Package org.sbml.jsbml

Examples of org.sbml.jsbml.Parameter


    return Double.isNaN(x);
  }

  @Before public void setUp() throws Exception
  {
    P = new  Parameter(3,1);
  }
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    @Test public void test_L3_Parameter_hasRequiredAttributes()
    {
      assertTrue(false); // TODO: we need to implement the method sbase.hasRequiredAttributes() for all element
     
      Parameter p = new  Parameter(3,1);
//      assertEquals( false, p.hasRequiredAttributes() );
      p.setId( "id");
//      assertEquals( false, p.hasRequiredAttributes() );
      p.setConstant(false);
//      assertEquals( true, p.hasRequiredAttributes() );
      p = null;
    }
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          }
        }
      }
      if (model.isSetListOfParameters()) {
        for (int i = 0; i < model.getParameterCount(); i++) {
          Parameter parameter = model.getParameter(i);
          if (parameter.isSetUnits()
              && !parameter.isSetUnitsInstance()) {
            log4jLogger.warn("No UnitDefinition matches the unitsID of parameter.");
          }
        }
      }
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              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(
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  /**
   * Test method for {@link org.sbml.jsbml.Model#removeParameter(java.lang.String)}.
   */
  @Test
  public void testRemoveParameterString() {
    Parameter r = modelL3.createParameter("p1");
    assertTrue(modelL3.getParameter(r.getId()) != null);

    modelL3.removeParameter(r.getId());
    assertTrue(modelL3.getParameter(r.getId()) == null);
  }
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    private Parameter P;

  @Before public void setUp() throws Exception
  {
    P = new  Parameter(2,4);
    if (P == null);
    {
    }
  }
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    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"));

  }
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    h.addCreator(c);
    model.setHistory(h);
//    model.appendNotes("This is a very interesting model.");
    model.appendNotes("<body xmlns=\"http://www.w3.org/1999/xhtml\"><h1>Model of &#8220;Apoptosis&#8221; in &#8220;Homo sapiens (human)&#8221;</h1>Apoptosis is a genetically controlled mechanisms of cell death involved in the regulation of tissue homeostasis. The 2 major pathways of apoptosis are the extrinsic (Fas and other TNFR superfamily members and ligands) and the intrinsic (mitochondria-associated) pathways, both of which are found in the cytoplasm. The extrinsic pathway is triggered by death receptor engagement, which initiates a signaling cascade mediated by caspase-8 activation. Caspase-8 both feeds directly into caspase-3 activation and stimulates the release of cytochrome c by the mitochondria. Caspase-3 activation leads to the degradation of cellular proteins necessary to maintain cell survival and integrity. The intrinsic pathway occurs when various apoptotic stimuli trigger the release of cytochrome c from the mitochondria (independently of caspase-8 activation). Cytochrome c interacts with Apaf-1 and caspase-9 to promote the activation of caspase-3. Recent studies point to the ER as a third subcellular compartment implicated in apoptotic execution. Alterations in Ca2+ homeostasis and accumulation of misfolded proteins in the ER cause ER stress. Prolonged ER stress can result in the activation of BAD and/or caspase-12, and execute apoptosis.<br/><a href=\"http://www.genome.jp/kegg/pathway/hsa/hsa04210.png\"><img src=\"http://www.genome.jp/kegg/pathway/hsa/hsa04210.png\" alt=\"http://www.genome.jp/kegg-bin/show_pathway?hsa04210\"/></a><br/><a href=\"http://www.genome.jp/kegg-bin/show_pathway?hsa04210\">Original Entry</a><br/><div align=\"right\"></div><br/></body>");
   
    Parameter k1 = model.createParameter("k1");
    Parameter k2 = model.createParameter("k2");
   
    k1.setConstant(false);
    k2.setConstant(false);
   
    k1.addCVTerm(new CVTerm(CVTerm.Qualifier.BQB_IS, "test"));
   
    Event event = model.createEvent("test_event");
   
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          setSpeciesCompartment(species, model);
        }
      }
      if (model.isSetListOfParameters()) {
        for (int i = 0; i < model.getParameterCount(); i++) {
          Parameter parameter = model.getParameter(i);
          setParameterUnits(parameter, model);
        }
      }

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

              return parameter;
            } else if (elementName.equals("algebraicRule")
                && list.getSBaseListType().equals(
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