public CVTerm remove(uint n) { IntPtr cPtr = libsbmlPINVOKE.CVTermList_remove(swigCPtr, n); CVTerm ret = (cPtr == IntPtr.Zero) ? null : new CVTerm(cPtr, false); return(ret); }
public CVTerm get(uint n) { global::System.IntPtr cPtr = libsbmlPINVOKE.CVTermList_get(swigCPtr, n); CVTerm ret = (cPtr == global::System.IntPtr.Zero) ? null : new CVTerm(cPtr, false); return(ret); }
public void test_SBase_addCVTerms() { CVTerm cv = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER); cv.setBiologicalQualifierType(libsbml.BQB_ENCODES); cv.addResource( "foo"); int i = S.addCVTerm(cv); assertTrue( i == libsbml.LIBSBML_MISSING_METAID ); assertTrue( S.getNumCVTerms() == 0 ); S.setMetaId( "_id"); i = S.addCVTerm(cv); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); assertTrue( S.getNumCVTerms() == 1 ); assertTrue( S.getCVTerms() != null ); i = S.addCVTerm(null); assertTrue( i == libsbml.LIBSBML_OPERATION_FAILED ); assertTrue( S.getNumCVTerms() == 1 ); assertTrue( S.getCVTerms() != null ); CVTerm cv2 = new CVTerm(libsbml.MODEL_QUALIFIER); i = S.addCVTerm(cv2); assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT ); assertTrue( S.getNumCVTerms() == 1 ); assertTrue( S.getCVTerms() != null ); cv = null; cv2 = null; }
public void test_CVTerm_create() { CVTerm term = new CVTerm(libsbml.MODEL_QUALIFIER); assertTrue( term != null ); assertTrue( term.getQualifierType() == libsbml.MODEL_QUALIFIER ); term = null; }
CVTerm(CVTerm orig) : this(libsbmlPINVOKE.new_CVTerm__SWIG_3(CVTerm.getCPtr(orig)), true) { if (libsbmlPINVOKE.SWIGPendingException.Pending) { throw libsbmlPINVOKE.SWIGPendingException.Retrieve(); } }
CVTerm clone() { IntPtr cPtr = libsbmlPINVOKE.CVTerm_clone(swigCPtr); CVTerm ret = (cPtr == IntPtr.Zero) ? null : new CVTerm(cPtr, true); return(ret); }
internal static HandleRef getCPtrAndDisown(CVTerm obj) { HandleRef ptr = new HandleRef(null, IntPtr.Zero); if (obj != null) { ptr = obj.swigCPtr; obj.swigCMemOwn = false; } return(ptr); }
public void test_Validation_CVTerm1() { CVTerm cv = new CVTerm(); assertTrue( cv != null ); assertEquals( false, (cv.hasRequiredAttributes()) ); cv.setQualifierType(libsbml.MODEL_QUALIFIER); assertEquals( false, (cv.hasRequiredAttributes()) ); cv.setModelQualifierType(libsbml.BQM_IS); assertEquals( false, (cv.hasRequiredAttributes()) ); cv.addResource("ggg"); assertEquals( true, (cv.hasRequiredAttributes()) ); cv = null; }
public void test_Validation_CVTerm2() { CVTerm cv = new CVTerm(); assertTrue( cv != null ); assertEquals( false, (cv.hasRequiredAttributes()) ); cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER); assertEquals( false, (cv.hasRequiredAttributes()) ); cv.setBiologicalQualifierType(libsbml.BQB_IS); assertEquals( false, (cv.hasRequiredAttributes()) ); cv.addResource("ggg"); assertEquals( true, (cv.hasRequiredAttributes()) ); cv = null; }
public void test_CVTerm_copyConstructor() { CVTerm CVTerm1 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER); CVTerm1.addResource("http://www.geneontology.org/#GO:0005892"); assertTrue( CVTerm1.getQualifierType() == libsbml.BIOLOGICAL_QUALIFIER ); assertTrue( CVTerm1.getResources().getLength() == 1 ); assertTrue( CVTerm1.getResources().getValue(0) == "http://www.geneontology.org/#GO:0005892" ); CVTerm CVTerm2 = new CVTerm(CVTerm1); assertTrue( CVTerm2.getQualifierType() == libsbml.BIOLOGICAL_QUALIFIER ); assertTrue( CVTerm2.getResources().getLength() == 1 ); assertTrue( CVTerm2.getResources().getValue(0) == "http://www.geneontology.org/#GO:0005892" ); CVTerm2 = null; CVTerm1 = null; }
