public void test_Reaction_ancestor_create()
{
Model m = new Model(2,4);
Reaction r = m.createReaction();
ListOf lo = m.getListOfReactions();
assertTrue( r.getAncestorOfType(libsbml.SBML_MODEL) == m );
assertTrue( r.getAncestorOfType(libsbml.SBML_LIST_OF) == lo );
assertTrue( r.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
assertTrue( r.getAncestorOfType(libsbml.SBML_EVENT) == null );
Reaction obj = m.getReaction(0);
assertTrue( obj.getAncestorOfType(libsbml.SBML_MODEL) == m );
assertTrue( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo );
assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
assertTrue( obj.getAncestorOfType(libsbml.SBML_EVENT) == null );
}
public void test_Reaction_parent_add()
{
Reaction ia = new Reaction(2,4);
Model m = new Model(2,4);
ia.setId("k");
m.addReaction(ia);
ia = null;
ListOf lo = m.getListOfReactions();
assertTrue( lo == m.getReaction(0).getParentSBMLObject() );
assertTrue( m == lo.getParentSBMLObject() );
}
public void test_ReadSBML_notes()
{
Reaction r;
KineticLaw kl;
string s = wrapSBML_L2v3("<listOfReactions>" +
"<reaction name='J1'>" +
" <kineticLaw formula='k1*X0'>" +
" <notes>This is a test note.</notes>" +
" <listOfParameters>" +
" <parameter name='k1' value='0'/>" +
" </listOfParameters>" +
" </kineticLaw>" +
"</reaction>" +
"</listOfReactions>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
r = M.getReaction(0);
kl = r.getKineticLaw();
assertTrue( kl.getNotes() != null );
string notes = kl.getNotes().getChild(0).getCharacters();
assertTrue( ( "This is a test note." != notes ) == false );
}
public void test_Reaction_ancestor_add()
{
Reaction ia = new Reaction(2,4);
Model m = new Model(2,4);
ia.setId("k");
m.addReaction(ia);
ia = null;
ListOf lo = m.getListOfReactions();
Reaction obj = m.getReaction(0);
assertTrue( obj.getAncestorOfType(libsbml.SBML_MODEL) == m );
assertTrue( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo );
assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
assertTrue( obj.getAncestorOfType(libsbml.SBML_EVENT) == null );
}
public void test_ReadSBML_metaid()
{
SBase sb;
string s = wrapSBML_L2v1("<listOfFunctionDefinitions>" +
" <functionDefinition metaid='fd'/>" +
"</listOfFunctionDefinitions>" +
"<listOfUnitDefinitions>" +
" <unitDefinition metaid='ud'/>" +
"</listOfUnitDefinitions>" +
"<listOfCompartments>" +
" <compartment metaid='c'/>" +
"</listOfCompartments>" +
"<listOfSpecies>" +
" <species metaid='s'/>" +
"</listOfSpecies>" +
"<listOfParameters>" +
" <parameter metaid='p'/>" +
"</listOfParameters>" +
"<listOfRules>" +
" <rateRule metaid='rr'/>" +
"</listOfRules>" +
"<listOfReactions>" +
" <reaction metaid='rx'/>" +
"</listOfReactions>" +
"<listOfEvents>" +
" <event metaid='e'/>" +
"</listOfEvents>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M != null );
sb = M.getFunctionDefinition(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "fd" == sb.getMetaId() ));
sb = M.getUnitDefinition(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "ud" == sb.getMetaId() ));
sb = M.getCompartment(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "c" == sb.getMetaId() ));
sb = M.getSpecies(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "s" == sb.getMetaId() ));
sb = M.getParameter(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "p" == sb.getMetaId() ));
sb = M.getRule(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "rr" == sb.getMetaId() ));
sb = M.getReaction(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "rx" == sb.getMetaId() ));
sb = M.getEvent(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "e" == sb.getMetaId() ));
}
public void test_ReadSBML_metaid_Reaction()
{
SBase sb;
Reaction r;
string s = wrapSBML_L2v1("<listOfReactions>" +
