Package org.sbml.jsbml

Examples of org.sbml.jsbml.Species

46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
  public static void main(String[] args) throws IOException, XMLStreamException {
   
    SBMLDocument doc = new SBMLDocument(2, 4);
    Model model = doc.createModel("model_test");
    Compartment c1 = model.createCompartment("c1");
    Species s1 = model.createSpecies("s1", c1);
    s1.setMetaId("meta_" + s1.getId());
   
    Species s2 = model.createSpecies("s2", c1);
    s2.setMetaId("meta_" + s2.getId());
   
    Reaction r = model.createReaction("r1");
    r.createReactant(s1);
    r.createProduct(s2);
   
View Full Code Here
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
          }
        }
      }
      if (model.isSetListOfSpecies()) {
        for (int i = 0; i < model.getSpeciesCount(); i++) {
          Species species = model.getSpecies(i);

          if (species.isSetSubstanceUnits()
              && !species.isSetSubstanceUnitsInstance()) {
            log4jLogger.warn("No UnitDefinition matches the subtsanceUnitsID of species.");
          }
          if (species.isSetSpeciesType()
              && !species.isSetSpeciesTypeInstance()) {
            log4jLogger.warn("No SpeciesType matches the speciesTypeID of species.");
          }
          if (species.isSetConversionFactor()
              && !species.isSetConversionFactorInstance()) {
            log4jLogger.warn("No Parameter matches the conversionFactorID of species.");
          }
          if (species.isSetCompartment()
              && !species.isSetCompartmentInstance()) {
            log4jLogger.warn("No Compartment matches the compartmentID of species.");
          }
          if (species.isSetSpatialSizeUnits()
              && !species.isSetSpatialSizeUnitsInstance()) {
            log4jLogger.warn("No UnitDefinition matches the spatialSizeUnitsID of species.");
          }
        }
      }
      if (model.isSetListOfParameters()) {
View Full Code Here
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
            } 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(
View Full Code Here
155
156
157
158
159
160
161
162
163
164
165
  /**
   * Test method for {@link org.sbml.jsbml.Model#removeSpecies(java.lang.String)}.
   */
  @Test
  public void testRemoveSpeciesString() {
    Species c = modelL3.createSpecies("s5");
    assertTrue(modelL3.getSpecies(c.getId()) != null);

    modelL3.removeSpecies(c.getId());
    assertTrue(modelL3.getSpecies(c.getId()) == null);
  }
View Full Code Here
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
   
    // assertTrue(model.getId().equals("")); // TODO: document. Different behavior than libsbml, we set the id as the name for SBML level 1 models.
    assertTrue(model.getId().equals("Branch"));
    assertTrue(model.getName().equals("Branch"));
   
    Species s1 = model.getSpecies("S1");
   
    assertTrue(s1 != null);
   
    assertTrue(s1.getName().equals("S1"));
    assertTrue(s1.getId().equals("S1")); // changed, was assertTrue(s1.getId().equals("")); cf comment above.
    assertTrue(s1.getCVTermCount() == 0);
   
    assertTrue(s1.getInitialAmount() == 0);
    assertTrue(s1.getBoundaryCondition() == false);
   
    Species x1 = model.getSpecies("X1");
   
    assertTrue(x1 != null);
   
    assertTrue(x1.getName().equals("X1"));
    assertTrue(x1.getInitialAmount() == 0);
    assertTrue(x1.getBoundaryCondition() == true);
   
   
    Reaction r1 = model.getReaction(0);
   
    assertTrue(r1 != null);
View Full Code Here
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
    assertTrue(model.getLevel() == 1 && model.getVersion() == 1);
   
    assertTrue(model.getId().equals(""));
    assertTrue(model.getName().equals(""));
   
    Species s1 = model.getSpecies("s1");
   
    assertTrue(s1 != null);
   
    assertTrue(s1.getName().equals("s1"));
    assertTrue(s1.getId().equals("s1")); // changed, was:  assertTrue(s1.getId().equals(""));
    assertTrue(s1.getCVTermCount() == 0);
   
    assertTrue(s1.getInitialAmount() == 1);
   
   
    UnitDefinition mls = model.getUnitDefinition(1);
   
    assertTrue(mls != null);
View Full Code Here
46
47
48
49
50
51
52
53
54
55
  private Species S;

  @Before public void setUp() throws Exception
  {
    S = new  Species(2,4);
    if (S == null);
    {
    }
  }
View Full Code Here
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
 
  @SuppressWarnings("deprecation")
@Test public void test_Species_setSpatialSizeUnits()
  {
    Species s = new  Species(2,1);
    String units =  "volume";;
    s.setSpatialSizeUnits(units);
    assertTrue(s.getSpatialSizeUnits().equals(units));
    assertEquals( true, s.isSetSpatialSizeUnits() );
    if (s.getSpatialSizeUnits() == units);
    {
    }
    s.setSpatialSizeUnits(s.getSpatialSizeUnits());
    assertTrue(s.getSpatialSizeUnits().equals(units));
    s.setSpatialSizeUnits("");
    assertEquals( false, s.isSetSpatialSizeUnits() );
    if (s.getSpatialSizeUnits() != null);
    {
    }
    s = null;
  }
View Full Code Here
43
44
45
46
47
48
49
50
51
52
   *
   * @see org.sbml.jsbml.util.Filter#accepts(java.lang.Object)
   */
  public boolean accepts(Object o) {
    if (o instanceof Species) {
      Species s = (Species) o;
      return s.isSetBoundaryCondition() && s.getBoundaryCondition();
    }
    return false;
  }
View Full Code Here
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
    model = doc.createModel("model");
   
    Compartment comp = model.createCompartment("cell");
    comp.setMetaId("cell");
   
    Species s1 = model.createSpecies("S1", comp);
    s1.setMetaId("S1");
   
    Species s2 = model.createSpecies("S2", comp);
    s2.setMetaId("S2");
   
    Reaction r1 = model.createReaction("R1");
    r1.setMetaId("R1");
   
    SpeciesReference reactant = model.createReactant("SP1");
View Full Code Here
TOP

Related Classes of org.sbml.jsbml.Species

  • org.mcisb.ontology.drugbank.DrugBankUtils
  • org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin
  • org.sbml.jsbml.test.HashCodeTest
  • org.sbml.jsbml.test.IdRegistrationTest
  • org.sbml.jsbml.test.ListenerTest
  • org.sbml.jsbml.test.MathMLTest
  • org.sbml.jsbml.test.RemoveFromModelTest
  • org.sbml.jsbml.test.sbml.TestModel
  • org.sbml.jsbml.test.sbml.TestReadFromFile1
  • org.sbml.jsbml.test.sbml.TestReadFromFile5
    • 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.