public void test_XMLNode_create() {
XMLNode node = new XMLNode();
assertTrue(node != null);
assertTrue(node.getNumChildren() == 0);
node = null;
node = new XMLNode();
assertTrue(node != null);
XMLNode node2 = new XMLNode();
assertTrue(node2 != null);
node.addChild(node2);
assertTrue(node.getNumChildren() == 1);
XMLNode node3 = new XMLNode();
assertTrue(node3 != null);
node.addChild(node3);
assertTrue(node.getNumChildren() == 2);
node = null;
node2 = null;
node3 = null;
}
public static void main(String[] args) {
System.loadLibrary("sbmlj");
if (args.length != 2) {
System.out.println(" usage: addingEvidenceCodes_2 <input-filename> <output-filename>");
System.out.println(" Adds controlled vocabulary term to a species");
System.out.println();
System.exit(2);
}
SBMLDocument d = libsbml.readSBML(args[0]);
long errors = d.getNumErrors();
if (errors > 0) {
System.out.println("Read Error(s):");
d.printErrors();
System.out.println("Correct the above and re-run.");
} else {
long n = d.getModel().getNumSpecies();
if (n <= 0) {
System.out.println("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]);
}
}
System.exit((int) errors);
}
public void test_XMLNode_remove() {
XMLAttributes attr = new XMLAttributes();
XMLTriple trp_p = new XMLTriple("parent", "", "");
XMLTriple trp_c1 = new XMLTriple("child1", "", "");
XMLTriple trp_c2 = new XMLTriple("child2", "", "");
XMLTriple trp_c3 = new XMLTriple("child3", "", "");
XMLTriple trp_c4 = new XMLTriple("child4", "", "");
XMLTriple trp_c5 = new XMLTriple("child5", "", "");
XMLNode p = new XMLNode(trp_p, attr);
XMLNode c1 = new XMLNode(trp_c1, attr);
XMLNode c2 = new XMLNode(trp_c2, attr);
XMLNode c3 = new XMLNode(trp_c3, attr);
XMLNode c4 = new XMLNode(trp_c4, attr);
XMLNode c5 = new XMLNode(trp_c5, attr);
XMLNode r;
p.addChild(c1);
p.addChild(c2);
p.addChild(c3);
p.addChild(c4);
p.addChild(c5);
r = p.removeChild(5);
assertTrue(r == null);
r = p.removeChild(1);
assertTrue(p.getNumChildren() == 4);
assertTrue(!r.getName().equals("child2") == false);
r = null;
r = p.removeChild(3);
assertTrue(p.getNumChildren() == 3);
assertTrue(!r.getName().equals("child5") == false);
r = null;
r = p.removeChild(0);
assertTrue(p.getNumChildren() == 2);
assertTrue(!r.getName().equals("child1") == false);
r = null;
r = p.removeChild(1);
assertTrue(p.getNumChildren() == 1);
assertTrue(!r.getName().equals("child4") == false);
r = null;
r = p.removeChild(0);
assertTrue(p.getNumChildren() == 0);
assertTrue(!r.getName().equals("child3") == false);
r = null;
p.addChild(c1);
p.addChild(c2);
p.addChild(c3);
p.addChild(c4);
p.addChild(c5);
r = p.removeChild(4);
assertTrue(p.getNumChildren() == 4);
assertTrue(!r.getName().equals("child5") == false);
r = null;
r = p.removeChild(3);
assertTrue(p.getNumChildren() == 3);
assertTrue(!r.getName().equals("child4") == false);
r = null;
r = p.removeChild(2);
assertTrue(p.getNumChildren() == 2);
assertTrue(!r.getName().equals("child3") == false);
r = null;
r = p.removeChild(1);
assertTrue(p.getNumChildren() == 1);
assertTrue(!r.getName().equals("child2") == false);
r = null;
r = p.removeChild(0);
assertTrue(p.getNumChildren() == 0);
assertTrue(!r.getName().equals("child1") == false);
r = null;
p.addChild(c1);
p.addChild(c2);
p.addChild(c3);
p.addChild(c4);
p.addChild(c5);
r = p.removeChild(0);
assertTrue(p.getNumChildren() == 4);
assertTrue(!r.getName().equals("child1") == false);
r = null;
r = p.removeChild(0);
assertTrue(p.getNumChildren() == 3);
assertTrue(!r.getName().equals("child2") == false);
r = null;
r = p.removeChild(0);
assertTrue(p.getNumChildren() == 2);
assertTrue(!r.getName().equals("child3") == false);
r = null;
r = p.removeChild(0);
assertTrue(p.getNumChildren() == 1);
assertTrue(!r.getName().equals("child4") == false);
r = null;
r = p.removeChild(0);
assertTrue(p.getNumChildren() == 0);
assertTrue(!r.getName().equals("child5") == false);
r = null;
p.addChild(c1);
p.addChild(c2);
p.addChild(c3);
p.addChild(c4);
p.addChild(c5);
r = p.removeChild(0);
assertTrue(!r.getName().equals("child1") == false);
p.insertChild(0, r);
assertTrue(p.getNumChildren() == 5);
assertTrue(!p.getChild(0).getName().equals("child1") == false);
