Examples with PropertyVetoException java.beans.PropertyVetoException used on opensource projects

Example 31 with PropertyVetoException

use of java.beans.PropertyVetoException in project vcell by virtualcell.

the class XmlReader method getGeometry.

/**
 * This method returns a Geometry object from a XML representation.
 * Creation date: (4/26/2001 12:12:18 PM)
 * @return cbit.vcell.geometry.Geometry
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
public Geometry getGeometry(Element param) throws XmlParseException {
    // Get the Extent object
    Extent newextent = getExtent(param.getChild(XMLTags.ExtentTag, vcNamespace));
    // Get VCimage information
    VCImage newimage = null;
    if (param.getChild(XMLTags.ImageTag, vcNamespace) != null) {
        try {
            newimage = getVCImage(param.getChild(XMLTags.ImageTag, vcNamespace), newextent);
        } catch (Throwable e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Get attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    int newdimension = Integer.parseInt(param.getAttributeValue(XMLTags.DimensionAttrTag));
    // Get Version
    Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    // Try to construct the geometry upon four different cases
    Geometry newgeometry = null;
    if (version != null && newimage != null) {
        newgeometry = new Geometry(version, newimage);
    } else if (version != null) {
        newgeometry = new Geometry(version, newdimension);
    } else if (newimage != null) {
        newgeometry = new Geometry(name, newimage);
    } else {
        newgeometry = new Geometry(name, newdimension);
    }
    // set attributes
    try {
        if (!newgeometry.getName().equalsIgnoreCase(name)) {
            newgeometry.setName(name);
        }
        // String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag);
        // if (annotation!=null) {
        // newgeometry.setDescription( unMangle(annotation) );
        // }
        // Add annotation
        String annotation = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotation != null && annotation.length() > 0) {
            newgeometry.setDescription(unMangle(annotation));
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException occurred when setting the name " + name + " to a Geometry object!", e);
    }
    // Add the Extent
    try {
        newgeometry.getGeometrySpec().setExtent(newextent);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException occurred while trying to set the Extent for the Geometry " + name, e);
    }
    // Add the Origin
    newgeometry.getGeometrySpec().setOrigin(getOrigin(param.getChild(XMLTags.OriginTag, vcNamespace)));
    // Add the SubVolumes
    List<Element> children = param.getChildren(XMLTags.SubVolumeTag, vcNamespace);
    SubVolume[] newsubvolumes = new SubVolume[children.size()];
    int subvolumeCounter = 0;
    for (Element child : children) {
        newsubvolumes[subvolumeCounter] = getSubVolume(child);
        subvolumeCounter++;
    }
    try {
        newgeometry.getGeometrySpec().setSubVolumes(newsubvolumes);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException was generated when ading the subvolumes to the Geometry " + name, e);
    }
    if (newgeometry.getDimension() > 0) {
        // Add SurfaceClasses
        List<Element> surfaceClassChildren = param.getChildren(XMLTags.SurfaceClassTag, vcNamespace);
        SurfaceClass[] newSurfaceClassArr = new SurfaceClass[surfaceClassChildren.size()];
        int surfClassCounter = 0;
        for (Element surfClassChild : surfaceClassChildren) {
            newSurfaceClassArr[surfClassCounter] = getSurfaceClass(surfClassChild, newgeometry);
            surfClassCounter++;
        }
        try {
            newgeometry.getGeometrySurfaceDescription().setSurfaceClasses(newSurfaceClassArr);
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace();
            throw new XmlParseException("A PropertyVetoException was generated when ading the subvolumes to the Geometry " + name, e);
        }
    }
    // read Filaments (if any)
    Iterator<Element> iterator = param.getChildren(XMLTags.FilamentTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempElement = iterator.next();
        String filname = unMangle(tempElement.getAttributeValue(XMLTags.NameAttrTag));
        Iterator<Element> curveiterator = tempElement.getChildren().iterator();
        while (curveiterator.hasNext()) {
            ControlPointCurve curve = getControlPointCurve(curveiterator.next());
            newgeometry.getGeometrySpec().getFilamentGroup().addCurve(filname, curve);
        }
    }
    // read Surface description (if any)
    Element sd = param.getChild(XMLTags.SurfaceDescriptionTag, vcNamespace);
    if (sd != null) {
        GeometrySurfaceDescription dummy = getGeometrySurfaceDescription(sd, newgeometry);
    }
    try {
        newgeometry.precomputeAll(new GeometryThumbnailImageFactoryAWT(), false, false);
    } catch (GeometryException e) {
        e.printStackTrace(System.out);
    } catch (ImageException e) {
        e.printStackTrace(System.out);
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
    }
    return newgeometry;
}

Example 32 with PropertyVetoException

use of java.beans.PropertyVetoException in project vcell by virtualcell.

the class XmlReader method getMathModel.