" <reaction metaid='r'>" +
" <listOfReactants metaid='lor'>" +
" <speciesReference metaid='sr1'/>" +
" </listOfReactants>" +
" <listOfProducts metaid='lop'>" +
" <speciesReference metaid='sr2'/>" +
" </listOfProducts>" +
" <listOfModifiers metaid='lom'>" +
" <modifierSpeciesReference metaid='msr'/>" +
" </listOfModifiers>" +
" <kineticLaw metaid='kl'/>" +
" </reaction>" +
"</listOfReactions>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M != null );
r = M.getReaction(0);
sb = r;
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "r" == sb.getMetaId() ));
sb = r.getListOfReactants();
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "lor" == sb.getMetaId() ));
sb = r.getReactant(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "sr1" == sb.getMetaId() ));
sb = r.getListOfProducts();
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "lop" == sb.getMetaId() ));
sb = r.getProduct(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "sr2" == sb.getMetaId() ));
sb = r.getListOfModifiers();
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "lom" == sb.getMetaId() ));
sb = r.getModifier(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "msr" == sb.getMetaId() ));
sb = r.getKineticLaw();
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "kl" == sb.getMetaId() ));
}
public void test_ReadSBML_KineticLaw_Parameter()
{
Reaction r;
KineticLaw kl;
Parameter p;
string s = wrapSBML_L1v2("<listOfReactions>" +
" <reaction name='J1'>" +
" <kineticLaw formula='k1*X0'>" +
" <listOfParameters>" +
" <parameter name='k1' value='0'/>" +
" </listOfParameters>" +
" </kineticLaw>" +
" </reaction>" +
"</listOfReactions>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M.getNumReactions() == 1 );
r = M.getReaction(0);
kl = r.getKineticLaw();
assertTrue(( "k1*X0" == kl.getFormula() ));
assertTrue( kl.getNumParameters() == 1 );
p = kl.getParameter(0);
assertTrue(( "k1" == p.getId() ));
assertTrue( p.getValue() == 0 );
}
public void test_ReadSBML_Reaction_L2_defaults()
{
Reaction r;
string s = wrapSBML_L2v1("<listOfReactions> <reaction id='r1'/> </listOfReactions>"
);
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M.getNumReactions() == 1 );
r = M.getReaction(0);
assertEquals( true, r.isSetId() );
assertEquals( false, r.isSetName() );
assertEquals( false, r.isSetFast() );
assertTrue(( "r1" == r.getId() ));
assertTrue( r.getReversible() == true );
}
public void test_ReadSBML_KineticLaw()
{
Reaction r;
KineticLaw kl;
string s = wrapSBML_L1v2("<listOfReactions>" +
" <reaction name='J1'>" +
" <kineticLaw formula='k1*X0'/>" +
" </reaction>" +
"</listOfReactions>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M.getNumReactions() == 1 );
r = M.getReaction(0);
kl = r.getKineticLaw();
assertTrue(( "k1*X0" == kl.getFormula() ));
}
public void test_ReadSBML_KineticLaw_L2()
{
Reaction r;
KineticLaw kl;
ASTNode math;
string formula;
string s = wrapSBML_L2v1("<listOfReactions>" +
" <reaction id='J1'>" +
" <kineticLaw>" +
" <math>" +
" <apply>" +
" <times/>" +
" <ci> k </ci>" +
" <ci> S2 </ci>" +
" <ci> X0 </ci>" +
" </apply>" +
" </math>" +
" </kineticLaw>" +
" </reaction>" +
"</listOfReactions>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M.getNumReactions() == 1 );
r = M.getReaction(0);
assertTrue( r != null );
kl = r.getKineticLaw();
assertTrue( kl != null );
assertEquals( true, kl.isSetMath() );
math = kl.getMath();
formula = kl.getFormula();
assertTrue( formula != null );
assertTrue(( "k * S2 * X0" == formula ));
}
public void test_ReadSBML_SpeciesReference_StoichiometryMath_2()
{
Reaction r;
SpeciesReference sr;
string s = wrapSBML_L2v1("<listOfReactions>" +
" <reaction name='r1'>" +
" <listOfReactants>" +
" <speciesReference species='X0'>" +
