Examples with Model com.microsoft.z3.Model used on opensource projects

Example 21 with Model

use of com.microsoft.z3.Model in project xtext-core by eclipse.

the class Bug250313SemanticSequencer method sequence.

@Override
public void sequence(ISerializationContext context, EObject semanticObject) {
    EPackage epackage = semanticObject.eClass().getEPackage();
    ParserRule rule = context.getParserRule();
    Action action = context.getAssignedAction();
    Set<Parameter> parameters = context.getEnabledBooleanParameters();
    if (epackage == Bug250313Package.eINSTANCE)
        switch(semanticObject.eClass().getClassifierID()) {
            case Bug250313Package.CHILD1:
                sequence_Child1(context, (Child1) semanticObject);
                return;
            case Bug250313Package.CHILD2:
                sequence_Child2(context, (Child2) semanticObject);
                return;
            case Bug250313Package.MODEL:
                sequence_Model(context, (Model) semanticObject);
                return;
        }
    if (errorAcceptor != null)
        errorAcceptor.accept(diagnosticProvider.createInvalidContextOrTypeDiagnostic(semanticObject, context));
}

Example 22 with Model

use of com.microsoft.z3.Model in project xtext-core by eclipse.

the class Bug302128TestLanguageSemanticSequencer method sequence.

@Override
public void sequence(ISerializationContext context, EObject semanticObject) {
    EPackage epackage = semanticObject.eClass().getEPackage();
    ParserRule rule = context.getParserRule();
    Action action = context.getAssignedAction();
    Set<Parameter> parameters = context.getEnabledBooleanParameters();
    if (epackage == Bug302128Package.eINSTANCE)
        switch(semanticObject.eClass().getClassifierID()) {
            case Bug302128Package.ELEMENT:
                sequence_Element(context, (Element) semanticObject);
                return;
            case Bug302128Package.MODEL:
                sequence_Model(context, (Model) semanticObject);
                return;
        }
    if (errorAcceptor != null)
        errorAcceptor.accept(diagnosticProvider.createInvalidContextOrTypeDiagnostic(semanticObject, context));
}

Example 23 with Model

use of com.microsoft.z3.Model in project libSBOLj by SynBioDex.

the class ModelOutput method main.

public static void main(String[] args) throws Exception {
    SBOLDocument document = new SBOLDocument();
    document.setTypesInURIs(false);
    document.setDefaultURIprefix("http://www.sbolstandard.org/examples/");
    Model model = document.createModel("pIKE_Toggle_1", "", URI.create("http://virtualparts.org/part/pIKE_Toggle_1"), URI.create("http://identifiers.org/edam/format_2585"), SystemsBiologyOntology.CONTINUOUS_FRAMEWORK);
    model.setName("pIKE_Toggle_1 toggle switch");
    SBOLWriter.write(document, (System.out));
}

Example 24 with Model

use of com.microsoft.z3.Model in project libSBOLj by SynBioDex.

the class ModuleDefinitionOutput method main.