public void test_CVTerm_addResource() { CVTerm term = new CVTerm(libsbml.MODEL_QUALIFIER); string resource = "GO6666"; XMLAttributes xa; assertTrue( term != null ); assertTrue( term.getQualifierType() == libsbml.MODEL_QUALIFIER ); term.addResource(resource); xa = term.getResources(); assertTrue( xa.getLength() == 1 ); assertTrue(( "rdf:resource" == xa.getName(0) )); assertTrue(( "GO6666" == xa.getValue(0) )); term = null; }
public void test_SBase_addCVTerms() { CVTerm cv = new CVTerm (libsbml.BIOLOGICAL_QUALIFIER); cv.setBiologicalQualifierType (libsbml.BQB_ENCODES); cv.addResource ("foo"); S.setMetaId ("sbase1"); S.addCVTerm (cv); assertTrue (S.getNumCVTerms () == 1); assertTrue (S.getCVTerms () != null); XMLAttributes res = S.getCVTerm (0).getResources (); assertTrue (("foo" == res.getValue (0))); CVTerm cv1 = new CVTerm (libsbml.BIOLOGICAL_QUALIFIER); cv1.setBiologicalQualifierType (libsbml.BQB_IS); cv1.addResource ("bar"); S.addCVTerm (cv1); assertTrue (S.getNumCVTerms () == 2); CVTerm cv2 = new CVTerm (libsbml.BIOLOGICAL_QUALIFIER); cv2.setBiologicalQualifierType (libsbml.BQB_IS); cv2.addResource ("bar1"); S.addCVTerm (cv2); assertTrue (S.getNumCVTerms () == 2); res = S.getCVTerm (1).getResources (); assertTrue (res.getLength () == 2); assertTrue (("bar" == res.getValue (0))); assertTrue (("bar1" == res.getValue (1))); CVTerm cv4 = new CVTerm (libsbml.BIOLOGICAL_QUALIFIER); cv4.setBiologicalQualifierType (libsbml.BQB_IS); cv4.addResource ("bar1"); S.addCVTerm (cv4); assertTrue (S.getNumCVTerms () == 2); res = S.getCVTerm (1).getResources (); assertTrue (res.getLength () == 2); assertTrue (("bar" == res.getValue (0))); assertTrue (("bar1" == res.getValue (1))); CVTerm cv5 = new CVTerm (libsbml.BIOLOGICAL_QUALIFIER); cv5.setBiologicalQualifierType (libsbml.BQB_HAS_PART); cv5.addResource ("bar1"); S.addCVTerm (cv5); assertTrue (S.getNumCVTerms () == 2); res = S.getCVTerm (1).getResources (); assertTrue (res.getLength () == 2); assertTrue (("bar" == res.getValue (0))); assertTrue (("bar1" == res.getValue (1))); cv = null; cv2 = null; cv1 = null; cv4 = null; }
public void test_CVTerm_removeResource() { CVTerm term = new CVTerm(libsbml.MODEL_QUALIFIER); string resource = "GO6666"; XMLAttributes xa; assertTrue( term != null ); assertTrue( term.getQualifierType() == libsbml.MODEL_QUALIFIER ); term.addResource(resource); xa = term.getResources(); assertTrue( xa.getLength() == 1 ); int i = term.removeResource( "CCC"); assertTrue( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE ); xa = term.getResources(); assertTrue( xa.getLength() == 1 ); i = term.removeResource(resource); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); xa = term.getResources(); assertTrue( xa.getLength() == 0 ); term = 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 void test_CVTerm_setBiolQualifierType() { CVTerm term = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER); assertTrue( term != null ); assertTrue( term.getQualifierType() == libsbml.BIOLOGICAL_QUALIFIER ); assertTrue( term.getModelQualifierType() == libsbml.BQM_UNKNOWN ); assertTrue( term.getBiologicalQualifierType() == libsbml.BQB_UNKNOWN ); int i = term.setBiologicalQualifierType(libsbml.BQB_IS); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); assertTrue( term.getQualifierType() == libsbml.BIOLOGICAL_QUALIFIER ); assertTrue( term.getBiologicalQualifierType() == libsbml.BQB_IS ); assertTrue( term.getModelQualifierType() == libsbml.BQM_UNKNOWN ); i = term.setQualifierType(libsbml.MODEL_QUALIFIER); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); assertTrue( term.getQualifierType() == libsbml.MODEL_QUALIFIER ); assertTrue( term.getModelQualifierType() == libsbml.BQM_UNKNOWN ); assertTrue( term.getBiologicalQualifierType() == libsbml.BQB_UNKNOWN ); i = term.setBiologicalQualifierType(libsbml.BQB_IS); assertTrue( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE ); assertTrue( term.getQualifierType() == libsbml.MODEL_QUALIFIER ); assertTrue( term.getModelQualifierType() == libsbml.BQM_UNKNOWN ); assertTrue( term.getBiologicalQualifierType() == libsbml.BQB_UNKNOWN ); term = null; }
