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)); }