Package org.sbml.jsbml

Examples of org.sbml.jsbml.UnitDefinition

495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
    assertEquals(M.getSpeciesType(0), c);
  }

  @Test
  public void test_Model_createUnit() {
    UnitDefinition ud;
    Unit u;
    M.createUnitDefinition();
    M.createUnitDefinition();
    u = M.createUnit(Kind.LITRE);
    assertTrue(u != null);
    assertTrue(M.getNumUnitDefinitions() == 2);
    ud = M.getUnitDefinition(1);
    assertTrue(ud.getNumUnits() == 1);
    assertEquals(ud.getUnit(0), u);
  }
View Full Code Here
509
510
511
512
513
514
515
516
517
518
    assertEquals(ud.getUnit(0), u);
  }

  @Test
  public void test_Model_createUnitDefinition() {
    UnitDefinition ud = M.createUnitDefinition();
    assertTrue(ud != null);
    assertTrue(M.getNumUnitDefinitions() == 1);
    assertEquals(M.getUnitDefinition(0), ud);
  }
View Full Code Here
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
    assertTrue(M.getSpecies("Glucose2") == null);
  }

  @Test
  public void test_Model_getUnitDefinition() {
    UnitDefinition ud1 = new UnitDefinition(2, 4);
    UnitDefinition ud2 = new UnitDefinition(2, 4);
    ud1.setId("mmls");
    ud2.setId("volume");
    ud1.createUnit(Kind.LITRE);
    ud2.createUnit(Kind.LITRE);
    M.addUnitDefinition(ud1);
    M.addUnitDefinition(ud2);
    assertTrue(M.getNumUnitDefinitions() == 2);
    ud1 = M.getUnitDefinition(0);
    ud2 = M.getUnitDefinition(1);
    assertTrue(ud1.getId().equals("mmls"));
    assertTrue(ud2.getId().equals("volume"));
  }
View Full Code Here
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
    assertTrue(ud2.getId().equals("volume"));
  }

  @Test
  public void test_Model_getUnitDefinitionById() {
    UnitDefinition ud1 = new UnitDefinition(2, 4);
    UnitDefinition ud2 = new UnitDefinition(2, 4);
    ud1.setId("mmls");
    ud2.setId("volume");
    ud1.createUnit(Kind.LITRE);
    ud2.createUnit(Kind.LITRE);
    M.addUnitDefinition(ud1);
    M.addUnitDefinition(ud2);
    assertTrue(M.getNumUnitDefinitions() == 2);
    // assertNotEquals(M.getUnitDefinition("mmls"), ud1);
    // assertNotEquals(M.getUnitDefinition("volume"), ud2);
View Full Code Here
988
989
990
991
992
993
994
995
996
997
998
    o3 = null;
  }

  @Test
  public void test_Model_removeUnitDefinition() {
    UnitDefinition o1, o2, o3;
    o1 = M.createUnitDefinition();
    o2 = M.createUnitDefinition();
    o3 = M.createUnitDefinition();
    o3.setId("test");
    assertTrue(M.removeUnitDefinition(0).equals(o1));
View Full Code Here
204
205
206
207
208
209
210
211
212
213
214
    LocalParameter lp;
    AssignmentRule ar;
    Reaction r;
    SpeciesReference sr;
    KineticLaw kl;
    UnitDefinition ud;
    Reaction r1;
    ListOf<Compartment> loc;
    Compartment c1;
    ListOf<Rule> lor;
    AssignmentRule ar1;
View Full Code Here
108
109
110
111
112
113
114
115
116
117
118
  /**
   * Test method for {@link org.sbml.jsbml.AbstractNamedSBaseWithUnit#setUnits(org.sbml.jsbml.UnitDefinition)}.
   */
  @Test
  public void testSetUnitsUnitDefinition() {
    UnitDefinition ud = sbase.getModel().getPredefinedUnitDefinition(
      kind.toString().toLowerCase());
    sbase.setUnits(ud);
    assertTrue(sbase.isSetUnits());
    assertTrue(sbase.isSetUnitsInstance());
    assertTrue(sbase.getUnits().equals(kind.toString().toLowerCase() + "_base"));
View Full Code Here
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
    assertTrue(s1.getNumCVTerms() == 0);
   
    assertTrue(s1.getInitialAmount() == 1);
   