public void test_CVTerm_getResources() { CVTerm term = new CVTerm(libsbml.MODEL_QUALIFIER); string resource = "GO6666"; string resource1 = "OtherURI"; long number; term.addResource(resource); term.addResource(resource1); number = term.getNumResources(); assertTrue( number == 2 ); assertTrue(( "GO6666" == term.getResourceURI(0) )); assertTrue(( "OtherURI" == term.getResourceURI(1) )); term = null; }
/** * Adds a copy of the given CVTerm object to the list of nested CVTerm * objects within this CVTerm object. * * @param term the CVTerm to assign. * * * @return integer value indicating success/failure of the * function. @if clike The value is drawn from the * enumeration #OperationReturnValues_t. @endif The possible values * returned by this function are: * @li @link libsbml#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@endlink * @li @link libsbml#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED@endlink * @li @link libsbml#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT@endlink */ public int addNestedCVTerm(CVTerm term) { int ret = libsbmlPINVOKE.CVTerm_addNestedCVTerm(swigCPtr, CVTerm.getCPtr(term)); return ret; }
/** * Copy constructor; creates a copy of a CVTerm object. * * @param orig the CVTerm instance to copy. */ public CVTerm(CVTerm orig) : this(libsbmlPINVOKE.new_CVTerm__SWIG_3(CVTerm.getCPtr(orig)), true) { if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve(); }
internal static HandleRef getCPtrAndDisown(CVTerm obj) { HandleRef ptr = new HandleRef(null, IntPtr.Zero); if (obj != null) { ptr = obj.swigCPtr; obj.swigCMemOwn = false; } return ptr; }
internal static HandleRef getCPtr(CVTerm obj) { return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr; }
public static int Main(string[] args) { SBMLDocument d; long errors, n; Species s; if (args.Length != 2) { Console.WriteLine(" usage: addCVTerms <input-filename> <output-filename>"); Console.WriteLine(" Adds controlled vocabulary term to a species"); return 2; } d = libsbml.readSBML(args[0]); errors = d.getNumErrors(); if (errors > 0) { Console.WriteLine("Read Error(s):"); d.printErrors(); Console.WriteLine("Correct the above and re-run."); } else { n = d.getModel().getNumSpecies(); if (n <= 0) { Console.WriteLine("Model has no species.\n Cannot add CV terms\n"); } else { s = d.getModel().getSpecies(0); CVTerm cv = new CVTerm(); cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER); cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF); cv.addResource("http://www.geneontology.org/#GO:0005892"); CVTerm cv2 = new CVTerm(); cv2.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER); cv2.setBiologicalQualifierType(libsbml.BQB_IS); cv2.addResource("http://www.geneontology.org/#GO:0005895"); CVTerm cv1 = new CVTerm(); cv1.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER); cv1.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF); cv1.addResource("http://www.ebi.ac.uk/interpro/#IPR002394"); s.addCVTerm(cv); s.addCVTerm(cv2); s.addCVTerm(cv1); libsbml.writeSBML(d, args[1]); } } return (int)errors; }
