Examples of SpeciesType

model.SpeciesType
@author Gary
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.

org.sbml.jsbml.ext.multi.SpeciesType

dels.net/sbo/">Systems Biology Ontology through the optional sboTerm attribute. The following table provides typical examples of component or domains (the list is absolutely not complete).

SBO identifier	Definition
SBO:0000242	channel
SBO:0000244	receptor
SBO:0000284	transporter
SBO:0000280	ligand
SBO:0000493	functional domain
SBO:0000494	binding site
SBO:0000495	catalytic site
SBO:0000496	transmembrane domain

@author Nicolas Rodriguez

Examples of org.sbml.jsbml.SpeciesType

    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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Examples of org.sbml.jsbml.SpeciesType

              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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Examples of org.sbml.jsbml.SpeciesType

  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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Examples of org.sbml.jsbml.SpeciesType

              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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Examples of org.sbml.jsbml.SpeciesType

    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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Examples of org.sbml.jsbml.SpeciesType

    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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Examples of org.sbml.jsbml.SpeciesType

  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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Examples of org.sbml.jsbml.ext.multi.SpeciesType

        return multiModel.getListOfSelectors();
      }
    } // end Model
    else if (contextObject instanceof SpeciesType)
    {
      SpeciesType speciesType = (SpeciesType) contextObject;


      if (elementName.equals(listOfStateFeatures)) {
        return speciesType.getListOfStateFeatures();
      }
    } // end SpeciesType
    else if (contextObject instanceof StateFeature)
    {
      StateFeature stateFeature = (StateFeature) contextObject;

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