Package org.sbml.jsbml

Examples of org.sbml.jsbml.KineticLaw

336
337
338
339
340
341
342
343
344
345
346
347
348
349
              setSpeciesReferenceSpecies(
                  modifierSpeciesReference, model);
            }
          }
          if (reaction.isSetKineticLaw()) {
            KineticLaw kineticLaw = reaction.getKineticLaw();
            if (kineticLaw.isSetListOfParameters()) {
              for (int j = 0; j < kineticLaw.getNumParameters(); j++) {
                LocalParameter parameter = kineticLaw
                    .getParameter(j);

                setParameterUnits(parameter, model);
              }
            }
View Full Code Here
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
   
    assertTrue(rdClk.getListOfReactants().get(0).getSpecies().equals("EmptySet"));
    assertTrue(rdClk.getListOfProducts().get(0).getSpecies().equals("dClk"));
    assertTrue(rdClk.getListOfModifiers().get(0).getSpecies().equals("dClkF"));
   
    KineticLaw rdClkKL = rdClk.getKineticLaw();
   
    assertTrue(rdClkKL.getListOfParameters().size() == 3);
    assertTrue(rdClkKL.getListOfParameters().get(2).getId().equals("parameter_0000009"));
    assertTrue(rdClkKL.getListOfParameters().get(2).getName().equals("tau2"));
    assertTrue(rdClkKL.getListOfParameters().get(2).getValue() == 10);
   
    Event event = model.getEvent(0);
   
    assertTrue(event.getMetaId().equals("metaid_0000015"));
    assertTrue(event.getNumEventAssignments() == 1);
View Full Code Here
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
              }
            } else {
              // TODO : SBML syntax error, throw an exception?
            }
          } else if (list.getParentSBMLObject() instanceof KineticLaw) {
            KineticLaw kineticLaw = (KineticLaw) list
                .getParentSBMLObject();

            if (elementName.equals("parameter")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfParameters)) {
              LocalParameter localParameter = (LocalParameter) newContextObject;
              kineticLaw.addParameter(localParameter);

              return localParameter;
            } else {
              // TODO : SBML syntax error, throw an exception?
            }
          } else {
            // TODO : SBML syntax error, throw an exception?
          }
        } 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 Reaction) {
          Reaction reaction = (Reaction) contextObject;

          if (elementName.equals("listOfReactants")) {
            ListOf listOfReactants = (ListOf) newContextObject;
            reaction.setListOfReactants(listOfReactants);
            listOfReactants
                .setSBaseListType(ListOf.Type.listOfReactants);

            return listOfReactants;
          } else if (elementName.equals("listOfProducts")) {
            ListOf listOfProducts = (ListOf) newContextObject;
            reaction.setListOfProducts(listOfProducts);
            listOfProducts
                .setSBaseListType(ListOf.Type.listOfProducts);

            return listOfProducts;
          } else if (elementName.equals("kineticLaw")) {
            KineticLaw kineticLaw = (KineticLaw) newContextObject;
            reaction.setKineticLaw(kineticLaw);

            return kineticLaw;
          } else {
            // TODO : SBML syntax error, throw an exception?
          }
        } else if (contextObject instanceof KineticLaw) {
          KineticLaw kineticLaw = (KineticLaw) contextObject;

          if (elementName.equals("listOfParameters")) {
            ListOf listOfLocalParameters = (ListOf) newContextObject;
            kineticLaw
                .setListOfLocalParameters(listOfLocalParameters);
            listOfLocalParameters
                .setSBaseListType(ListOf.Type.listOfParameters);

            return listOfLocalParameters;
View Full Code Here
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
   
    /*
     * Local Parameters
     */
    logger.debug("==== LocalParameters ====");
    KineticLaw kl = r1.createKineticLaw();
    LocalParameter parameter = kl.createLocalParameter("lp1");
    parameter.setValue(2d);
    kl.getListOfLocalParameters().add(new LocalParameter("lp2"));
    try {
      kl.createLocalParameter("lp1");
      fail();
    } catch (IllegalArgumentException exc) {
      logger.debug(exc.getLocalizedMessage());
      assertTrue(kl.getListOfLocalParameters()
                   .filterList(new NameFilter(parameter.getId())).size() == 1);
    }
    kl.removeLocalParameter(parameter);
    assertTrue(kl.getListOfLocalParameters()
               .filterList(new NameFilter(parameter.getId())).size() == 0);
    assertTrue(kl.getLocalParameter(parameter.getId()) == null);
    // remove ListOfLocalParameters
    ListOf<LocalParameter> listOfLP = kl.getListOfLocalParameters();
    kl.unsetListOfLocalParameters();
    assertTrue(!listOfLP.contains(parameter));
    assertTrue(kl.getLocalParameter("lp2") == null);
    // add ListOfLocalParameters
    listOfLP.add(parameter);
    kl.setListOfLocalParameters(listOfLP);
    assertTrue(kl.getLocalParameter(parameter.getId()) != null);
   
    /*
     * Compartments
     */
    logger.debug("==== Compartments ====");
View Full Code Here
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
        if (listOfElementsToWrite.isEmpty()) {
          listOfElementsToWrite = null;
        }
      } else if (sbase instanceof KineticLaw) {
        KineticLaw kineticLaw = (KineticLaw) sbase;

        if (kineticLaw.isSetListOfLocalParameters()) {
          listOfElementsToWrite = new ArrayList<Object>();
          listOfElementsToWrite.add(kineticLaw.getListOfLocalParameters());
        }
      } else if (sbase instanceof SpeciesReference) {
        SpeciesReference speciesReference = (SpeciesReference) sbase;

        if (speciesReference.isSetStoichiometryMath()) {
View Full Code Here
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
                    modifierSpeciesReference.getId(), modifierSpeciesReference.getElementName()));
              }
            }
          }
          if (reaction.isSetKineticLaw()) {
            KineticLaw kineticLaw = reaction.getKineticLaw();
            if (kineticLaw.isSetTimeUnits()
                && !kineticLaw.isSetTimeUnitsInstance()) {
              log4jLogger.warn("No UnitDefinition matches the timeUnitsID of kineticLaw.");
            }
            if (kineticLaw.isSetSubstanceUnits()
                && !kineticLaw.isSetSubstanceUnitsInstance()) {
              log4jLogger.warn("No UnitDefinition matches the substanceUnitsID of kineticLaw.");
            }
            if (kineticLaw.isSetListOfLocalParameters()) {
              for (int j = 0; j < kineticLaw.getNumLocalParameters(); j++) {
                LocalParameter parameter = kineticLaw
                    .getLocalParameter(j);
                if (parameter.isSetUnits()
                    && !parameter.isSetUnitsInstance()) {
                  log4jLogger.warn(String.format(
                    "No UnitDefinition matches the unitsID '%s'of the parameter %s.",
View Full Code Here
TOP

Related Classes of org.sbml.jsbml.KineticLaw

  • cysbml.SBMLGraphReader
  • org.sbml.jsbml.ext.multi.ReactionRule
  • org.sbml.jsbml.test.IdRegistrationTest
  • org.sbml.jsbml.test.MathMLTest
  • org.sbml.jsbml.test.sbml.TestModel
  • org.sbml.jsbml.test.sbml.TestReadFromFile1
  • org.sbml.jsbml.test.sbml.TestReadFromFile5
  • org.sbml.jsbml.test.TestLocalParameterIdentification
  • org.sbml.jsbml.xml.parsers.RDFAnnotationParser
  • org.sbml.jsbml.xml.parsers.SBMLCoreParser
    • 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.