" <stoichiometryMath>" +
" <math> <cn type='rational'> 3 <sep/> 2 </cn> </math>" +
" </stoichiometryMath>" +
" </speciesReference>" +
" </listOfReactants>" +
" </reaction>" +
"</listOfReactions>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M.getNumReactions() == 1 );
r = M.getReaction(0);
assertTrue( r != null );
assertTrue( r.getNumReactants() == 1 );
sr = r.getReactant(0);
assertTrue( sr != null );
assertEquals( false, sr.isSetStoichiometryMath() );
assertTrue( sr.getStoichiometry() == 3 );
assertTrue( sr.getDenominator() == 2 );
}
public void test_ReadSBML_SpeciesReference_StoichiometryMath_1()
{
Reaction r;
SpeciesReference sr;
StoichiometryMath math;
string formula;
string s = wrapSBML_L2v1("<listOfReactions>" +
" <reaction name='r1'>" +
" <listOfReactants>" +
" <speciesReference species='X0'>" +
" <stoichiometryMath>" +
" <math> <ci> x </ci> </math>" +
" </stoichiometryMath>" +
" </speciesReference>" +
" </listOfReactants>" +
" </reaction>" +
"</listOfReactions>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M.getNumReactions() == 1 );
r = M.getReaction(0);
assertTrue( r != null );
assertTrue( r.getNumReactants() == 1 );
sr = r.getReactant(0);
assertTrue( sr != null );
assertEquals( true, sr.isSetStoichiometryMath() );
math = sr.getStoichiometryMath();
formula = libsbml.formulaToString(math.getMath());
assertTrue( formula != null );
assertTrue(( "x" == formula ));
}
public void test_ReadSBML_SpeciesReference_defaults()
{
Reaction r;
SpeciesReference sr;
string s = wrapSBML_L1v2("<listOfReactions>" +
" <reaction name='reaction_1' reversible='false'>" +
" <listOfReactants>" +
" <speciesReference species='X0'/>" +
" </listOfReactants>" +
" </reaction>" +
"</listOfReactions>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M.getNumReactions() == 1 );
r = M.getReaction(0);
assertTrue(( "reaction_1" == r.getId() ));
assertTrue( r.getReversible() == false );
assertTrue( r.getNumReactants() == 1 );
sr = r.getReactant(0);
assertTrue(( "X0" == sr.getSpecies() ));
assertTrue( sr.getStoichiometry() == 1 );
assertTrue( sr.getDenominator() == 1 );
}
public void test_Reaction_parent_create()
{
Model m = new Model(2,4);
Reaction r = m.createReaction();
ListOf lo = m.getListOfReactions();
assertTrue( lo == m.getReaction(0).getParentSBMLObject() );
assertTrue( lo == r.getParentSBMLObject() );
assertTrue( m == lo.getParentSBMLObject() );
}
public void test_ReadSBML_line_col_numbers()
{
//setXMLParser();
SBase sb;
string s = "<?xml version='1.0' encoding='UTF-8'?>\n" +
"<sbml xmlns='http://www.sbml.org/sbml/level2' level='2' version='1'>\n" +
" <model id='testModel' name='testModel'>\n" +
" <listOfReactions> <reaction/> </listOfReactions>\n" +
" </model>\n" +
"</sbml>\n";
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M != null );
sb = M;
sb = M.getListOfReactions();
sb = M.getReaction(0);
}
/// <summary>
/// [ ReactionStruct ]
/// [[ Id , Name , [ KineticLawStruct ] , Reversible , Fast , [ ReactantStruct ] , [ ProductStruct ] , [ ModifierSpecies ] ]]
/// </summary>
/// <param name="aSBMLmodel"></param>
/// <returns></returns>
public static List<ReactionStruct> getReaction(Model aSBMLmodel)
{
List<ReactionStruct> list = new List<ReactionStruct>();
ListOfReactions reactions = aSBMLmodel.getListOfReactions();
for (int i = 0; i < reactions.size(); i++ )
{
Reaction aReaction = aSBMLmodel.getReaction(i);
string anId = aReaction.getId();
string aName =aReaction.getName();
//----------KineticLaw----------------------------------
List<KineticLawStruct> ListOfKineticLaw = new List<KineticLawStruct>();
if( aReaction.isSetKineticLaw())
{
KineticLaw aKineticLaw = aReaction.getKineticLaw();
if( aKineticLaw != null)
{
string aFormula_KL;
if( aKineticLaw.isSetFormula())