public void test_RDFAnnotation_testMissingMetaId() { SBMLDocument doc = new SBMLDocument ( 3,1 ); Model model = doc.createModel(); assertTrue( model != null ); model.setId("test1"); CVTerm term = new CVTerm ( libsbml.MODEL_QUALIFIER ); term.addResource("testResource"); term.setModelQualifierType(libsbml.BQM_IS); model.setMetaId("t1"); model.addCVTerm(term); model.setMetaId(""); string test = model.toSBML(); assertTrue( test == "<model id=\"test1\"/>" ); }
public void prepend(CVTerm item) { libsbmlPINVOKE.CVTermList_prepend(swigCPtr, CVTerm.getCPtr(item)); }
internal static HandleRef getCPtr(CVTerm obj) { return((obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr); }
public void test_SBase_unsetAnnotationWithCVTerms() { CVTerm cv; string annt = "<annotation>\n" + " <test:test xmlns:test=\"http://test.org/test\">this is a test node</test:test>\n" + "</annotation>"; string annt_with_cvterm = "<annotation>\n" + " <test:test xmlns:test=\"http://test.org/test\">this is a test node</test:test>\n" + " <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" " + "xmlns:dc=\"http://purl.org/dc/elements/1.1/\" " + "xmlns:dcterms=\"http://purl.org/dc/terms/\" " + "xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" " + "xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" " + "xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n" + " <rdf:Description rdf:about=\"#_000001\">\n" + " <bqbiol:is>\n" + " <rdf:Bag>\n" + " <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0005895\"/>\n" + " </rdf:Bag>\n" + " </bqbiol:is>\n" + " </rdf:Description>\n" + " </rdf:RDF>\n" + "</annotation>"; S.setAnnotation (annt); assertTrue (S.isSetAnnotation () == true); assertTrue ((annt == S.getAnnotationString ())); S.unsetAnnotation (); assertTrue (S.isSetAnnotation () == false); assertTrue (S.getAnnotation () == null); S.setAnnotation (annt); S.setMetaId ("_000001"); cv = new CVTerm (libsbml.BIOLOGICAL_QUALIFIER); cv.setBiologicalQualifierType (libsbml.BQB_IS); cv.addResource ("http://www.geneontology.org/#GO:0005895"); S.addCVTerm (cv); assertTrue (S.isSetAnnotation () == true); assertTrue ((annt_with_cvterm == S.getAnnotationString ())); S.unsetAnnotation (); assertTrue (S.isSetAnnotation () == false); assertTrue (S.getAnnotation () == null); cv = null; }
/** * Adds a copy of the given CVTerm object to this SBML object. * * @param term the CVTerm to assign. * * @param newBag if @c true, creates a new RDF bag with the same identifier * as a previous bag, and if @c false, adds the term to an existing * RDF bag with the same type of qualifier as the term being added. * * @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 * @li @link libsbmlcs.libsbml.LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink * @li @link libsbmlcs.libsbml.LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink, if * this object lacks a 'metaid' attribute * @li @link libsbmlcs.libsbml.LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink * * @note Since the CV Term uses the 'metaid' attribute of the object as a * reference, if the object has no 'metaid' attribute value set, then the * CVTerm will not be added. * * * * @note This method should be used with some caution. The fact that this * method @em copies the object passed to it means that the caller will be * left holding a physically different object instance than the one contained * inside this object. Changes made to the original object instance (such as * resetting attribute values) will <em>not affect the instance in this * object</em>. In addition, the caller should make sure to free the * original object if it is no longer being used, or else a memory leak will * result. Please see other methods on this class (particularly a * corresponding method whose name begins with the word <code>create</code>) * for alternatives that do not lead to these issues. * * * * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif */ public int addCVTerm(CVTerm term, bool newBag) { int ret = libsbmlPINVOKE.SBase_addCVTerm__SWIG_0(swigCPtr, CVTerm.getCPtr(term), newBag); return ret; }
