public getListOfReactions ( ) : ListOfReactions | ||
Результат | ListOfReactions |
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() ); }
/// <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_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_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_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_ListOf() { SBase sb; string s = wrapSBML_L2v1("<listOfFunctionDefinitions metaid='lofd'/>" + "<listOfUnitDefinitions metaid='loud'/>" + "<listOfCompartments metaid='loc'/>" + "<listOfSpecies metaid='los'/>" + "<listOfParameters metaid='lop'/>" + "<listOfRules metaid='lor'/>" + "<listOfReactions metaid='lorx'/>" + "<listOfEvents metaid='loe'/>"); D = libsbml.readSBMLFromString(s); M = D.getModel(); assertTrue( M != null ); sb = M.getListOfFunctionDefinitions(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "lofd" == sb.getMetaId() )); sb = M.getListOfUnitDefinitions(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "loud" == sb.getMetaId() )); sb = M.getListOfCompartments(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "loc" == sb.getMetaId() )); sb = M.getListOfSpecies(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "los" == sb.getMetaId() )); sb = M.getListOfParameters(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "lop" == sb.getMetaId() )); sb = M.getListOfRules(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "lor" == sb.getMetaId() )); sb = M.getListOfReactions(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "lorx" == sb.getMetaId() )); sb = M.getListOfEvents(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "loe" == sb.getMetaId() )); }
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); }