aFormula_KL = aKineticLaw.getFormula();
else
aFormula_KL = "";
List<string> aString_KL = new List<string>();
if (aSBMLmodel.getLevel() == 1)
{
aString_KL.Add( "" );
}
else
{
if (aKineticLaw.isSetMath())
{
ASTNode anASTNode_KL = aKineticLaw.getMath();
aString_KL.Add( libsbml.libsbml.formulaToString( anASTNode_KL ) );
}
else
aString_KL.Add( "" );
}
string aTimeUnit_KL = aKineticLaw.getTimeUnits();
string aSubstanceUnit_KL = aKineticLaw.getSubstanceUnits();
List<ParameterStruct> listOfParameters = new List<ParameterStruct>();
ListOfParameters parameters = aKineticLaw.getListOfParameters();
for (int j = 0; j < parameters.size(); j++ )
{
Parameter aParameter = aKineticLaw.getParameter(j);
if (aParameter == null)
continue;
string anId_KL_P = aParameter.getId();
string aName_KL_P = aParameter.getName();
double aValue_KL_P = aParameter.getValue();
string aUnit_KL_P = aParameter.getUnits();
bool aConstant_KL_P = aParameter.getConstant();
ParameterStruct parameter = new ParameterStruct(
anId_KL_P,
aName_KL_P,
aValue_KL_P,
aUnit_KL_P,
aConstant_KL_P);
listOfParameters.Add( parameter );
}
XMLNode anExpressionAnnotation = aKineticLaw.getAnnotation();
KineticLawStruct kineticLaw = new KineticLawStruct(
aFormula_KL,
aString_KL,
aTimeUnit_KL,
aSubstanceUnit_KL,
listOfParameters,
anExpressionAnnotation );
ListOfKineticLaw.Add(kineticLaw);
}
}
bool aReversible = aReaction.getReversible();
bool aFast = aReaction.getFast();
//----------Reactants----------------------------------
List<ReactantStruct> ListOfReactants = new List<ReactantStruct>();
ListOfSpeciesReferences reactants = aReaction.getListOfReactants();
for (int k = 0; k < reactants.size(); k++ )
{
SpeciesReference aSpeciesReference = aReaction.getReactant(k);
string aSpecies_R = aSpeciesReference.getSpecies();
int aStoichiometry_R = (int)aSpeciesReference.getStoichiometry();
string aString_R = GetStoichiometryMath(aSpeciesReference);
int aDenominator_R = aSpeciesReference.getDenominator();
ReactantStruct reactant = new ReactantStruct(
aSpecies_R,
aStoichiometry_R,
aString_R,
aDenominator_R);
ListOfReactants.Add( reactant );
}
//----------Products----------------------------------
List<ProductStruct> ListOfProducts = new List<ProductStruct>();
ListOfSpeciesReferences products = aReaction.getListOfProducts();
long max = products.size();
for (int l = 0; l < max; l++)
{
SpeciesReference aSpeciesReference = aReaction.getProduct(l);
string aSpecies_P = aSpeciesReference.getSpecies();
double aStoichiometry_P = aSpeciesReference.getStoichiometry();
string aString_P = GetStoichiometryMath(aSpeciesReference);
int aDenominator_P = aSpeciesReference.getDenominator();
ProductStruct product = new ProductStruct(
aSpecies_P,
aStoichiometry_P,
aString_P,
aDenominator_P);
ListOfProducts.Add( product );
}
//----------Modifiers----------------------------------
List<string> ListOfModifiers = new List<string>();
ListOfSpeciesReferences modifiers = aReaction.getListOfModifiers();
for (long l = 0; l < modifiers.size(); l++ )
{
ModifierSpeciesReference aSpeciesReference = aReaction.getModifier(l);
string aSpecies_M = aSpeciesReference.getSpecies();
ListOfModifiers.Add( aSpecies_M );
}
ReactionStruct reaction = new ReactionStruct(
anId,
aName,
ListOfKineticLaw,
aReversible,
aFast,
ListOfReactants,
ListOfProducts,
ListOfModifiers );
list.Add(reaction);
}
return list;
}
public void test_ReadSBML_Reaction_defaults()
{
Reaction r;
string s = wrapSBML_L1v2("<listOfReactions>" +
" <reaction name='reaction_1'/>" +
"</listOfReactions>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M.getNumReactions() == 1 );
r = M.getReaction(0);
assertTrue(( "reaction_1" == r.getId() ));
assertTrue( r.getReversible() != false );
assertTrue( r.getFast() == false );
}