Package org.sbml.jsbml

Examples of org.sbml.jsbml.Species

97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
    } catch (IllegalArgumentException e) {
      assertTrue(true);
      // success
    }

    Species s3 = new Species();
    s3.setId("SP1");
   
    try {
      model.addSpecies(s3);
      fail("We should not be able to register twice the same id.");
    } catch (IllegalArgumentException e) {
      assertTrue(true);
      // success
    }
    assertTrue(model.getSpecies("S3") == null);

    s3.setId("LP1");
   
    try {
      model.addSpecies(s3);
      assertTrue(true);
    } catch (IllegalArgumentException e) {
      fail("We should be able to register an id that is the same as a local parameter id.");
    }

    model.removeSpecies(s3);
    assertTrue(model.getSpecies("S3") == null);
   
    // Testing again after having removed the Species
    try {
      model.addSpecies(s3);
      assertTrue(true);
    } catch (IllegalArgumentException e) {
      fail("We should be able to register an id that is the same as a local parameter id.");
    }

    model.removeSpecies(s3);
    assertTrue(model.getSpecies("S3") == null);
   
    // Setting the same metaid as a SpeciesReference
    try {
      s3.setMetaId("SP1");
      assertTrue(true);
    } catch (IdentifierException e) {
      fail("We should be able to put any metaId to a Species removed from a model.");
    }

    try {
      model.addSpecies(s3);
      fail("We should not be able to register twice the same metaid.");
    } catch (IllegalArgumentException e) {
      assertTrue(true);
      // success
    }

    assertTrue(model.getSpecies("S3") == null);

    try {
      s3.setId("S1");
      assertTrue(true);
    } catch (IdentifierException e) {
      fail("We should be able to put any id to a Species removed from a model.");
    }

    try {
      model.addSpecies(s3);
      fail("We should not be able to register twice the same id.");
    } catch (IllegalArgumentException e) {
      assertTrue(true);
      // success
    }
   
    assertTrue(model.getSpecies("S3") == null);

    // Setting the same metaid as a LocalParameter

    try {
      s3.setMetaId("LP1");
      assertTrue(true);
    } catch (IdentifierException e) {
      fail("We should be able to put any metaId to a Species not linked to a model.");
    }
View Full Code Here
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
  /**
   *
   */
  @Test public void testRegister2() {
   
    Species s3 = new Species();
    // Setting the same id as a LocalParameter
    s3.setId("LP1");

    // Setting the same metaid as a LocalParameter
    try {
      s3.setMetaId("LP1");
      assertTrue(true);
    } catch (IdentifierException e) {
      fail("We should be able to put any metaId to a Species not linked to a model.");
    }

View Full Code Here
482
483
484
485
486
487
488
489
490
491
492
493
  /**
   *
   */
  @Test public void testRegister6() {
   
    Species s3 = new Species();
    s3.setId("S3");
   
    model.addSpecies(s3);

    // calling the registerChild by hand !!
    model.registerChild(s3);// This call does nothing if the parent of the SBase we try to register is already defined
View Full Code Here
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
    // assertTrue(model.findNamedSBase("LP1") == null);
    assertTrue(doc.findSBase("SP1") == null);
    assertTrue(doc.findSBase("R1") == null);
    assertTrue(doc.findSBase("LP1") == null);
   
    Species s3 = new Species();
   
    // Setting the same id as a removed SpeciesReference
    s3.setId("SP1");

    // Setting the same metaid as a removed LocalParameter
    try {
      s3.setMetaId("LP1");
      assertTrue(true);
    } catch (IdentifierException e) {
      fail("We should be able to put any metaId to a Species not linked to a model.");
    }
View Full Code Here
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
    // assertTrue(model.findNamedSBase("LP1") == null);
    assertTrue(doc.findSBase("SP1") == null);
    assertTrue(doc.findSBase("R1") == null);
    assertTrue(doc.findSBase("LP1") == null);
   
    Species s3 = new Species();
   
    // Setting the same id as a removed SpeciesReference
    s3.setId("SP1");

    // Setting the same metaid as a removed LocalParameter
    try {
      s3.setMetaId("LP1");
      assertTrue(true);
    } catch (IdentifierException e) {
      fail("We should be able to put any metaId to a Species not linked to a model.");
    }
View Full Code Here
49
50
51
52
53
54
55
56
57
58
59
60
  @SuppressWarnings("deprecation")
  public static void main(String args[]) throws ParseException, XMLStreamException, SBMLException {
    SBMLDocument doc = new SBMLDocument(1, 2);
    Model m = doc.createModel();
    Compartment c = m.createCompartment("c1");
    Species s1 = m.createSpecies("s1", c);
    Species s2 = m.createSpecies("s2", c);
    Reaction r = m.createReaction("r1");
    r.createReactant(null, s1);
    r.createProduct(null, s2);
    KineticLaw kl = r.createKineticLaw();
    kl.setFormula("s1 * 3");
 
View Full Code Here
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
   */
  @Test public void checkHashCode() throws ParseException {
    SBMLDocument doc1 = new SBMLDocument(3, 1);
    Model model = doc1.createModel("test_model");
    Compartment c = model.createCompartment("c1");
    Species s = model.createSpecies("s1", c);
    s.addCVTerm(new CVTerm(CVTerm.Qualifier.BQB_IS, "urn:miriam:kegg.compound:C00001"));
    Rule r = model.createAlgebraicRule();
    r.setMath(ASTNode.parseFormula("sin(3) + 1"));
   
    SBMLDocument doc2 = doc1.clone();
    try {
      (new SBMLWriter()).write(doc1, System.out);
      System.out.println("\n==================");
      (new SBMLWriter()).write(doc2, System.out);
    } catch (SBMLException e) {
      e.printStackTrace();
    } catch (XMLStreamException e) {
      e.printStackTrace();
    }
    assertTrue(doc1.hashCode() == doc2.hashCode());
    assertTrue(model.hashCode() != doc2.hashCode());
    assertTrue(s.getCVTerm(0).equals(new CVTerm(CVTerm.Qualifier.BQB_IS, "urn:miriam:kegg.compound:C00001")));
    assertTrue(s.getCVTerm(0).hashCode() == (new CVTerm(CVTerm.Qualifier.BQB_IS, "urn:miriam:kegg.compound:C00001")).hashCode());
    assertTrue(doc1.equals(doc2));
    assertTrue(doc2.equals(doc1));
  }
View Full Code Here
350
351
352
353
354
355
356
357
358
359
360
          }
        }
      }
      if (model.isSetListOfSpecies()) {
        for (int i = 0; i < model.getSpeciesCount(); i++) {
          Species species = model.getSpecies(i);
          setSpeciesSubstanceUnits(species, model);
          setSpeciesSpeciesType(species, model);
          setSpeciesConversionFactor(species, model);
          setSpeciesCompartment(species, model);
        }
View Full Code Here
492
493
494
495
496
497
498
499
500
501
502
              return compartment;
            } else if (elementName.equals("specie")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfSpecies)) {
              Species species = (Species) newContextObject;
              model.addSpecies(species);

              return species;
            } else if (elementName.equals("parameter")
                && list.getSBaseListType().equals(
View Full Code Here
654
655
656
657
658
659
660
661
662
663
664
    if (rule.isSetVariable()) {
      String variableID = rule.getVariable();

      Compartment compartment = model.getCompartment(variableID);
      Species species = null;
      SpeciesReference speciesReference = null;
      Parameter parameter = null;

      if (compartment == null) {
        species = model.getSpecies(variableID);
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.