r = null;
r = p.removeChild(1);
assertTrue(!r.getName().equals("child2") == false);
p.insertChild(1, r);
assertTrue(p.getNumChildren() == 5);
assertTrue(!p.getChild(1).getName().equals("child2") == false);
r = null;
r = p.removeChild(2);
assertTrue(!r.getName().equals("child3") == false);
p.insertChild(2, r);
assertTrue(p.getNumChildren() == 5);
assertTrue(!p.getChild(2).getName().equals("child3") == false);
r = null;
r = p.removeChild(3);
assertTrue(!r.getName().equals("child4") == false);
p.insertChild(3, r);
assertTrue(p.getNumChildren() == 5);
assertTrue(!p.getChild(3).getName().equals("child4") == false);
r = null;
r = p.removeChild(4);
assertTrue(!r.getName().equals("child5") == false);
p.insertChild(4, r);
assertTrue(p.getNumChildren() == 5);
assertTrue(!p.getChild(4).getName().equals("child5") == false);
r = null;
p = null;
c1 = null;
c2 = null;
c3 = null;
c4 = null;
c5 = null;
attr = null;
trp_p = null;
trp_c1 = null;
trp_c2 = null;
trp_c3 = null;
trp_c4 = null;
trp_c5 = null;
}
public void test_XMLNode_insert() {
XMLAttributes attr = new XMLAttributes();
XMLTriple trp_p = new XMLTriple("parent", "", "");
XMLTriple trp_c1 = new XMLTriple("child1", "", "");
XMLTriple trp_c2 = new XMLTriple("child2", "", "");
XMLTriple trp_c3 = new XMLTriple("child3", "", "");
XMLTriple trp_c4 = new XMLTriple("child4", "", "");
XMLTriple trp_c5 = new XMLTriple("child5", "", "");
XMLNode p = new XMLNode(trp_p, attr);
XMLNode c1 = new XMLNode(trp_c1, attr);
XMLNode c2 = new XMLNode(trp_c2, attr);
XMLNode c3 = new XMLNode(trp_c3, attr);
XMLNode c4 = new XMLNode(trp_c4, attr);
XMLNode c5 = new XMLNode(trp_c5, attr);
p.addChild(c2);
p.addChild(c4);
p.insertChild(0, c1);
p.insertChild(2, c3);
p.insertChild(4, c5);
assertTrue(p.getNumChildren() == 5);
assertTrue(!p.getChild(0).getName().equals("child1") == false);
assertTrue(!p.getChild(1).getName().equals("child2") == false);
assertTrue(!p.getChild(2).getName().equals("child3") == false);
assertTrue(!p.getChild(3).getName().equals("child4") == false);
assertTrue(!p.getChild(4).getName().equals("child5") == false);
p.removeChildren();
p.insertChild(0, c1);
p.insertChild(0, c2);
p.insertChild(0, c3);
p.insertChild(0, c4);
p.insertChild(0, c5);
assertTrue(p.getNumChildren() == 5);
assertTrue(!p.getChild(0).getName().equals("child5") == false);
assertTrue(!p.getChild(1).getName().equals("child4") == false);
assertTrue(!p.getChild(2).getName().equals("child3") == false);
assertTrue(!p.getChild(3).getName().equals("child2") == false);
assertTrue(!p.getChild(4).getName().equals("child1") == false);
p.removeChildren();
p.insertChild(1, c1);
p.insertChild(2, c2);
p.insertChild(3, c3);
p.insertChild(4, c4);
p.insertChild(5, c5);
assertTrue(p.getNumChildren() == 5);
assertTrue(!p.getChild(0).getName().equals("child1") == false);
assertTrue(!p.getChild(1).getName().equals("child2") == false);
assertTrue(!p.getChild(2).getName().equals("child3") == false);
assertTrue(!p.getChild(3).getName().equals("child4") == false);
assertTrue(!p.getChild(4).getName().equals("child5") == false);
p.removeChildren();
XMLNode tmp;
tmp = p.insertChild(0, c1);
assertTrue(!tmp.getName().equals("child1") == false);
tmp = p.insertChild(0, c2);
assertTrue(!tmp.getName().equals("child2") == false);
tmp = p.insertChild(0, c3);
assertTrue(!tmp.getName().equals("child3") == false);
tmp = p.insertChild(0, c4);
assertTrue(!tmp.getName().equals("child4") == false);
tmp = p.insertChild(0, c5);
assertTrue(!tmp.getName().equals("child5") == false);
p.removeChildren();
tmp = p.insertChild(1, c1);
assertTrue(!tmp.getName().equals("child1") == false);
tmp = p.insertChild(2, c2);
assertTrue(!tmp.getName().equals("child2") == false);
tmp = p.insertChild(3, c3);
assertTrue(!tmp.getName().equals("child3") == false);
tmp = p.insertChild(4, c4);
assertTrue(!tmp.getName().equals("child4") == false);
tmp = p.insertChild(5, c5);
assertTrue(!tmp.getName().equals("child5") == false);
p = null;
c1 = null;
c2 = null;
c3 = null;
c4 = null;
c5 = null;
attr = null;
trp_p = null;
trp_c1 = null;
trp_c2 = null;
trp_c3 = null;
trp_c4 = null;
trp_c5 = null;
}