C# libsbmlcs.XMLTriple类代码示例

 public void test_Node_clone()
 {
     XMLAttributes att = new XMLAttributes();
       XMLTriple t = new XMLTriple("sarah", "http://foo.org/", "bar");
       XMLToken token = new XMLToken(t,att,3,4);
       XMLNode node = new XMLNode(token);
       XMLNode child = new XMLNode();
       node.addChild(child);
       assertTrue( node.getNumChildren() == 1 );
       assertTrue( node.getName() ==  "sarah" );
       assertTrue( node.getURI() ==  "http://foo.org/" );
       assertTrue( node.getPrefix() ==  "bar" );
       assertTrue( node.isEnd() == false );
       assertTrue( node.isEOF() == false );
       assertTrue( node.getLine() == 3 );
       assertTrue( node.getColumn() == 4 );
       XMLNode node2 = (XMLNode) node.clone();
       assertTrue( node2.getNumChildren() == 1 );
       assertTrue( node2.getName() ==  "sarah" );
       assertTrue( node2.getURI() ==  "http://foo.org/" );
       assertTrue( node2.getPrefix() ==  "bar" );
       assertTrue( node2.isEnd() == false );
       assertTrue( node2.isEOF() == false );
       assertTrue( node2.getLine() == 3 );
       assertTrue( node2.getColumn() == 4 );
       t = null;
       token = null;
       node = null;
       node2 = null;
 }

 public void test_XMLNode_clearAttributes()
 {
     XMLTriple triple = new  XMLTriple("test","","");
       XMLAttributes attr = new  XMLAttributes();
       XMLNode node = new XMLNode(triple,attr);
       XMLTriple xt2 = new  XMLTriple("name3",  "http://name3.org/", "p3");
       XMLTriple xt1 = new  XMLTriple("name5",  "http://name5.org/", "p5");
       int i = node.addAttr( "name1", "val1");
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       assertTrue( node.getAttributes().getLength() == 1 );
       i = node.addAttr( "name2", "val2",  "http://name1.org/", "p1");
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       assertTrue( node.getAttributes().getLength() == 2 );
       i = node.addAttr(xt2, "val2");
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       assertTrue( node.getAttributes().getLength() == 3 );
       i = node.addAttr( "name4", "val4");
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       assertTrue( node.getAttributes().getLength() == 4 );
       i = node.clearAttributes();
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       assertTrue( node.getAttributes().getLength() == 0 );
       xt1 = null;
       xt2 = null;
       triple = null;
       attr = null;
       node = null;
 }

 public void test_XMLToken_newSetters_addAttributes1()
 {
     XMLTriple triple = new  XMLTriple("test","","");
       XMLAttributes attr = new  XMLAttributes();
       XMLToken token = new  XMLToken(triple,attr);
       XMLTriple xt2 = new  XMLTriple("name3",  "http://name3.org/", "p3");
       int i = token.addAttr( "name1", "val1");
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       assertTrue( token.getAttributesLength() == 1 );
       assertTrue( token.isAttributesEmpty() == false );
       assertTrue( (  "name1" != token.getAttrName(0) ) == false );
       assertTrue( (  "val1"  != token.getAttrValue(0) ) == false );
       i = token.addAttr( "name2", "val2",  "http://name1.org/", "p1");
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       assertTrue( token.getAttributesLength() == 2 );
       assertTrue( token.isAttributesEmpty() == false );
       assertTrue( (  "name2" != token.getAttrName(1) ) == false );
       assertTrue( (  "val2"  != token.getAttrValue(1) ) == false );
       assertTrue( (  "http://name1.org/" != token.getAttrURI(1) ) == false );
       assertTrue( (  "p1"    != token.getAttrPrefix(1) ) == false );
       i = token.addAttr(xt2, "val2");
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       assertTrue( token.getAttributesLength() == 3 );
       assertTrue( token.isAttributesEmpty() == false );
       assertTrue( (  "name3" != token.getAttrName(2) ) == false );
       assertTrue( (  "val2"  != token.getAttrValue(2) ) == false );
       assertTrue( (  "http://name3.org/" != token.getAttrURI(2) ) == false );
       assertTrue( (  "p3"    != token.getAttrPrefix(2) ) == false );
       xt2 = null;
       triple = null;
       attr = null;
       token = null;
 }

