Examples with Parameter org.sbml.jsbml.Parameter used on opensource projects

Example 6 with Parameter

use of org.sbml.jsbml.Parameter in project vcell by virtualcell.

the class MathModel_SBMLExporter method getSBMLString.

/**
 * Insert the method's description here.
 * Creation date: (4/11/2006 11:38:26 AM)
 * @return org.sbml.libsbml.Model
 * @param mathModel cbit.vcell.mathmodel.MathModel
 * @throws XMLStreamException
 * @throws SBMLException
 */
public static String getSBMLString(cbit.vcell.mathmodel.MathModel mathModel, long level, long version) throws cbit.vcell.parser.ExpressionException, java.io.IOException, SBMLException, XMLStreamException {
    if (mathModel.getMathDescription().isSpatial()) {
        throw new RuntimeException("spatial models export to SBML not supported");
    }
    if (mathModel.getMathDescription().hasFastSystems()) {
        throw new RuntimeException("math models with fast systems cannot be exported to SBML");
    }
    if (mathModel.getMathDescription().isNonSpatialStoch()) {
        throw new RuntimeException("stochastic math models cannot be exported to SBML");
    }
    if (!mathModel.getMathDescription().isValid()) {
        throw new RuntimeException("math model has an invalid Math Description, cannot export to SBML");
    }
    String dummyID = "ID_0";
    String compartmentId = "compartment";
    SBMLDocument sbmlDocument = new SBMLDocument((int) level, (int) version);
    Model sbmlModel = sbmlDocument.createModel();
    sbmlModel.setId("MathModel_" + TokenMangler.mangleToSName(mathModel.getName()));
    if (mathModel.getMathDescription().isSpatial()) {
        addGeometry(sbmlModel, mathModel);
    }
    Compartment compartment = sbmlModel.createCompartment();
    compartment.setId(compartmentId);
    // ------ For spatial SBML when implemented -----
    // if (vcMathModel.getMathDescription().isSpatial()){
    // // for spatial model, compartment(s) created in addGeometry(), based on number of subVolumes/surfaceClasses.
    // addGeometry();
    // } else {
    // // for non-spatial mathmodel, only 1 compartment; create it here.
    // String compartmentId = "compartment";
    // org.sbml.libsbml.Compartment compartment = sbmlModel.createCompartment();
    // compartment.setId(compartmentId);
    // }
    MathDescription mathDesc = mathModel.getMathDescription();
    Enumeration<Variable> enumVars = mathDesc.getVariables();
    while (enumVars.hasMoreElements()) {
        Variable vcVar = (Variable) enumVars.nextElement();
        // 
        if (vcVar instanceof cbit.vcell.math.VolVariable) {
        // 
        // skip for now, define later when defining ODEEquations.
        // 
        // org.sbml.libsbml.Species species = model.createSpecies();
        // species.setId(vcVar.getName());
        // species.setCompartment(compartmentId);
        } else if (vcVar instanceof cbit.vcell.math.Constant && ((cbit.vcell.math.Constant) vcVar).getExpression().isNumeric()) {
            Parameter param = sbmlModel.createParameter();
            param.setId(TokenMangler.mangleToSName(vcVar.getName()));
            param.setConstant(true);
            param.setValue(vcVar.getExpression().evaluateConstant());
        } else if (vcVar instanceof cbit.vcell.math.Constant || vcVar instanceof cbit.vcell.math.Function) {
            Parameter param = sbmlModel.createParameter();
            param.setId(TokenMangler.mangleToSName(vcVar.getName()));
            param.setConstant(false);
            // 
            // Function or Constant with expressions - create assignment rule and add to model.
            // 
            ASTNode mathNode = getFormulaFromExpression(vcVar.getExpression(), MathType.REAL);
            AssignmentRule assignmentRule = sbmlModel.createAssignmentRule();
            dummyID = TokenMangler.getNextEnumeratedToken(dummyID);
            assignmentRule.setId(dummyID);
            assignmentRule.setVariable(TokenMangler.mangleToSName(vcVar.getName()));
            assignmentRule.setMath(mathNode);
        // Create a parameter for this function/non-numeric constant, set its value to be 'not-constant',
        // add to model.
        }
    }
    cbit.vcell.math.CompartmentSubDomain subDomain = (cbit.vcell.math.CompartmentSubDomain) mathDesc.getSubDomains().nextElement();
    // System.out.println(model.toSBML());
    Enumeration<Equation> enumEqu = subDomain.getEquations();
    while (enumEqu.hasMoreElements()) {