public void test_SBase_CVTerms() { CVTerm cv = new CVTerm (libsbml.BIOLOGICAL_QUALIFIER); cv.setBiologicalQualifierType (libsbml.BQB_IS); cv.addResource ("foo"); assertTrue (S.getNumCVTerms () == 0); assertTrue (S.getCVTerms () == null); S.setMetaId ("_id"); S.addCVTerm (cv); assertTrue (S.getNumCVTerms () == 1); assertTrue (S.getCVTerms () != null); assertTrue (S.getCVTerm (0) != cv); cv = null; }
public void test_SBase_getQualifiersFromResources() { CVTerm cv = new CVTerm (libsbml.BIOLOGICAL_QUALIFIER); cv.setBiologicalQualifierType (libsbml.BQB_ENCODES); cv.addResource ("foo"); S.setMetaId ("sbase1"); S.addCVTerm (cv); assertTrue (S.getResourceBiologicalQualifier ("foo") == libsbml.BQB_ENCODES); CVTerm cv1 = new CVTerm (libsbml.MODEL_QUALIFIER); cv1.setModelQualifierType (libsbml.BQM_IS); cv1.addResource ("bar"); S.addCVTerm (cv1); assertTrue (S.getResourceModelQualifier ("bar") == libsbml.BQM_IS); cv = null; cv1 = null; }
public void test_CVTerm_set_get() { CVTerm term = new CVTerm(libsbml.MODEL_QUALIFIER); assertTrue( term != null ); assertTrue( term.getQualifierType() == libsbml.MODEL_QUALIFIER ); term.setModelQualifierType(libsbml.BQM_IS); assertTrue( term != null ); assertTrue( term.getQualifierType() == libsbml.MODEL_QUALIFIER ); assertTrue( term.getModelQualifierType() == libsbml.BQM_IS ); term.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER); term.setBiologicalQualifierType(libsbml.BQB_IS); assertTrue( term.getQualifierType() == libsbml.BIOLOGICAL_QUALIFIER ); assertTrue( term.getBiologicalQualifierType() == libsbml.BQB_IS ); term = 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#", "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; }
public void prepend(CVTerm item) { libsbmlPINVOKE.CVTermList_prepend(swigCPtr, CVTerm.getCPtr(item)); }
public void test_RDFAnnotation_parseCVTerms() { XMLNode node = RDFAnnotationParser.parseCVTerms(m.getCompartment(0)); assertTrue( node.getNumChildren() == 1 ); XMLNode rdf = node.getChild(0); assertTrue(( "RDF" == rdf.getName() )); assertTrue(( "rdf" == rdf.getPrefix() )); assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == rdf.getURI() )); assertTrue( rdf.getNumChildren() == 1 ); XMLNode desc = rdf.getChild(0); assertTrue(( "Description" == desc.getName() )); assertTrue(( "rdf" == desc.getPrefix() )); assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == desc.getURI() )); assertTrue( desc.getNumChildren() == 1 ); XMLNode is1 = desc.getChild(0); assertTrue(( "is" == is1.getName() )); assertTrue(( "bqbiol" == is1.getPrefix() )); assertTrue( is1.getNumChildren() == 1 ); XMLNode Bag = is1.getChild(0); assertTrue(( "Bag" == Bag.getName() )); assertTrue(( "rdf" == Bag.getPrefix() )); assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == Bag.getURI() )); assertTrue( Bag.getNumChildren() == 4 ); XMLNode li = Bag.getChild(0); assertTrue(( "li" == li.getName() )); assertTrue(( "rdf" == li.getPrefix() )); assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li.getURI() )); assertTrue( li.getNumChildren() == 0 ); XMLNode li1 = Bag.getChild(1); assertTrue(( "li" == li1.getName() )); assertTrue(( "rdf" == li1.getPrefix() )); assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li1.getURI() )); assertTrue( li1.getNumChildren() == 0 ); XMLNode li2 = Bag.getChild(2); assertTrue(( "li" == li2.getName() )); assertTrue(( "rdf" == li2.getPrefix() )); assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li2.getURI() )); assertTrue( li2.getNumChildren() == 