getListOfSpecies() public method

public getListOfSpecies ( ) : ListOfSpecies
return ListOfSpecies
Ejemplo n.º 1
0
        /// <summary>
        /// [ SpeciesStruct ]
        /// [[ Id , Name , Compartment , InitialAmount , InitialConcentration , SubstanceUnit , SpatialSizeUnit , Unit , HasOnlySubstanceUnit , BoundaryCondition , Charge , Constant ]]
        /// </summary>
        /// <param name="aSBMLmodel"></param>
        /// <returns></returns>
        public static List<SpeciesStruct> getSpecies(Model aSBMLmodel)
        {
            List<SpeciesStruct> list = new List<SpeciesStruct>();

            ListOfSpecies listOfSpecies = aSBMLmodel.getListOfSpecies();
            for (int i = 0; i < listOfSpecies.size(); i++ )
            {
                Species aSpecies = aSBMLmodel.getSpecies(i);

                string anId_Sp = aSpecies.getId();
                string aName_Sp = aSpecies.getName();
                string aCompartment_Sp = aSpecies.getCompartment();

                double anInitialAmount_Sp = GetInitialAmount(aSpecies);
                double anInitialConcentration_Sp = GetInitialConcentration(aSpecies);

                string aSubstanceUnit_Sp = aSpecies.getSubstanceUnits();
                string aSpatialSizeUnit_Sp = aSpecies.getSpatialSizeUnits();
                string anUnit_Sp = aSpecies.getUnits();
                bool aHasOnlySubstanceUnit_Sp = aSpecies.getHasOnlySubstanceUnits();
                bool aBoundaryCondition_Sp = aSpecies.getBoundaryCondition();
                int aCharge_Sp = aSpecies.getCharge();
                bool aConstant_Sp = aSpecies.getConstant();

                SpeciesStruct species = new SpeciesStruct(
                    anId_Sp,
                    aName_Sp,
                    aCompartment_Sp,
                    anInitialAmount_Sp,
                    anInitialConcentration_Sp,
                    aSubstanceUnit_Sp,
                    aSpatialSizeUnit_Sp,
                    anUnit_Sp,
                    aHasOnlySubstanceUnit_Sp,
                    aBoundaryCondition_Sp,
                    aCharge_Sp,
                    aConstant_Sp);

                list.Add( species );
            }

            return list;
        }
Ejemplo n.º 2
0
 public void test_Species_parent_create()
 {
     Model m = new Model(2,4);
       Species s = m.createSpecies();
       ListOf lo = m.getListOfSpecies();
       assertTrue( lo == s.getParentSBMLObject() );
       assertTrue( lo == m.getSpecies(0).getParentSBMLObject() );
       assertTrue( m == lo.getParentSBMLObject() );
 }
Ejemplo n.º 3
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 public void test_Species_parent_add()
 {
     Species ia = new Species(2,4);
       ia.setId("s");
       ia.setCompartment("c");
       Model m = new Model(2,4);
       m.addSpecies(ia);
       ia = null;
       ListOf lo = m.getListOfSpecies();
       assertTrue( lo == m.getSpecies(0).getParentSBMLObject() );
       assertTrue( m == lo.getParentSBMLObject() );
 }
Ejemplo n.º 4
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 public void test_Species_ancestor_create()
 {
     Model m = new Model(2,4);
       Species s = m.createSpecies();
       ListOf lo = m.getListOfSpecies();
       assertTrue( s.getAncestorOfType(libsbml.SBML_MODEL) == m );
       assertTrue( s.getAncestorOfType(libsbml.SBML_LIST_OF) == lo );
       assertTrue( s.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
       assertTrue( s.getAncestorOfType(libsbml.SBML_EVENT) == null );
       Species obj = m.getSpecies(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 );
 }
Ejemplo n.º 5
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 public void test_Species_ancestor_add()
 {
     Species ia = new Species(2,4);
       Model m = new Model(2,4);
       ia.setId("s");
       ia.setCompartment("c");
       m.addSpecies(ia);
       ia = null;
       ListOf lo = m.getListOfSpecies();
       Species obj = m.getSpecies(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 );
 }
Ejemplo n.º 6
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 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() ));
 }