        cbit.vcell.math.Equation equ = (cbit.vcell.math.Equation) enumEqu.nextElement();
        if (equ instanceof cbit.vcell.math.OdeEquation) {
            // For ODE equations, add the ode variable as a parameter, add rate as a rate rule and init condition as an initial assignment rule.
            Parameter param = sbmlModel.createParameter();
            param.setId(TokenMangler.mangleToSName(equ.getVariable().getName()));
            param.setConstant(false);
            // try to obtain the constant to which the init expression evaluates.
            RateRule rateRule = sbmlModel.createRateRule();
            rateRule.setVariable(TokenMangler.mangleToSName(equ.getVariable().getName()));
            rateRule.setMath(getFormulaFromExpression(equ.getRateExpression(), MathType.REAL));
            InitialAssignment initialAssignment = sbmlModel.createInitialAssignment();
            dummyID = TokenMangler.getNextEnumeratedToken(dummyID);
            initialAssignment.setId(dummyID);
            initialAssignment.setMath(getFormulaFromExpression(equ.getInitialExpression(), MathType.REAL));
            initialAssignment.setVariable(TokenMangler.mangleToSName(equ.getVariable().getName()));
        } else {
            throw new RuntimeException("equation type " + equ.getClass().getName() + " not supported");
        }
    }
    Iterator<Event> vcellEvents = mathDesc.getEvents();
    while (vcellEvents.hasNext()) {
        Event vcellEvent = vcellEvents.next();
        addSbmlEvent(sbmlModel, vcellEvent);
    }
    System.out.println(new SBMLWriter().writeSBMLToString(sbmlDocument));
    // validate the sbml document
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.GENERAL_CONSISTENCY, true);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.IDENTIFIER_CONSISTENCY, true);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.MATHML_CONSISTENCY, true);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.MODELING_PRACTICE, false);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.OVERDETERMINED_MODEL, true);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.SBO_CONSISTENCY, false);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.UNITS_CONSISTENCY, false);
    sbmlDocument.checkConsistency();
    // sbmlDocument.checkConsistencyOffline();
    long internalErrCount = sbmlDocument.getNumErrors();
    if (internalErrCount > 0) {
        StringBuffer sbmlErrbuf = new StringBuffer();
        for (int i = 0; i < internalErrCount; i++) {
            SBMLError sbmlErr = sbmlDocument.getError(i);
            if (sbmlErr.isError() || sbmlErr.isFatal()) {
                sbmlErrbuf.append(sbmlErr.getCategory() + " :: " + sbmlErr.getSeverity() + " :: " + sbmlErr.getMessage() + "\n");
            }
        }
        if (sbmlErrbuf.length() > 0) {
            throw new RuntimeException("SBML Internal consistency checks failed: \n" + sbmlErrbuf.toString());
        }
    }
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.GENERAL_CONSISTENCY, true);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.IDENTIFIER_CONSISTENCY, true);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.UNITS_CONSISTENCY, false);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.MATHML_CONSISTENCY, true);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.SBO_CONSISTENCY, false);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.OVERDETERMINED_MODEL, true);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.MODELING_PRACTICE, false);
    sbmlDocument.checkConsistency();
    // sbmlDocument.checkConsistencyOffline();
    long errCount = sbmlDocument.getNumErrors();
    if (errCount > 0) {
        StringBuffer sbmlErrbuf = new StringBuffer();
        for (int i = 0; i < errCount; i++) {
            SBMLError sbmlErr = sbmlDocument.getError(i);
            if (sbmlErr.isError() || sbmlErr.isFatal()) {
                sbmlErrbuf.append(sbmlErr.getCategory() + " :: " + sbmlErr.getSeverity() + " :: " + sbmlErr.getMessage() + "\n");
            }
        }
        if (sbmlErrbuf.length() > 0) {
            throw new RuntimeException("SBML validation failed: \n" + sbmlErrbuf.toString());
        }
    }
    // end of validation
    // start writing
    SBMLWriter sbmlWriter = new SBMLWriter();
    String sbmlStr = sbmlWriter.writeSBMLToString(sbmlDocument);
    // Error check - use libSBML's document.printError to print to outputstream
    System.out.println("\n\nSBML Export Error Report");
    sbmlDocument.printErrors(System.out);
    return sbmlStr;
}