0 ); XMLNode li3 = Bag.getChild(3); assertTrue(( "li" == li3.getName() )); assertTrue(( "rdf" == li3.getPrefix() )); assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li3.getURI() )); assertTrue( li3.getNumChildren() == 0 ); node = null; XMLNode node1 = RDFAnnotationParser.parseCVTerms(null); assertTrue( node1 == null ); node1 = RDFAnnotationParser.createCVTerms(null); assertTrue( node1 == null ); node1 = RDFAnnotationParser.parseCVTerms(m.getCompartment(2)); assertTrue( node1 == null ); node1 = RDFAnnotationParser.createCVTerms(m.getCompartment(2)); assertTrue( node1 == null ); node1 = RDFAnnotationParser.parseCVTerms(m); assertTrue( node1 == null ); node1 = RDFAnnotationParser.createCVTerms(m); assertTrue( node1 == null ); Compartment c = new Compartment(3,1); c.setMetaId("_002"); node1 = RDFAnnotationParser.parseCVTerms(c); assertTrue( node1 == null ); node1 = RDFAnnotationParser.createCVTerms(c); assertTrue( node1 == null ); CVTerm cv = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER); cv.setBiologicalQualifierType(23); cv.addResource("http://myres"); c.addCVTerm(cv); node1 = RDFAnnotationParser.createCVTerms(c); assertTrue( node1 == null ); c = null; Model m1 = new Model(3,1); m1.setMetaId("_002"); cv = new CVTerm(libsbml.MODEL_QUALIFIER); cv.setModelQualifierType(23); cv.addResource("http://myres"); m1.addCVTerm(cv); node1 = RDFAnnotationParser.createCVTerms(m1); assertTrue( node1 == null ); }
public static int Main(string[] args) { SBMLDocument d; long errors, n; Reaction r; if (args.Length != 2) { Console.Write(Environment.NewLine + " usage: addingEvidenceCodes_1 <input-filename> <output-filename>" + Environment.NewLine + " Adds controlled vocabulary term to a reaction" + Environment.NewLine + Environment.NewLine); return 2; } d = libsbml.readSBML(args[1]); errors = d.getNumErrors(); if (errors > 0) { Console.Write("Read Error(s):" + Environment.NewLine); d.printErrors(); Console.Write("Correct the above and re-run." + Environment.NewLine); } else { n = d.getModel().getNumReactions(); if (n <= 0) { Console.Write("Model has no reactions.\n Cannot add CV terms\n"); } else { r = d.getModel().getReaction(0); /* check that the reaction has a metaid * no CVTerms will be added if there is no metaid to reference */ if (!r.isSetMetaId()) r.setMetaId("metaid_0000052"); CVTerm cv1 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER); cv1.setBiologicalQualifierType(libsbml.BQB_IS_DESCRIBED_BY); cv1.addResource("urn:miriam:obo.eco:ECO%3A0000183"); r.addCVTerm(cv1); CVTerm cv2 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER); cv2.setBiologicalQualifierType(libsbml.BQB_IS); cv2.addResource("urn:miriam:kegg.reaction:R00756"); cv2.addResource("urn:miriam:reactome:REACT_736"); r.addCVTerm(cv2); libsbml.writeSBML(d, args[1]); } } return (int)errors; }
public void test_SBase_unsetCVTerms() { CVTerm cv = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER); cv.setBiologicalQualifierType(libsbml.BQB_ENCODES); cv.addResource( "foo"); S.setMetaId( "_id"); S.addCVTerm(cv); CVTerm cv1 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER); cv1.setBiologicalQualifierType(libsbml.BQB_IS); cv1.addResource( "bar"); S.addCVTerm(cv1); CVTerm cv2 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER); cv2.setBiologicalQualifierType(libsbml.BQB_IS); cv2.addResource( "bar1"); S.addCVTerm(cv2); CVTerm cv4 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER); cv4.setBiologicalQualifierType(libsbml.BQB_IS); cv4.addResource( "bar1"); S.addCVTerm(cv4); assertTrue( S.getNumCVTerms() == 2 ); int i = S.unsetCVTerms(); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); assertTrue( S.getNumCVTerms() == 0 ); assertTrue( S.getCVTerms() == null ); cv = null; cv2 = null; cv1 = null; cv4 = null; }