   
    UnitDefinition mls = model.getUnitDefinition(1);
   
    assertTrue(mls != null);
    assertTrue(mls.getNumUnits() == 3);
    assertTrue(mls.getName().equals("mls"));
    assertTrue(mls.getUnit(0).getScale() == -3);
    assertTrue(mls.getUnit(0).getKind().getName().equals("mole"));
   
    assertTrue(mls.getUnit(2).getExponent() == -1);
    assertTrue(mls.getUnit(2).getKind().getName().equals("second"));
    assertTrue(mls.getUnit(2).getKind().equals(Kind.SECOND));

    Parameter vm = model.getParameter(0);
   
    assertTrue(vm != null);
    assertTrue(vm.getUnits().equals("mls"));
View Full Code Here
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
            SBase element = listOf.get(i);

            if (element != null) {
              boolean add = true;
              if (element instanceof UnitDefinition) {
                UnitDefinition ud = (UnitDefinition) element;
                if (ud.isPredefined()) {
                  add = false;
                }
              }
              if (add) {
                listOfElementsToWrite.add(element);
              }
            }
          }
          if (listOfElementsToWrite.isEmpty()) {
            listOfElementsToWrite = null;
          }
        }
      } else if (sbase instanceof UnitDefinition) {
        UnitDefinition unitDefinition = (UnitDefinition) sbase;

        if (unitDefinition.isSetListOfUnits()) {
          listOfElementsToWrite = new ArrayList<Object>();
          listOfElementsToWrite.add(unitDefinition.getListOfUnits());
        }
      } else if (sbase instanceof Reaction) {
        Reaction reaction = (Reaction) sbase;
        listOfElementsToWrite = new ArrayList<Object>();
View Full Code Here
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
              return functionDefinition;
            } else if (elementName.equals("unitDefinition")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfUnitDefinitions)) {
              UnitDefinition unitDefinition = (UnitDefinition) newContextObject;
              model.addUnitDefinition(unitDefinition);

              return unitDefinition;
            } else if (elementName.equals("compartment")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfCompartments)) {
              Compartment compartment = (Compartment) newContextObject;
              compartment.initDefaults();
              model.addCompartment(compartment);

              return compartment;
            } else if (elementName.equals("species")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfSpecies)
                && ((model.getLevel() == 1 && model
                    .getVersion() > 1) || model.getLevel() > 1)) {
              Species species = (Species) newContextObject;
              species.initDefaults();
              model.addSpecies(species);

              return species;
            }
            // level 1 : species => specie
            else if (elementName.equals("specie")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfSpecies)
                && model.getLevel() == 1
                && model.getVersion() == 1) {
              Species species = (Species) newContextObject;
              species.initDefaults();
              model.addSpecies(species);

              return species;
            } else if (elementName.equals("parameter")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfParameters)) {
              Parameter parameter = (Parameter) newContextObject;
              parameter.initDefaults();
              model.addParameter(parameter);

              return parameter;
            } else if (elementName.equals("initialAssignment")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfInitialAssignments)
                && ((model.getLevel() == 2 && model
                    .getVersion() > 1) || model.getLevel() >= 3)) {
              InitialAssignment initialAssignment = (InitialAssignment) newContextObject;
              model.addInitialAssignment(initialAssignment);

              return initialAssignment;
            } else if (elementName.equals("algebraicRule")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfRules)) {
              AlgebraicRule rule = (AlgebraicRule) newContextObject;
              model.addRule(rule);