Example 7 with Parameter

use of org.sbml.jsbml.Parameter in project vcell by virtualcell.

the class MathModel_SBMLExporter method addGeometry.

private static void addGeometry(Model sbmlModel, MathModel vcMathModel) {
    SpatialModelPlugin mplugin = (SpatialModelPlugin) sbmlModel.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
    // Creates a geometry object via SpatialModelPlugin object.
    org.sbml.jsbml.ext.spatial.Geometry sbmlGeometry = mplugin.getGeometry();
    sbmlGeometry.setCoordinateSystem(GeometryKind.cartesian);
    Geometry vcGeometry = vcMathModel.getGeometry();
    // 
    // list of CoordinateComponents : 1 if geometry is 1-d, 2 if geometry is 2-d, 3 if geometry is 3-d
    // 
    int dimension = vcGeometry.getDimension();
    Extent vcExtent = vcGeometry.getExtent();
    Origin vcOrigin = vcGeometry.getOrigin();
    // add x coordinate component
    CoordinateComponent coordCompX = sbmlGeometry.createCoordinateComponent();
    coordCompX.setSpatialId("CoordCompX");
    coordCompX.setType(CoordinateKind.cartesianX);
    Boundary minX = coordCompX.getBoundaryMaximum();
    minX.setSpatialId("Xmin");
    minX.setValue(vcOrigin.getX());
    Boundary maxX = coordCompX.getBoundaryMaximum();
    maxX.setSpatialId("Xmax");
    maxX.setValue(vcOrigin.getX() + (vcExtent.getX()));
    Parameter parameterX = sbmlModel.createParameter();
    // note for exporting BioModels rather than MathModels, get ReservedSymbol from Model with Role of ReservedSymbolRole.X
    parameterX.setId(ReservedVariable.X.getName());
    SpatialSymbolReference coordXSpatialRef = new SpatialSymbolReference();
    coordXSpatialRef.setSpatialRef(coordCompX.getSpatialId());
    SpatialParameterPlugin parameterXSpatialPlugin = (SpatialParameterPlugin) parameterX.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
    parameterXSpatialPlugin.setParamType(coordXSpatialRef);
    // add y coordinate component
    if (dimension == 2 || dimension == 3) {
        CoordinateComponent coordCompY = sbmlGeometry.createCoordinateComponent();
        coordCompY.setSpatialId("CoordCompY");
        coordCompY.setType(CoordinateKind.cartesianY);
        Boundary minY = coordCompY.getBoundaryMinimum();
        minY.setId("Ymin");
        minY.setValue(vcOrigin.getY());
        Boundary maxY = coordCompY.getBoundaryMaximum();
        maxY.setId("Ymax");
        maxY.setValue(vcOrigin.getY() + (vcExtent.getY()));
        Parameter parameterY = sbmlModel.createParameter();
        // note for exporting BioModels rather than MathModels, get ReservedSymbol from Model with Role of ReservedSymbolRole.Y
        parameterY.setId(ReservedVariable.Y.getName());
        SpatialSymbolReference coordYSpatialRef = new SpatialSymbolReference();
        coordYSpatialRef.setSpatialRef(coordCompY.getSpatialId());
        SpatialParameterPlugin parameterYSpatialPlugin = (SpatialParameterPlugin) parameterY.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
        parameterYSpatialPlugin.setParamType(coordYSpatialRef);
    }
    // add z coordinate component
    if (dimension == 3) {
        CoordinateComponent coordCompZ = sbmlGeometry.createCoordinateComponent();
        coordCompZ.setSpatialId("CoordCompZ");
        coordCompZ.setType(CoordinateKind.cartesianZ);
        Boundary minZ = coordCompZ.getBoundaryMinimum();
        minZ.setId("Zmin");
        minZ.setValue(vcOrigin.getZ());
        Boundary maxZ = coordCompZ.getBoundaryMaximum();
        maxZ.setId("Zmax");
        maxZ.setValue(vcOrigin.getZ() + (vcExtent.getZ()));
        Parameter parameterZ = sbmlModel.createParameter();
        // note for exporting BioModels rather than MathModels, get ReservedSymbol from Model with Role of ReservedSymbolRole.Y
