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()) );
}
{
}
}