              return rule;
            } else if (elementName.equals("assignmentRule")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfRules)
                && model.getLevel() > 1) {
              AssignmentRule rule = (AssignmentRule) newContextObject;
              model.addRule(rule);

              return rule;
            } else if (elementName.equals("parameterRule")
                && list.getSBaseListType().equals(ListOf.Type.listOfRules)
                && model.getLevel() == 1)
            {
              ExplicitRule rule = (ExplicitRule) newContextObject;
              model.addRule(rule);

              return rule;
            } else if (elementName.equals("specieConcentrationRule")
                && list.getSBaseListType().equals(ListOf.Type.listOfRules)
                && model.getLevel() == 1
                && model.getVersion() == 1)
            {
              ExplicitRule rule = (ExplicitRule) newContextObject;
              model.addRule(rule);

              return rule;
            } else if (elementName.equals("speciesConcentrationRule")
                && list.getSBaseListType().equals(ListOf.Type.listOfRules)
                && model.getLevel() == 1
                && model.getVersion() == 2)
            {
              ExplicitRule rule = (ExplicitRule) newContextObject;
              model.addRule(rule);

              return rule;
            } else if (elementName.equals("compartmentVolumeRule")
                && list.getSBaseListType().equals(ListOf.Type.listOfRules)
                && model.getLevel() == 1)
            {
              ExplicitRule rule = (ExplicitRule) newContextObject;
              model.addRule(rule);

              return rule;
            } else if (elementName.equals("rateRule")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfRules)) {
              RateRule rule = (RateRule) newContextObject;
              model.addRule(rule);

              return rule;
            } else if (elementName.equals("constraint")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfConstraints)
                && ((model.getLevel() == 2 && model
                    .getVersion() > 1) || model.getLevel() >= 3)) {
              Constraint constraint = (Constraint) newContextObject;
              model.addConstraint(constraint);

              return constraint;
            } else if (elementName.equals("reaction")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfReactions)) {
              Reaction reaction = (Reaction) newContextObject;
              model.addReaction(reaction);
              reaction.initDefaults();

              return reaction;
            } else if (elementName.equals("event")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfEvents)
                && model.getLevel() > 1) {
              Event event = (Event) newContextObject;
              model.addEvent(event);
              event.initDefaults();

              return event;
            } else if (elementName.equals("compartmentType")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfCompartmentTypes)
                && (model.getLevel() == 2 && model.getVersion() > 1)) {
              CompartmentType compartmentType = (CompartmentType) newContextObject;
              model.addCompartmentType(compartmentType);

              return compartmentType;
            } else if (elementName.equals("speciesType")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfSpeciesTypes)
                && (model.getLevel() == 2 && model.getVersion() > 1)) {
              SpeciesType speciesType = (SpeciesType) newContextObject;
              model.addSpeciesType(speciesType);

              return speciesType;
            } else {
              log4jLogger.warn("The element " + elementName + " is not recognized");
            }
          } else if (list.getParentSBMLObject() instanceof UnitDefinition) {
            UnitDefinition unitDefinition = (UnitDefinition) list
                .getParentSBMLObject();

            if (elementName.equals("unit")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfUnits)) {
              Unit unit = (Unit) newContextObject;
              unit.initDefaults();
              unitDefinition.addUnit(unit);

              return unit;
            } else {
              log4jLogger.warn("The element " + elementName + " is not recognized");
            }
          } else if (list.getParentSBMLObject() instanceof Reaction) {
            Reaction reaction = (Reaction) list
                .getParentSBMLObject();

            if (elementName.equals("speciesReference")
                && (reaction.getLevel() > 1 || (reaction
                    .getLevel() == 1 && reaction
                    .getVersion() == 2))) {
              SpeciesReference speciesReference = (SpeciesReference) newContextObject;
              speciesReference.initDefaults();

              if (list.getSBaseListType().equals(
                  ListOf.Type.listOfReactants)) {
                reaction.addReactant(speciesReference);