        parameterZ.setId(ReservedVariable.Z.getName());
        SpatialSymbolReference coordZSpatialRef = new SpatialSymbolReference();
        coordZSpatialRef.setSpatialRef(coordCompZ.getSpatialId());
        SpatialParameterPlugin parameterZSpatialPlugin = (SpatialParameterPlugin) parameterZ.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
        parameterZSpatialPlugin.setParamType(coordZSpatialRef);
    }
    // 
    // list of domain types : subvolumes and surface classes from VC
    // Also create compartments - one compartment for each geometryClass. set id and spatialDimension based on type of geometryClass.
    // 
    boolean bAnalyticGeom = false;
    boolean bImageGeom = false;
    GeometryClass[] vcGeomClasses = vcGeometry.getGeometryClasses();
    int numVCGeomClasses = vcGeomClasses.length;
    for (int i = 0; i < numVCGeomClasses; i++) {
        DomainType domainType = sbmlGeometry.createDomainType();
        domainType.setId(vcGeomClasses[i].getName());
        if (vcGeomClasses[i] instanceof SubVolume) {
            if (((SubVolume) vcGeomClasses[i]) instanceof AnalyticSubVolume) {
                bAnalyticGeom = true;
            } else if (((SubVolume) vcGeomClasses[i]) instanceof ImageSubVolume) {
                bImageGeom = true;
            }
            domainType.setSpatialDimensions(3);
        } else if (vcGeomClasses[i] instanceof SurfaceClass) {
            domainType.setSpatialDimensions(2);
        }
    }
    // 
    // list of domains, adjacent domains : from VC geometricRegions
    // 
    GeometrySurfaceDescription vcGSD = vcGeometry.getGeometrySurfaceDescription();
    if (vcGSD.getRegionImage() == null) {
        try {
            vcGSD.updateAll();
        } catch (Exception e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Unable to generate region images for geometry");
        }
    }
    GeometricRegion[] vcGeometricRegions = vcGSD.getGeometricRegions();
    ISize sampleSize = vcGSD.getVolumeSampleSize();
    int numX = sampleSize.getX();
    int numY = sampleSize.getY();
    int numZ = sampleSize.getZ();
    double ox = vcOrigin.getX();
    double oy = vcOrigin.getY();
    double oz = vcOrigin.getZ();
    RegionInfo[] regionInfos = vcGSD.getRegionImage().getRegionInfos();
    Compartment compartment = null;
    for (int i = 0; i < vcGeometricRegions.length; i++) {
        // domains
        Domain domain = sbmlGeometry.createDomain();
        domain.setId(vcGeometricRegions[i].getName());
        compartment = sbmlModel.createCompartment();
        compartment.setId("compartment" + i);
        if (vcGeometricRegions[i] instanceof VolumeGeometricRegion) {
            domain.setDomainType(((VolumeGeometricRegion) vcGeometricRegions[i]).getSubVolume().getName());
            // domain.setImplicit(false);
            compartment.setSpatialDimensions(3);
            InteriorPoint interiorPt = domain.createInteriorPoint();
            int regionID = ((VolumeGeometricRegion) vcGeometricRegions[i]).getRegionID();
            boolean bFound = false;
            int regInfoIndx = 0;
            for (int j = 0; j < regionInfos.length; j++) {
                regInfoIndx = j;
                if (regionInfos[j].getRegionIndex() == regionID) {
                    int volIndx = 0;
                    for (int z = 0; z < numZ && !bFound; z++) {
                        for (int y = 0; y < numY && !bFound; y++) {
                            for (int x = 0; x < numX && !bFound; x++) {
                                if (regionInfos[j].isIndexInRegion(volIndx)) {
                                    bFound = true;
                                    double unit_z = (numZ > 1) ? ((double) z) / (numZ - 1) : 0.5;
                                    double coordZ = oz + vcExtent.getZ() * unit_z;