/*
public RateRuleVariable[] getRateRuleVariables(Element rateRuleVarsElement, Model model) throws XmlParseException  {
	Iterator<Element> rateRuleVarsIterator = rateRuleVarsElement.getChildren(XMLTags.RateRuleVariableTag, vcNamespace).iterator();
	Vector<RateRuleVariable> rateRuleVarsVector = new Vector<RateRuleVariable>();
	while (rateRuleVarsIterator.hasNext()) {
		Element rrvElement = (Element) rateRuleVarsIterator.next();

		RateRuleVariable newRateRuleVar = null;
		try {
			String rrvName = unMangle(rrvElement.getAttributeValue(XMLTags.NameAttrTag));
		    String rrvStructureName = unMangle(rrvElement.getAttributeValue(XMLTags.StructureAttrTag));
		    // structure can be null
		    Structure rrvStructure = null;
		    if (rrvStructureName != null) {
		    	rrvStructure = (Structure) model.getStructure(rrvStructureName);
		    }
//		    if (structureref == null) {
//		    	throw new XmlParseException("The structure " + rrvStructureName + "could not be resolved!");
//		    }
		    String rrvRoleStr = rrvElement.getAttributeValue(XMLTags.ParamRoleAttrTag);
		    int rrvRole = RateRuleVariable.getParamRoleFromDesc(rrvRoleStr);
		    Element rrvParamElement = rrvElement.getChild(XMLTags.ParameterTag, vcNamespace);
		    ModelParameter rrvParameter = getModelParameter(rrvParamElement, model);
		    newRateRuleVar = new RateRuleVariable(rrvName, rrvStructure, rrvParameter, rrvRole);
			newRateRuleVar.bind();
		} catch (ExpressionBindingException e) {
			e.printStackTrace(System.out);
			throw new XmlParseException(e.getMessage());
		}
		if (newRateRuleVar != null) {
			rateRuleVarsVector.add(newRateRuleVar);
		}
	}
	
	return ((RateRuleVariable[])BeanUtils.getArray(rateRuleVarsVector, RateRuleVariable.class));
}
*/
/**
 * This method returns a MathModel object from a XML Element.
 * Creation date: (3/13/2001 12:35:00 PM)
 * @return cbit.vcell.mathmodel.MathModel
 * @param param org.jdom.Element
 */
public MathModel getMathModel(Element param) throws XmlParseException {
    // Create it
    // set Metadata (version), if any
    Version versionObject = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    MathModel mathmodel = new MathModel(versionObject);
    // Set attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    try {
        mathmodel.setName(name);
        // String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag);
        // if (annotation!=null) {
        // mathmodel.setDescription(unMangle(annotation));
        // }
        // Add annotation
        String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotationText != null && annotationText.length() > 0) {
            mathmodel.setDescription(unMangle(annotationText));
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("An error occurred while trying to set the name " + param.getAttributeValue(XMLTags.NameAttrTag) + "to a MathModel!", e);
    }
    // set Geometry (if any)
    Element tempElem = param.getChild(XMLTags.GeometryTag, vcNamespace);
    Geometry tempGeometry = getGeometry(tempElem);
    // set MathDescription
    tempElem = param.getChild(XMLTags.MathDescriptionTag, vcNamespace);
    MathDescription mathDesc = getMathDescription(tempElem, tempGeometry);
    if (tempElem != null) {
        mathmodel.setMathDescription(mathDesc);
    } else {
        throw new XmlParseException("MathDescription missing in this MathModel!");
    }
    // set output functions (outputfunctionContext)
    Element outputFunctionsElement = param.getChild(XMLTags.OutputFunctionsTag, vcNamespace);
    if (outputFunctionsElement != null) {
        ArrayList<AnnotatedFunction> outputFunctions = getOutputFunctions(outputFunctionsElement);
        try {
            // construct OutputFnContext from mathmodel and add output functions that were read in from XML.
            OutputFunctionContext outputFnContext = mathmodel.getOutputFunctionContext();
            for (AnnotatedFunction outputFunction : outputFunctions) {
                outputFnContext.addOutputFunction(outputFunction);
            }
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException(e);
        }
    }
    // Set simulations contexts (if any)
    List<Element> childList = param.getChildren(XMLTags.SimulationTag, vcNamespace);
    Simulation[] simList = new Simulation[childList.size()];
    int simCounter = 0;
    for (Element simElement : childList) {
        simList[simCounter] = getSimulation(simElement, mathDesc);
        simCounter++;
    }
    try {
        mathmodel.setSimulations(simList);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException occurred when adding the Simulations to the MathModel " + name, e);
    }
    return mathmodel;
}