 public void test_XMLNode_addChild3()
 {
     XMLTriple triple = new  XMLTriple("test","","");
       XMLNode node = new XMLNode(triple);
       XMLNode node2 = new XMLNode();
       int i = node.addChild(node2);
       assertTrue( i == libsbml.LIBSBML_INVALID_XML_OPERATION );
       assertTrue( node.getNumChildren() == 0 );
       triple = null;
       node = null;
       node2 = null;
 }

 public void test_XMLNode_addChild2()
 {
     XMLTriple triple = new  XMLTriple("test","","");
       XMLAttributes attr = new  XMLAttributes();
       XMLNode node = new XMLNode(triple,attr);
       XMLNode node2 = new XMLNode();
       int i = node.addChild(node2);
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       assertTrue( node.getNumChildren() == 1 );
       triple = null;
       attr = null;
       node = null;
       node2 = null;
 }

 public void test_XMLAttributes_add1()
 {
     XMLAttributes xa = new  XMLAttributes();
       XMLTriple xt2 = new  XMLTriple("name2", "http://name2.org/", "p2");
       int i = xa.add( "name1", "val1", "http://name1.org/", "p1");
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       i = xa.add(xt2, "val2");
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       assertTrue( xa.getLength() == 2 );
       assertTrue( xa.isEmpty() == false );
       i = xa.add( "noprefix", "val3");
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       assertTrue( xa.getLength() == 3 );
       assertTrue( xa.isEmpty() == false );
       xa = null;
       xt2 = 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_XMLToken_newSetters_addAttributes2()
 {
     XMLTriple triple = new  XMLTriple("test","","");
       XMLToken token = new  XMLToken(triple);
       XMLTriple xt2 = new  XMLTriple("name3",  "http://name3.org/", "p3");
       int i = token.addAttr( "name1", "val1");
       assertTrue( i == libsbml.LIBSBML_INVALID_XML_OPERATION );
       assertTrue( token.getAttributesLength() == 0 );
       assertTrue( token.isAttributesEmpty() == true );
       i = token.addAttr( "name2", "val2",  "http://name1.org/", "p1");
       assertTrue( i == libsbml.LIBSBML_INVALID_XML_OPERATION );
       assertTrue( token.getAttributesLength() == 0 );
       assertTrue( token.isAttributesEmpty() == true );
       i = token.addAttr(xt2, "val2");
       assertTrue( i == libsbml.LIBSBML_INVALID_XML_OPERATION );
       assertTrue( token.getAttributesLength() == 0 );
       assertTrue( token.isAttributesEmpty() == true );
       xt2 = null;
       triple = null;
       token = null;
 }

 public void test_XMLTriple_create()
 {
     XMLTriple t = new  XMLTriple();
       assertTrue( t != null );
       assertTrue( t.isEmpty() != false );
       t = null;
       t = new  XMLTriple("attr", "uri", "prefix");
       assertTrue( (  "attr" != t.getName() ) == false );
       assertTrue( (  "uri" != t.getURI() ) == false );
       assertTrue( (  "prefix" != t.getPrefix() ) == false );
       assertTrue( (  "prefix:attr" != t.getPrefixedName() ) == false );
       assertTrue( t.isEmpty() == false );
       t = null;
       t = new  XMLTriple("attr", "uri", "");
       assertTrue( (  "attr" != t.getName() ) == false );
       assertTrue( (  "uri" != t.getURI() ) == false );
       assertTrue( t.getPrefix() == "" );
       assertTrue( (  "attr" != t.getPrefixedName() ) == false );
       assertTrue( t.isEmpty() == false );
       t = null;
 }

