Examples of org.sbml.jsbml.SpeciesType

org.sbml.jsbml.SpeciesType
Represents the speciesType XML element of a SBML file. It is deprecated since level 3 and not defined in SBML before Level 2 Version 2. @author Andreas Dräger @since 0.8 @version $Rev: 1525 $ @deprecated Only valid in SBML Level 2 for Versions 2 through 4.

    assertTrue(M.getSpecies(0).equals(s) == true);
  }


  @Test
  public void test_Model_createSpeciesType() {
    SpeciesType c = M.createSpeciesType();
    assertTrue(c != null);
    assertTrue(M.getSpeciesTypeCount() == 1);
    assertEquals(M.getSpeciesType(0), c);
  }

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    o3 = null;
  }


  @Test
  public void test_Model_removeSpeciesType() {
    SpeciesType o1, o2, o3;
    o1 = M.createSpeciesType();
    o2 = M.createSpeciesType();
    o3 = M.createSpeciesType();
    o3.setId("test");
    assertTrue(M.removeSpeciesType(0).equals(o1));

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              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");

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  /**
   * Test method for {@link org.sbml.jsbml.Model#removeSpeciesType(java.lang.String)}.
   */
  @Test
  public void testRemoveSpeciesTypeString() {
    SpeciesType st = modelL2V4.createSpeciesType("st");
    assertTrue(modelL2V4.getSpeciesType(st.getId()) != null);
    
    modelL2V4.removeSpeciesType(st.getId());
    assertTrue(modelL2V4.getSpeciesType(st.getId()) == null);
  }

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  private void setSpeciesSpeciesType(Species species, Model model) {


    if (species.isSetSpeciesType()) {
      String speciesTypeID = species.getSpeciesType();


      SpeciesType speciesType = model.getSpeciesType(speciesTypeID);


      if (speciesType != null) {
        species.setSpeciesType(speciesType);
      } else {
        // TODO: the speciesType ID doesn't match a speciesType, throw

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    assertTrue(M.getSpecies(0).equals(s) == true);
  }


  @Test
  public void test_Model_createSpeciesType() {
    SpeciesType c = M.createSpeciesType();
    assertTrue(c != null);
    assertTrue(M.getNumSpeciesTypes() == 1);
    assertEquals(M.getSpeciesType(0), c);
  }

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    o3 = null;
  }


  @Test
  public void test_Model_removeSpeciesType() {
    SpeciesType o1, o2, o3;
    o1 = M.createSpeciesType();
    o2 = M.createSpeciesType();
    o3 = M.createSpeciesType();
    o3.setId("test");
    assertTrue(M.removeSpeciesType(0).equals(o1));

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              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");

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  private void setSpeciesSpeciesType(Species species, Model model) {


    if (species.isSetSpeciesType()) {
      String speciesTypeID = species.getSpeciesType();


      SpeciesType speciesType = model.getSpeciesType(speciesTypeID);


      if (speciesType != null) {
        species.setSpeciesType(speciesType);
      } else {
        // TODO : the speciesType ID doesn't match a speciesType, throw

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              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");

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Related Classes of org.sbml.jsbml.SpeciesType

org.sbml.jsbml.test.RemoveFromModelTest

org.sbml.jsbml.test.sbml.TestModel

org.sbml.jsbml.xml.parsers.SBMLCoreParser

org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser

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