                                    double unit_y = (numY > 1) ? ((double) y) / (numY - 1) : 0.5;
                                    double coordY = oy + vcExtent.getY() * unit_y;
                                    double unit_x = (numX > 1) ? ((double) x) / (numX - 1) : 0.5;
                                    double coordX = ox + vcExtent.getX() * unit_x;
                                    interiorPt.setCoord1(coordX);
                                    interiorPt.setCoord2(coordY);
                                    interiorPt.setCoord3(coordZ);
                                }
                                volIndx++;
                            }
                        // end - for x
                        }
                    // end - for y
                    }
                // end - for z
                }
            // end if
            }
            // end for regionInfos
            if (!bFound) {
                throw new RuntimeException("Unable to find interior point for region '" + regionInfos[regInfoIndx].toString());
            }
        } else if (vcGeometricRegions[i] instanceof SurfaceGeometricRegion) {
            SurfaceGeometricRegion vcSurfaceGeomReg = (SurfaceGeometricRegion) vcGeometricRegions[i];
            GeometricRegion geomRegion0 = vcSurfaceGeomReg.getAdjacentGeometricRegions()[0];
            GeometricRegion geomRegion1 = vcSurfaceGeomReg.getAdjacentGeometricRegions()[1];
            SurfaceClass surfaceClass = vcGSD.getSurfaceClass(((VolumeGeometricRegion) geomRegion0).getSubVolume(), ((VolumeGeometricRegion) geomRegion1).getSubVolume());
            domain.setDomainType(surfaceClass.getName());
            // domain.setImplicit(true);
            compartment.setSpatialDimensions(2);
            // adjacent domains : 2 adjacent domain objects for each surfaceClass in VC.
            // adjacent domain 1
            AdjacentDomains adjDomain = sbmlGeometry.createAdjacentDomain();
            adjDomain.setId(TokenMangler.mangleToSName(vcSurfaceGeomReg.getName() + "_" + geomRegion0.getName()));
            adjDomain.setDomain1(vcSurfaceGeomReg.getName());
            adjDomain.setDomain2(geomRegion0.getName());
            // adjacent domain 2
            adjDomain = sbmlGeometry.createAdjacentDomain();
            adjDomain.setId(TokenMangler.mangleToSName(vcSurfaceGeomReg.getName() + "_" + geomRegion1.getName()));
            adjDomain.setDomain1(vcSurfaceGeomReg.getName());
            adjDomain.setDomain2(geomRegion1.getName());
        }
        // 
        // Mathmodel does not have structureMapping, hence creating compartmentMapping while creating domains.
        // @TODO : how to assign unitSize for compartmentMapping?
        // 
        SpatialCompartmentPlugin cplugin = (SpatialCompartmentPlugin) compartment.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
        CompartmentMapping compMapping = cplugin.getCompartmentMapping();
        String compMappingId = TokenMangler.mangleToSName(domain.getDomainType() + "_" + compartment.getId());
        compMapping.setId(compMappingId);
        compMapping.setDomainType(TokenMangler.mangleToSName(domain.getDomainType()));
    // try {
    // compMapping.setUnitSize(1.0);
    // } catch (ExpressionException e) {
    // e.printStackTrace(System.out);
    // throw new RuntimeException("Unable to create compartment mapping for structureMapping '" + compMapping.getId() +"' : " + e.getMessage());
    // }
    }
    AnalyticGeometry sbmlAnalyticGeom = null;
    SampledFieldGeometry sbmlSFGeom = null;
    // both image and analytic subvolumes?? == not handled in SBML at this time.
    if (bAnalyticGeom && !bImageGeom) {
        sbmlAnalyticGeom = sbmlGeometry.createAnalyticGeometry();