Example 33 with PropertyVetoException

use of java.beans.PropertyVetoException in project vcell by virtualcell.

the class XmlReader method getMeshSpecification.

/**
 * This method returns a MeshSpecification object from a XML Element.
 * Creation date: (5/22/2001 12:05:21 PM)
 * @return cbit.vcell.mesh.MeshSpecification
 * @param param org.jdom.Element
 */
private MeshSpecification getMeshSpecification(Element param, Geometry geometry) throws XmlParseException {
    // *** create new MeshSpecification ***
    MeshSpecification meshSpec = new MeshSpecification(geometry);
    // get ISize
    Element size = param.getChild(XMLTags.SizeTag, vcNamespace);
    int x = Integer.parseInt(size.getAttributeValue(XMLTags.XAttrTag));
    int y = Integer.parseInt(size.getAttributeValue(XMLTags.YAttrTag));
    int z = Integer.parseInt(size.getAttributeValue(XMLTags.ZAttrTag));
    ISize newsize = new ISize(x, y, z);
    // set ISize
    try {
        meshSpec.setSamplingSize(newsize);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException was fired when setting the ISize object to a new MeshSpecification", e);
    }
    return meshSpec;
}

Example 34 with PropertyVetoException

use of java.beans.PropertyVetoException in project vcell by virtualcell.

the class XmlReader method getImageSubVolume.

/**
 * This method returns an ImageSubVolume object from a XML representation.
 * Creation date: (5/1/2001 5:26:17 PM)
 * @return cbit.vcell.geometry.ImageSubVolume
 * @param param org.jdom.Element
 */
private ImageSubVolume getImageSubVolume(Element param) throws XmlParseException {
    // retrieve the attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    int handle = Integer.parseInt(param.getAttributeValue(XMLTags.HandleAttrTag));
    int imagePixelValue = Integer.parseInt(param.getAttributeValue(XMLTags.ImagePixelValueTag));
    // Get the PixelClass from image (image should be a sibling of this subVolume element)
    Element imageElement = ((Element) param.getParent()).getChild(XMLTags.ImageTag, vcNamespace);
    if (imageElement == null) {
        throw new XmlParseException("image not found in geometry corresponding to ImageSubVolume");
    }
    List<Element> pixelClassList = imageElement.getChildren(XMLTags.PixelClassTag, vcNamespace);
    VCPixelClass pixelClass = null;
    for (Element pixelClassElement : pixelClassList) {
        VCPixelClass pc = getPixelClass(pixelClassElement);
        if (pc.getPixel() == imagePixelValue) {
            pixelClass = pc;
        }
    }
    if (pixelClass == null) {
        throw new XmlParseException("image pixelclass(pixel=" + imagePixelValue + ") not found while creating ImageSubVolume " + name);
    }
    // retrieve the key if there is one
    KeyValue key = null;
    String stringkey = param.getAttributeValue(XMLTags.KeyValueAttrTag);
    if (stringkey != null && stringkey.length() > 0 && this.readKeysFlag) {
        key = new KeyValue(stringkey);
    }
    // Create the new Image SubVolume
    ImageSubVolume newsubvolume = new ImageSubVolume(key, pixelClass, handle);
    // set name
    try {
        newsubvolume.setName(name);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A propertyVetoException was generated when setting the name " + name + " to an ImageSubvolume object!", e);
    }
    return newsubvolume;
}

Example 35 with PropertyVetoException

use of java.beans.PropertyVetoException in project vcell by virtualcell.

the class XmlReader method getFluxReaction.