public static void main(String[] args) throws Exception {
    SBOLDocument document = new SBOLDocument();
    setDefaultNameSpace(document, pr.getNamespaceURI());
    ComponentDefinition gfp = createComponenDefinition(document, pr.withLocalPart("BBa_E0040"), "gfp", Terms.biopaxTerms.DnaRegion, Terms.soTerms.CDS, "gfp coding sequence");
    ComponentDefinition tetR = createComponenDefinition(document, pr.withLocalPart("BBa_C0040"), "tetR", Terms.biopaxTerms.DnaRegion, Terms.soTerms.CDS, "tetR coding sequence");
    ComponentDefinition lacI = createComponenDefinition(document, pr.withLocalPart("BBa_C0012"), "lacI", Terms.biopaxTerms.DnaRegion, Terms.soTerms.CDS, "lacI coding sequence");
    ComponentDefinition placI = createComponenDefinition(document, pr.withLocalPart("BBa_R0010"), "pLacI", Terms.biopaxTerms.DnaRegion, Terms.soTerms.promoter, "pLacI promoter");
    ComponentDefinition ptetR = createComponenDefinition(document, pr.withLocalPart("BBa_R0040"), "pTetR", Terms.biopaxTerms.DnaRegion, Terms.soTerms.promoter, "pTet promoter");
    ComponentDefinition rbslacI = createComponenDefinition(document, pr.withLocalPart("BBa_J61101"), "BBa_J61101 RBS", Terms.biopaxTerms.DnaRegion, Terms.soTerms.RBS, "RBS1");
    ComponentDefinition rbstetR = createComponenDefinition(document, pr.withLocalPart("BBa_J61120"), "BBa_J61101 RBS", Terms.biopaxTerms.DnaRegion, Terms.soTerms.RBS, "RBS2");
    ComponentDefinition rbsgfp = createComponenDefinition(document, pr.withLocalPart("BBa_J61130"), "BBa_J61101 RBS", Terms.biopaxTerms.DnaRegion, Terms.soTerms.RBS, "RBS2");
    setDefaultNameSpace(document, uniprot.getNamespaceURI());
    ComponentDefinition GFP = createComponenDefinition(document, uniprot.withLocalPart("P42212"), "GFP", Terms.biopaxTerms.Protein, Terms.sboTerms.product, "GFP protein");
    ComponentDefinition TetR = createComponenDefinition(document, uniprot.withLocalPart("Q6QR72"), "TetR", Terms.biopaxTerms.Protein, Terms.sboTerms.inhibitor, "TetR protein");
    ComponentDefinition LacI = createComponenDefinition(document, uniprot.withLocalPart("P03023"), "LacI", Terms.biopaxTerms.Protein, Terms.sboTerms.inhibitor, "LacI protein");
    setDefaultNameSpace(document, pr.getNamespaceURI());
    ComponentDefinition lacITerminator = createComponenDefinition(document, pr.withLocalPart("ECK120029600"), "ECK120029600", Terms.biopaxTerms.DnaRegion, Terms.soTerms.terminator, "Terminator1");
    ComponentDefinition tetRTerminator = createComponenDefinition(document, pr.withLocalPart("ECK120033736"), "ECK120033736", Terms.biopaxTerms.DnaRegion, Terms.soTerms.terminator, "Terminator2");
    setDefaultNameSpace(document, vpr.getNamespaceURI());
    ComponentDefinition tetRInverter = createComponenDefinition(document, vpr.withLocalPart("pIKELeftCassette_1"), "TetR Inverter", Terms.biopaxTerms.DnaRegion, Terms.soTerms.engineeredGene, "TetR Inverter");
    ComponentDefinition lacIInverter = createComponenDefinition(document, vpr.withLocalPart("pIKERightCassette_1"), "LacI Inverter", Terms.biopaxTerms.DnaRegion, Terms.soTerms.engineeredGene, "LacI Inverter");
    ComponentDefinition toggleSwitch = createComponenDefinition(document, vpr.withLocalPart("pIKE_Toggle_1"), "LacI/TetR Toggle Switch", Terms.biopaxTerms.DnaRegion, Terms.soTerms.engineeredGene, "LacI/TetR Toggle Switch");
    // tetR inverter sequences
    addPRSequence(document, ptetR, "tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac");
    addPRSequence(document, rbslacI, "aaagacaggacc");
    addPRSequence(document, lacI, "atggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagacagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcaggctgcaaacgacgaaaactacgctttagtagcttaataa");
    addPRSequence(document, lacITerminator, "ttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa");