        sbmlAnalyticGeom.setId(TokenMangler.mangleToSName(vcGeometry.getName()));
    } else if (bImageGeom && !bAnalyticGeom) {
        // assuming image based geometry if not analytic geometry
        sbmlSFGeom = sbmlGeometry.createSampledFieldGeometry();
        sbmlSFGeom.setId(TokenMangler.mangleToSName(vcGeometry.getName()));
    } else if (bAnalyticGeom && bImageGeom) {
        throw new RuntimeException("Export to SBML of a combination of Image-based and Analytic geometries is not supported yet.");
    } else if (!bAnalyticGeom && !bImageGeom) {
        throw new RuntimeException("Unknown geometry type.");
    }
    // 
    for (int i = 0; i < vcGeomClasses.length; i++) {
        if (vcGeomClasses[i] instanceof AnalyticSubVolume) {
            // add analytiVols to sbmlAnalyticGeometry
            if (sbmlAnalyticGeom != null) {
                AnalyticVolume analyticVol = sbmlAnalyticGeom.createAnalyticVolume();
                analyticVol.setId(vcGeomClasses[i].getName());
                analyticVol.setDomainType(vcGeomClasses[i].getName());
                analyticVol.setFunctionType(FunctionKind.layered);
                analyticVol.setOrdinal(i);
                Expression expr = ((AnalyticSubVolume) vcGeomClasses[i]).getExpression();
                try {
                    String mathMLStr = ExpressionMathMLPrinter.getMathML(expr, true);
                    ASTNode mathMLNode = ASTNode.readMathMLFromString(mathMLStr);
                    analyticVol.setMath(mathMLNode);
                } catch (Exception e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException("Error converting VC subvolume expression to mathML" + e.getMessage());
                }
            } else {
                throw new RuntimeException("SBML AnalyticGeometry is null.");
            }
        } else if (vcGeomClasses[i] instanceof ImageSubVolume) {
            // add sampledVols to sbmlSFGeometry
            if (sbmlSFGeom != null) {
                SampledVolume sampledVol = sbmlSFGeom.createSampledVolume();
                sampledVol.setId(vcGeomClasses[i].getName());
                sampledVol.setDomainType(vcGeomClasses[i].getName());
                sampledVol.setSampledValue(((ImageSubVolume) vcGeomClasses[i]).getPixelValue());
            } else {
                throw new RuntimeException("SBML SampledFieldGeometry is null.");
            }
        }
    }
    if (sbmlSFGeom != null) {
        // add sampledField to sampledFieldGeometry
        SampledField sampledField = sbmlGeometry.createSampledField();
        VCImage vcImage = vcGeometry.getGeometrySpec().getImage();
        sampledField.setId(vcImage.getName());
        sampledField.setNumSamples1(vcImage.getNumX());
        if (vcImage.getNumY() > 1) {
            sampledField.setNumSamples2(vcImage.getNumY());
        }
        if (vcImage.getNumZ() > 1) {
            sampledField.setNumSamples3(vcImage.getNumZ());
        }
        sampledField.setInterpolationType(InterpolationKind.nearestneighbor);
        sampledField.setDataType(DataKind.UINT8);
        // add image from vcGeometrySpec to sampledField.
        try {
            StringBuffer sb = new StringBuffer();
            byte[] imagePixelsBytes = vcImage.getPixelsCompressed();
            for (int i = 0; i < imagePixelsBytes.length; i++) {
                int uint8_sample = ((int) imagePixelsBytes[i]) & 0xff;
                sb.append(uint8_sample + " ");
            }
            sampledField.setSamplesLength(vcImage.getNumXYZ());
            sampledField.setSamples(sb.toString().trim());
        } catch (ImageException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Unable to export image from VCell to SBML : " + e.getMessage());
        }
    }
}