                return speciesReference;
              } else if (list.getSBaseListType().equals(
                  ListOf.Type.listOfProducts)) {
                reaction.addProduct(speciesReference);

                return speciesReference;
              } else {
                log4jLogger.warn("The element " + elementName + " is not recognized");
              }
            } else if (elementName.equals("specieReference")
                && reaction.getLevel() == 1) {
              SpeciesReference speciesReference = (SpeciesReference) newContextObject;
              speciesReference.initDefaults();

              if (list.getSBaseListType().equals(
                  ListOf.Type.listOfReactants)) {
                reaction.addReactant(speciesReference);

                return speciesReference;
              } else if (list.getSBaseListType().equals(
                  ListOf.Type.listOfProducts)) {
                reaction.addProduct(speciesReference);

                return speciesReference;
              } else {
                log4jLogger.warn("The element " + elementName + " is not recognized");
              }
            } else if (elementName
                .equals("modifierSpeciesReference")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfModifiers)
                && reaction.getLevel() > 1) {
              ModifierSpeciesReference modifierSpeciesReference = (ModifierSpeciesReference) newContextObject;
              reaction.addModifier(modifierSpeciesReference);

              return modifierSpeciesReference;
            } else {
              log4jLogger.warn("The element " + elementName + " is not recognized");
            }
          } else if (list.getParentSBMLObject() instanceof KineticLaw) {
            KineticLaw kineticLaw = (KineticLaw) list
                .getParentSBMLObject();
            // Level 3 : parameter and listOfParameters =>
            // localParameter and listOfLocalParameter
            if (elementName.equals("localParameter")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfLocalParameters)
                && kineticLaw.getLevel() >= 3) {
              LocalParameter localParameter = (LocalParameter) newContextObject;
              kineticLaw.addParameter(localParameter);

              return localParameter;
            } else if (elementName.equals("parameter")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfLocalParameters)
                && kineticLaw.isSetLevel()
                && kineticLaw.getLevel() < 3) {
              LocalParameter localParameter = new LocalParameter(
                  (Parameter) newContextObject);
              kineticLaw.addParameter(localParameter);

              return localParameter;
            } else {
              log4jLogger.warn("The element " + elementName + " is not recognized");
            }
          } else if (list.getParentSBMLObject() instanceof Event) {
            Event event = (Event) list.getParentSBMLObject();

            if (elementName.equals("eventAssignment")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfEventAssignments)
                && event.getLevel() > 1) {
              EventAssignment eventAssignment = (EventAssignment) newContextObject;
              event.addEventAssignment(eventAssignment);

              return eventAssignment;
            } else {
              log4jLogger.warn("The element " + elementName + " is not recognized");
            }
          } else {
            log4jLogger.warn("The element " + elementName + " is not recognized");
          }
        } else if (contextObject instanceof UnitDefinition) {
          UnitDefinition unitDefinition = (UnitDefinition) contextObject;

          if (elementName.equals("listOfUnits")) {
            ListOf<Unit> listOfUnits = (ListOf<Unit>) newContextObject;
            unitDefinition.setListOfUnits(listOfUnits);

            return listOfUnits;
          }
        } else if (contextObject instanceof Event) {
          Event event = (Event) contextObject;
View Full Code Here
TOP

Related Classes of org.sbml.jsbml.UnitDefinition

  • org.sbml.jsbml.test.RemoveFromModelTest
  • org.sbml.jsbml.test.sbml.TestModel
  • org.sbml.jsbml.test.sbml.TestReadFromFile1
  • org.sbml.jsbml.test.sbml.TestReadFromFile5
  • org.sbml.jsbml.test.sbml.TestUnitSimplification
  • org.sbml.jsbml.test.UnitDefinitionTest
  • org.sbml.jsbml.Unit.Kind
  • org.sbml.jsbml.util.compilers.ASTNodeValue
  • org.sbml.jsbml.util.compilers.UnitsCompiler
  • org.sbml.jsbml.util.SubModel
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.