Inheritance: IDisposable
Exemplo n.º 1
0
 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;
 }
Exemplo n.º 5
0
 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;
 }
Exemplo n.º 7
0
 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 );
 }
Exemplo n.º 10
0
 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;
 }
Exemplo n.º 11
0
 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));
 }
Exemplo n.º 13
0
 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;
    }
Exemplo n.º 15
0
 XMLNamespaces(XMLNamespaces orig) : this(libsbmlPINVOKE.new_XMLNamespaces__SWIG_1(XMLNamespaces.getCPtr(orig)), true)
 {
     if (libsbmlPINVOKE.SWIGPendingException.Pending)
     {
         throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
     }
 }
Exemplo n.º 16
0
 /**
    * 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&nbsp;3) packages used in addition to SBML Level&nbsp;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;
 }
Exemplo n.º 17
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 internal static HandleRef getCPtr(XMLNamespaces obj)
 {
     return((obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr);
 }
Exemplo n.º 18
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        int addPkgNamespaces(XMLNamespaces xmlns)
        {
            int ret = libsbmlPINVOKE.SBMLNamespaces_addPkgNamespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));

            return(ret);
        }
Exemplo n.º 19
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 /**
    * 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();
 }
Exemplo n.º 20
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 internal static HandleRef getCPtr(XMLNamespaces obj)
 {
     return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
 }
Exemplo n.º 21
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        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);
        }
Exemplo n.º 22
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        internal static HandleRef getCPtrAndDisown(XMLNamespaces obj)
        {
            HandleRef ptr = new HandleRef(null, IntPtr.Zero);

            if (obj != null)
            {
            ptr             = obj.swigCPtr;
            obj.swigCMemOwn = false;
            }

            return ptr;
        }
Exemplo n.º 23
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 /**
    * 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;
 }
Exemplo n.º 25
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 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;
 }
Exemplo n.º 26
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 /**
    * 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));
 }
Exemplo n.º 27
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 /**
    * 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();
 }
Exemplo n.º 28
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 /**
    * 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;
 }
Exemplo n.º 29
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 void addL2Namespaces(XMLNamespaces xmlns)
 {
     libsbmlPINVOKE.SBMLExtensionRegistry_addL2Namespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));
 }
Exemplo n.º 30
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 /**
    * 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;
 }
Exemplo n.º 31
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 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;
 }
Exemplo n.º 32
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 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;
 }
Exemplo n.º 33
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 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;
 }
Exemplo n.º 34
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 /**
    * 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>&lt;html&gt;</code>, <code>&lt;body&gt;</code>,
    * <code>&lt;annotation&gt;</code>, or <code>&lt;notes&gt;</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;
 }
Exemplo n.º 35
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 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;
 }
Exemplo n.º 36
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 /** */
 /* libsbml-internal */
 public int addPkgNamespaces(XMLNamespaces xmlns)
 {
     int ret = libsbmlPINVOKE.SBMLNamespaces_addPkgNamespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));
     return ret;
 }
Exemplo n.º 37
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 void removeL2Namespaces(XMLNamespaces xmlns)
 {
     libsbmlPINVOKE.SBMLExtension_removeL2Namespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));
 }