Example 8 with Parameter

use of org.sbml.jsbml.Parameter in project vcell by virtualcell.

the class SBMLImporter method substituteGlobalParamRulesInPlace.

/**
 * substituteGlobalParamRulesInPlace:
 *
 * @param sbmlExpr
 * @param expandedExpr
 * @throws ExpressionException
 */
private void substituteGlobalParamRulesInPlace(Expression sbmlExpr, boolean bReplaceValues) throws ExpressionException {
    boolean bParamChanged = true;
    while (bParamChanged) {
        bParamChanged = false;
        String[] symbols = sbmlExpr.getSymbols();
        for (int i = 0; symbols != null && i < symbols.length; i++) {
            Parameter sbmlParam = sbmlModel.getParameter(symbols[i]);
            if (sbmlParam != null) {
                Expression paramExpression = getValueFromAssignmentRule(sbmlParam.getId());
                if (paramExpression != null) {
                    sbmlExpr.substituteInPlace(new Expression(sbmlParam.getId()), paramExpression);
                    bParamChanged = true;
                } else if (bReplaceValues) {
                    sbmlExpr.substituteInPlace(new Expression(sbmlParam.getId()), new Expression(sbmlParam.getValue()));
                }
            }
        }
    }
}

Example 9 with Parameter

use of org.sbml.jsbml.Parameter in project vcell by virtualcell.

the class SBMLImporter method checkIdentifiersNameLength.

private void checkIdentifiersNameLength() throws Exception {
    // Check compartment name lengths
    ListOf listofIds = sbmlModel.getListOfCompartments();
    boolean bLongCompartmentName = false;
    SBase issueSource = null;
    for (int i = 0; i < sbmlModel.getNumCompartments(); i++) {
        Compartment compartment = (Compartment) listofIds.get(i);
        String compartmentName = compartment.getId();
        if (compartmentName.length() > 64) {
            bLongCompartmentName = true;
            issueSource = compartment;
        }
    }
    // Check species name lengths
    listofIds = sbmlModel.getListOfSpecies();
    boolean bLongSpeciesName = false;
    for (int i = 0; i < sbmlModel.getNumSpecies(); i++) {
        org.sbml.jsbml.Species species = (org.sbml.jsbml.Species) listofIds.get(i);
        String speciesName = species.getId();
        if (speciesName.length() > 64) {
            bLongSpeciesName = true;
            issueSource = species;
        }
    }
    // Check parameter name lengths
    listofIds = sbmlModel.getListOfParameters();
    boolean bLongParameterName = false;
    for (int i = 0; i < sbmlModel.getNumParameters(); i++) {
        Parameter param = (Parameter) listofIds.get(i);
        String paramName = param.getId();
        if (paramName.length() > 64) {
            bLongParameterName = true;
            issueSource = param;
        }
    }
    // Check reaction name lengths
    listofIds = sbmlModel.getListOfReactions();
    boolean bLongReactionName = false;
    for (int i = 0; i < sbmlModel.getNumReactions(); i++) {
        Reaction rxn = (Reaction) listofIds.get(i);
        String rxnName = rxn.getId();
        if (rxnName.length() > 64) {
            bLongReactionName = true;
            issueSource = rxn;
        }
    }
    if (bLongCompartmentName || bLongSpeciesName || bLongParameterName || bLongReactionName) {
        String warningMsg = "WARNING: The imported model has one or more ";
        if (bLongCompartmentName) {
            warningMsg = warningMsg + "compartments, ";
        }
        if (bLongSpeciesName) {
            warningMsg = warningMsg + "species, ";
        }
        if (bLongParameterName) {
            warningMsg = warningMsg + "global parameters, ";
        }
        if (bLongReactionName) {
            warningMsg = warningMsg + "reactions ";
        }
        warningMsg = warningMsg + "that have ids/names that are longer than 64 characters. \n\nUser is STRONGLY recommeded to shorten " + "the names to avoid problems with the length of expressions these names might be used in.";
        localIssueList.add(new Issue(new SBMLIssueSource(issueSource), issueContext, IssueCategory.SBMLImport_UnsupportedAttributeOrElement, warningMsg, Issue.SEVERITY_WARNING));
    // logger.sendMessage(VCLogger.Priority.MediumPriority,
    // VCLogger.ErrorType.UnsupportedConstruct, warningMsg);
    }
}

Example 10 with Parameter

use of org.sbml.jsbml.Parameter in project vcell by virtualcell.

the class ModelParameterInputPanel method setModel.

public void setModel(VCellModel vCellModel) {
    this.vCellModel = vCellModel;
    parameterTable.clear();
    removeAll();
    GridBagConstraints c = new GridBagConstraints();
    c.fill = GridBagConstraints.HORIZONTAL;
    c.gridy = 0;
    for (Parameter parameter : vCellModel.getParameters()) {
        addParameterInput(parameter, vCellModel, c);
    }
    // Add empty panel to occupy any extra space at bottom (pushes components to the top of the panel)
    c.gridy++;
    c.weighty = 1.0;
    add(new JPanel(), c);
    revalidate();
}