/** * Adds a copy of the given CVTerm object to this SBML object. * * @param term the CVTerm to assign. * * @param newBag if @c true, creates a new RDF bag with the same identifier * as a previous bag, and if @c false, adds the term to an existing * RDF bag with the same type of qualifier as the term being added. * * @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 * @li @link libsbmlcs.libsbml.LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink * @li @link libsbmlcs.libsbml.LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink, if * this object lacks a 'metaid' attribute * @li @link libsbmlcs.libsbml.LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink * * @note Since the CV Term uses the 'metaid' attribute of the object as a * reference, if the object has no 'metaid' attribute value set, then the * CVTerm will not be added. * * * * @note This method should be used with some caution. The fact that this * method @em copies the object passed to it means that the caller will be * left holding a physically different object instance than the one contained * inside this object. Changes made to the original object instance (such as * resetting attribute values) will <em>not affect the instance in this * object</em>. In addition, the caller should make sure to free the * original object if it is no longer being used, or else a memory leak will * result. Please see other methods on this class (particularly a * corresponding method whose name begins with the word <code>create</code>) * for alternatives that do not lead to these issues. * * * * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif */ public int addCVTerm(CVTerm term) { int ret = libsbmlPINVOKE.SBase_addCVTerm__SWIG_1(swigCPtr, CVTerm.getCPtr(term)); return ret; }
public void test_RDFAnnotation2_modelWithHistoryAndCVTerms() { ModelHistory h = new ModelHistory(); ModelCreator c = new ModelCreator(); c.setFamilyName("Keating"); c.setGivenName("Sarah"); h.addCreator(c); Date d = new Date(2008,11,17,18,37,0,0,0,0); h.setCreatedDate(d); h.setModifiedDate(d); m2.unsetModelHistory(); m2.setModelHistory(h); CVTerm cv = new CVTerm(); cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER); cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF); cv.addResource("http://www.geneontology.org/#GO:0005892"); m2.addCVTerm(cv); XMLNode ann = RDFAnnotationParser.parseModelHistory(m2); string expected = "<annotation>\n" + " <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n" + " <rdf:Description rdf:about=\"#_000001\">\n" + " <dc:creator rdf:parseType=\"Resource\">\n" + " <rdf:Bag>\n" + " <rdf:li rdf:parseType=\"Resource\">\n" + " <vCard:N rdf:parseType=\"Resource\">\n" + " <vCard:Family>Keating</vCard:Family>\n" + " <vCard:Given>Sarah</vCard:Given>\n" + " </vCard:N>\n" + " </rdf:li>\n" + " </rdf:Bag>\n" + " </dc:creator>\n" + " <dcterms:created rdf:parseType=\"Resource\">\n" + " <dcterms:W3CDTF>2008-11-17T18:37:00Z</dcterms:W3CDTF>\n" + " </dcterms:created>\n" + " <dcterms:modified rdf:parseType=\"Resource\">\n" + " <dcterms:W3CDTF>2008-11-17T18:37:00Z</dcterms:W3CDTF>\n" + " </dcterms:modified>\n" + " <bqbiol:isVersionOf>\n" + " <rdf:Bag>\n" + " <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0005892\"/>\n" + " </rdf:Bag>\n" + " </bqbiol:isVersionOf>\n" + " </rdf:Description>\n" + " </rdf:RDF>\n" + "</annotation>"; if (ann != null); { assertEquals( true, equals(expected,ann.toXMLString()) ); } { } }