    // lacI inverter sequences
    addPRSequence(document, placI, "tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac");
    addPRSequence(document, rbstetR, "aaagacaggacc");
    addPRSequence(document, tetR, "atgtccagattagataaaagtaaagtgattaacagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtccgctgcaaacgacgaaaactacgctttagtagcttaataa");
    addPRSequence(document, rbsgfp, "aaagaaacgaca");
    addPRSequence(document, gfp, "atgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataa");
    addPRSequence(document, tetRTerminator, "ttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa");
    addSubComponents(document, tetRInverter, ptetR, rbslacI, lacI, lacITerminator);
    addSubComponents(document, lacIInverter, placI, rbstetR, tetR, rbsgfp, gfp, tetRTerminator);
    addSubComponents(document, toggleSwitch, tetRInverter, lacIInverter);
    setDefaultNameSpace(document, example.getNamespaceURI());
    ModuleDefinition laciInverterModuleDef = document.createModuleDefinition("laci_inverter");
    laciInverterModuleDef.addRole(Terms.moduleRoles.inverter);
    ModuleDefinition tetRInverterModuleDef = document.createModuleDefinition("tetr_inverter");
    tetRInverterModuleDef.addRole(Terms.moduleRoles.inverter);
    createInverter(document, laciInverterModuleDef, placI, LacI);
    createInverter(document, tetRInverterModuleDef, ptetR, TetR);
    ModuleDefinition toggleSwitchModuleDef = document.createModuleDefinition("toggle_switch");
    toggleSwitchModuleDef.addRole(toURI(example.withLocalPart("module_role/toggle_switch")));
    FunctionalComponent toggleSwitchModuleDef_TetR = toggleSwitchModuleDef.createFunctionalComponent("TetR", AccessType.PUBLIC, TetR.getIdentity(), DirectionType.INOUT);
    FunctionalComponent toggleSwitchModuleDef_LacI = toggleSwitchModuleDef.createFunctionalComponent("LacI", AccessType.PUBLIC, LacI.getIdentity(), DirectionType.INOUT);
    Module lacInverterSubModule = toggleSwitchModuleDef.createModule("laci_inverter", laciInverterModuleDef.getIdentity());
    lacInverterSubModule.createMapsTo("LacI_mapping", RefinementType.USEREMOTE, toggleSwitchModuleDef_LacI.getIdentity(), laciInverterModuleDef.getFunctionalComponent("TF").getIdentity());
    Module tetRInverterSubModule = toggleSwitchModuleDef.createModule("tetr_inverter", tetRInverterModuleDef.getIdentity());
    tetRInverterSubModule.createMapsTo("TetR_mapping", RefinementType.USEREMOTE, toggleSwitchModuleDef_TetR.getIdentity(), tetRInverterModuleDef.getFunctionalComponent("TF").getIdentity());
    Model model = document.createModel("toogleswitch", URI.create("http://virtualparts.org/part/pIKE_Toggle_1"), EDAMOntology.SBML, SystemsBiologyOntology.CONTINUOUS_FRAMEWORK);
    toggleSwitchModuleDef.addModel(model.getIdentity());
    SBOLWriter.write(document, (System.out));
}

Example 25 with Model

use of com.microsoft.z3.Model in project libSBOLj by SynBioDex.

the class ModuleDefinitionTest method test_modelMethods.

@Test
public void test_modelMethods() throws SBOLValidationException {
    Model model = doc.createModel("pIKE_Toggle_1", "1.0", URI.create("http://virtualparts.org/part/pIKE_Toggle_1"), URI.create("http://identifiers.org/edam/format_2585"), SystemsBiologyOntology.CONTINUOUS_FRAMEWORK);
    assertTrue(geneticToggleSwitch.addModel("pIKE_Toggle_1"));
    assertTrue(doc.getModuleDefinition("geneticToggleSwitch", "").getModels().contains(model));
    assertTrue(geneticToggleSwitch.removeModel(model.getPersistentIdentity()));
    assertTrue(geneticToggleSwitch.addModel("pIKE_Toggle_1", "1.0"));
    assertTrue(doc.getModuleDefinition("geneticToggleSwitch", "").getModels().contains(model));
    assertTrue(geneticToggleSwitch.containsModel(model.getIdentity()));
}