libSBML C++ API
libSBML 5.18.0 C++ API
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Adds evidence codes to a species in a model.
#include <iostream>
using namespace std;
int
main (int argc, char *argv[])
{
unsigned int errors, n;
if (argc != 3)
{
cout << endl
<< " usage: addingEvidenceCodes_2 <input-filename> <output-filename>" << endl
<< " Adds controlled vocabulary term to a species" << endl
<< endl;
return 2;
}
if (errors > 0)
{
cout << "Read Error(s):" << endl;
cout << "Correct the above and re-run." << endl;
}
else
{
if (n <= 0)
{
cout << "Model has no species.\n Cannot add CV terms\n";
}
else
{
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
resource_att.
add(
"rdf:resource",
"http://biomodels.net/biology-qualifiers/occursIn");
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
resource_att.
add(
"rdf:resource",
"urn:miriam:obo.go:GO%3A0005764");
"http://biomodels.net/biology-qualifiers/",
"bqbiol");
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
resource_att.
add(
"rdf:resource",
"urn:miriam:obo.eco:ECO%3A0000004");
resource_att.
add(
"rdf:resource",
"urn:miriam:pubmed:7017716");
li_token =
XMLToken(li_triple, resource_att);
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");
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
}
}
delete d;
return errors;
}
virtual int appendAnnotation(const XMLNode *annotation)
Appends the given annotation to the "annotation" subelement of this object.
Definition: SBase.cpp:1488
int clear()
Removes all attributes in this XMLAttributes object.
Definition: XMLAttributes.cpp:250
const Species * getSpecies(unsigned int n) const
Get the nth Species object in this Model.
Definition: Model.cpp:2676
const Model * getModel() const
Returns the Model object stored in this SBMLDocument.
Definition: SBMLDocument.cpp:361
Include all SBML types in a single header file.
int add(const std::string &name, const std::string &value, const std::string namespaceURI="", const std::string prefix="")
Adds an attribute to this list of attributes.
Definition: XMLAttributes.cpp:135
bool isSetMetaId() const
Predicate returning true if this object's "metaid" attribute is set.
Definition: SBase.cpp:1132
A MIRIAM-compliant controlled vocabulary term.
Definition: CVTerm.h:478
A qualified XML name.
Definition: XMLTriple.h:88
int addCVTerm(CVTerm *term, bool newBag=false)
Adds a copy of the given CVTerm object to this SBML object.
Definition: SBase.cpp:2745
SBMLDocument_t * readSBML(const char *filename)
int add(const std::string &uri, const std::string prefix="")
Appends an XML namespace prefix and URI pair to this list of namespace declarations.
Definition: XMLNamespaces.cpp:114
@ BQB_OCCURS_IN
Definition: CVTerm.h:440
unsigned int getNumErrors() const
Returns the number of errors or warnings encountered during parsing, consistency checking,...
Definition: SBMLDocument.cpp:1184
An XML Namespace.
Definition: XMLNamespaces.h:84
@ BIOLOGICAL_QUALIFIER
Definition: CVTerm.h:327
A list of attributes on an XML element.
Definition: XMLAttributes.h:251
int setBiologicalQualifierType(BiolQualifierType_t type)
Sets the BiolQualifierType_t value of this CVTerm object.
Definition: CVTerm.cpp:297
int addResource(const std::string &resource)
Adds a resource reference to this CVTerm object.
Definition: CVTerm.cpp:448
void printErrors(std::ostream &stream=std::cerr) const
Prints all the errors or warnings encountered trying to parse, check, or translate this SBML document...
Definition: SBMLDocument.cpp:1207
A node in libSBML's XML document tree.
Definition: XMLNode.h:172
unsigned int getNumSpecies() const
Get the number of Species objects in this Model.
Definition: Model.cpp:3235
int addChild(const XMLNode &node)
Adds a copy of node as a child of this XMLNode.
Definition: XMLNode.cpp:237
const std::string & getMetaId() const
Returns the value of the "metaid" attribute of this SBML object.
Definition: SBase.cpp:693
Definition of a CVTerm class for adding annotations to a Model.
int setMetaId(const std::string &metaid)
Sets the value of the meta-identifier attribute of this SBML object.
Definition: SBase.cpp:1216
An SBML species – a pool of entities.
Definition: Species.h:423
A token in an XML stream.
Definition: XMLToken.h:141
#define LIBSBML_CPP_NAMESPACE_USE
Definition: libsbml-namespace.h:67
Overall SBML container object.
Definition: SBMLDocument.h:342
int writeSBML(const SBMLDocument_t *d, const char *filename)
Writes the given SBML document d to the file named by filename.
int setEnd()
Declares that this token represents an XML element end tag.
Definition: XMLToken.cpp:1171