 public void test_CVTerm_createFromNode()
 {
     XMLAttributes xa;
       XMLTriple qual_triple = new  XMLTriple("is", "", "bqbiol");
       XMLTriple bag_triple = new  XMLTriple();
       XMLTriple li_triple = new  XMLTriple();
       XMLAttributes att = new  XMLAttributes();
       att.add( "", "This is my resource");
       XMLAttributes att1 = new  XMLAttributes();
       XMLToken li_token = new  XMLToken(li_triple,att);
       XMLToken bag_token = new  XMLToken(bag_triple,att1);
       XMLToken qual_token = new  XMLToken(qual_triple,att1);
       XMLNode li = new XMLNode(li_token);
       XMLNode bag = new XMLNode(bag_token);
       XMLNode node = new XMLNode(qual_token);
       bag.addChild(li);
       node.addChild(bag);
       CVTerm term = new  CVTerm(node);
       assertTrue( term != null );
       assertTrue( term.getQualifierType() == libsbml.BIOLOGICAL_QUALIFIER );
       assertTrue( term.getBiologicalQualifierType() == libsbml.BQB_IS );
       xa = term.getResources();
       assertTrue( xa.getLength() == 1 );
       assertTrue((  "rdf:resource" == xa.getName(0) ));
       assertTrue((  "This is my resource" == xa.getValue(0) ));
       qual_triple = null;
       bag_triple = null;
       li_triple = null;
       li_token = null;
       bag_token = null;
       qual_token = null;
       att = null;
       att1 = null;
       term = null;
       node = null;
       bag = null;
       li = null;
 }

    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#",
//.........这里部分代码省略.........

 /**
    * Return the index of an attribute with the given XMLTriple.
    *
    * @param triple an XMLTriple, the XML triple of the attribute for which
    *        the index is required.
    *
    * @return the index of an attribute with the given XMLTriple, or <code>-1</code> if not present.
    */
 public int getAttrIndex(XMLTriple triple)
 {
     int ret = libsbmlPINVOKE.XMLToken_getAttrIndex__SWIG_2(swigCPtr, XMLTriple.getCPtr(triple));
     if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
     return ret;
 }

 /**
    * Return a value of an attribute with the given XMLTriple.
    *
    * @param triple an XMLTriple, the XML triple of the attribute whose
    *        value is required.
    *
    * @return The attribute value as a string.
    *
    * @note If an attribute with the
    * given XMLTriple does not exist, an empty string will be returned.
    * Use XMLToken::hasAttr(@if java [email protected])
    * to test for attribute existence.
    */
 public string getAttrValue(XMLTriple triple)
 {
     string ret = libsbmlPINVOKE.XMLToken_getAttrValue__SWIG_3(swigCPtr, XMLTriple.getCPtr(triple));
     if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
     return ret;
 }

 /**
    * Sets the XMLTripe (name, uri and prefix) of this XML element.
    * Nothing will be done if this XML element is a text node.
    *
    * @param triple XMLTriple to be added to this XML element.
    *
    * @return integer value indicating success/failure of the
    * function.   The possible values
    * returned by this function are:
    * @li @link libsbmlcs#LIBSBML_OPERATION_SUCCESS [email protected]
    * @li @link libsbmlcs#LIBSBML_OPERATION_FAILED [email protected]
    * @li @link libsbmlcs#LIBSBML_INVALID_XML_OPERATION [email protected]
    * @li @link libsbmlcs#LIBSBML_INVALID_OBJECT [email protected]
    */
 public int setTriple(XMLTriple triple)
 {
     int ret = libsbmlPINVOKE.XMLToken_setTriple(swigCPtr, XMLTriple.getCPtr(triple));
     if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
     return ret;
 }

 /**
    * Adds an attribute with the given XMLTriple/value pair to the attribute set
    * in this XMLToken.
    * Nothing will be done if this XMLToken is not a start element.
    *
    * @note if local name with the same namespace URI already exists in the
    * attribute set, its value and prefix will be replaced.
    *
    * @param triple an XMLTriple, the XML triple of the attribute.
    * @param value a string, the value of the attribute.
    *
    * @return integer value indicating success/failure of the
    * function.   The possible values
    * returned by this function are:
    * @li @link libsbmlcs#LIBSBML_OPERATION_SUCCESS [email protected]
    * @li @link libsbmlcs#LIBSBML_INVALID_XML_OPERATION [email protected]
    */
 public int addAttr(XMLTriple triple, string value)
 {
     int ret = libsbmlPINVOKE.XMLToken_addAttr__SWIG_3(swigCPtr, XMLTriple.getCPtr(triple), value);
     if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
     return ret;
 }