarations for this XML element.
*/
public XMLNamespaces getNamespaces()
{
XMLNamespaces ret = new XMLNamespaces(libsbmlPINVOKE.XMLToken_getNamespaces(swigCPtr), false);
return ret;
}
public void test_L3_Reaction_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3,1);
sbmlns.addNamespaces(xmlns);
Reaction r = new Reaction(sbmlns);
assertTrue( r.getTypeCode() == libsbml.SBML_REACTION );
assertTrue( r.getMetaId() == "" );
assertTrue( r.getNotes() == null );
assertTrue( r.getAnnotation() == null );
assertTrue( r.getLevel() == 3 );
assertTrue( r.getVersion() == 1 );
assertTrue( r.getNamespaces() != null );
assertTrue( r.getNamespaces().getLength() == 2 );
assertTrue( r.getId() == "" );
assertTrue( r.getName() == "" );
assertTrue( r.getCompartment() == "" );
assertTrue( r.getFast() == false );
assertTrue( r.getReversible() == true );
assertEquals( false, r.isSetId() );
assertEquals( false, r.isSetName() );
assertEquals( false, r.isSetCompartment() );
assertEquals( false, r.isSetFast() );
assertEquals( false, r.isSetReversible() );
r = null;
}
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;
}
public void test_XMLToken_newSetters_setNamespaces1()
{
XMLTriple triple = new XMLTriple("test","","");
XMLAttributes attr = new XMLAttributes();
XMLToken token = new XMLToken(triple,attr);
XMLNamespaces ns = new XMLNamespaces();
assertTrue( token.getNamespacesLength() == 0 );
assertTrue( token.isNamespacesEmpty() == true );
ns.add( "http://test1.org/", "test1");
int i = token.setNamespaces(ns);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( token.getNamespacesLength() == 1 );
assertTrue( token.isNamespacesEmpty() == false );
attr = null;
triple = null;
token = null;
ns = null;
}
/**
* Returns an XMLNode which is derived from a string containing XML
* content.
*
* The XML namespace must be defined using argument @p xmlns if the
* corresponding XML namespace attribute is not part of the string of the
* first argument.
*
* @param xmlstr string to be converted to a XML node.
* @param xmlns XMLNamespaces the namespaces to set (default value is @c null).
*
* @note The caller owns the returned XMLNode and is reponsible for
* deleting it. The returned XMLNode object is a dummy root (container)
* XMLNode if the top-level element in the given XML string is NOT
* <code><html></code>, <code><body></code>,
* <code><annotation></code>, or <code><notes></code>. In
* the dummy root node, each top-level element in the given XML string is
* contained as a child XMLNode. XMLToken::isEOF() can be used to
* identify if the returned XMLNode object is a dummy node.
*
* @return a XMLNode which is converted from string @p xmlstr. If the
* conversion failed, this method returns @c null.
*
* @ifnot hasDefaultArgs @htmlinclude warn-default-args-in-docs.html @endif
*/
public static XMLNode convertStringToXMLNode(string xmlstr, XMLNamespaces xmlns)
{
IntPtr cPtr = libsbmlPINVOKE.XMLNode_convertStringToXMLNode__SWIG_0(xmlstr, XMLNamespaces.getCPtr(xmlns));
XMLNode ret = (cPtr == IntPtr.Zero) ? null : new XMLNode(cPtr, true);
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
return ret;
}
public void test_XMLToken_newSetters_setNamespaces2()
{
int i;
XMLTriple triple = new XMLTriple("test","","");
XMLToken token = new XMLToken(triple);
XMLNamespaces ns = new XMLNamespaces();
assertTrue( token.getNamespacesLength() == 0 );
assertTrue( token.isNamespacesEmpty() == true );
ns.add( "http://test1.org/", "test1");
i = token.setNamespaces(ns);
assertTrue( i == libsbml.LIBSBML_INVALID_XML_OPERATION );
assertTrue( token.getNamespacesLength() == 0 );
assertTrue( token.isNamespacesEmpty() == true );
triple = null;
token = null;
ns = null;
}
/** */
/* libsbml-internal */
public int addPkgNamespaces(XMLNamespaces xmlns)
{
int ret = libsbmlPINVOKE.SBMLNamespaces_addPkgNamespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));
return ret;
}
void removeL2Namespaces(XMLNamespaces xmlns)
{
libsbmlPINVOKE.SBMLExtension_removeL2Namespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));
}