/**
 * This method returns a FluxReaction object from a XML element.
 * Creation date: (3/16/2001 11:52:02 AM)
 * @return cbit.vcell.model.FluxReaction
 * @param param org.jdom.Element
 * @throws XmlParseException
 * @throws PropertyVetoException
 * @throws ModelException
 * @throws Exception
 */
private FluxReaction getFluxReaction(Element param, Model model) throws XmlParseException, PropertyVetoException {
    // retrieve the key if there is one
    KeyValue key = null;
    String keystring = param.getAttributeValue(XMLTags.KeyValueAttrTag);
    if (keystring != null && keystring.length() > 0 && this.readKeysFlag) {
        key = new KeyValue(keystring);
    }
    // resolve reference to the Membrane
    String structureName = unMangle(param.getAttributeValue(XMLTags.StructureAttrTag));
    Membrane structureref = (Membrane) model.getStructure(structureName);
    if (structureref == null) {
        throw new XmlParseException("The membrane " + structureName + " could not be resolved in the dictionnary!");
    }
    // -- Instantiate new FluxReaction --
    FluxReaction fluxreaction = null;
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String reversibleAttributeValue = param.getAttributeValue(XMLTags.ReversibleAttrTag);
    boolean bReversible = true;
    if (reversibleAttributeValue != null) {
        if (Boolean.TRUE.toString().equals(reversibleAttributeValue)) {
            bReversible = true;
        } else if (Boolean.FALSE.toString().equals(reversibleAttributeValue)) {
            bReversible = false;
        } else {
            throw new RuntimeException("unexpected value " + reversibleAttributeValue + " for reversible flag for reaction " + name);
        }
    }
    try {
        fluxreaction = new FluxReaction(model, structureref, key, name, bReversible);
        fluxreaction.setModel(model);
    } catch (Exception e) {
        e.printStackTrace();
        throw new XmlParseException("An exception occurred while trying to create the FluxReaction " + name, e);
    }
    // resolve reference to the fluxCarrier
    if (param.getAttribute(XMLTags.FluxCarrierAttrTag) != null) {
        String speciesname = unMangle(param.getAttributeValue(XMLTags.FluxCarrierAttrTag));
        Species specieref = model.getSpecies(speciesname);
        if (specieref != null) {
            Feature insideFeature = model.getStructureTopology().getInsideFeature(structureref);
            try {
                if (insideFeature != null) {
                    SpeciesContext insideSpeciesContext = model.getSpeciesContext(specieref, insideFeature);
                    fluxreaction.addProduct(insideSpeciesContext, 1);
                }
                Feature outsideFeature = model.getStructureTopology().getOutsideFeature(structureref);
                if (outsideFeature != null) {
                    SpeciesContext outsideSpeciesContext = model.getSpeciesContext(specieref, outsideFeature);
                    fluxreaction.addReactant(outsideSpeciesContext, 1);
                }
            } catch (ModelException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException(e.getMessage());
            }
        }
    }
    // Annotation
    // String rsAnnotation = null;
    // String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
    // if (annotationText!=null && annotationText.length()>0) {
    // rsAnnotation = unMangle(annotationText);
    // }
    // fluxreaction.setAnnotation(rsAnnotation);
    // set the fluxOption
    String fluxOptionString = null;
    fluxOptionString = param.getAttributeValue(XMLTags.FluxOptionAttrTag);
    if (fluxOptionString != null && fluxOptionString.length() > 0) {
        try {
            if (fluxOptionString.equals(XMLTags.FluxOptionElectricalOnly)) {
                fluxreaction.setPhysicsOptions(FluxReaction.PHYSICS_ELECTRICAL_ONLY);
            } else if (fluxOptionString.equals(XMLTags.FluxOptionMolecularAndElectrical)) {
                fluxreaction.setPhysicsOptions(FluxReaction.PHYSICS_MOLECULAR_AND_ELECTRICAL);
            } else if (fluxOptionString.equals(XMLTags.FluxOptionMolecularOnly)) {
                fluxreaction.setPhysicsOptions(FluxReaction.PHYSICS_MOLECULAR_ONLY);
            }
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("A propertyVetoException was fired when setting the fluxOption to the flux reaction " + name, e);
        }
    }
    // Add Reactants, if any
    try {
        Iterator<Element> iterator = param.getChildren(XMLTags.ReactantTag, vcNamespace).iterator();
        while (iterator.hasNext()) {
            Element temp = iterator.next();
            // Add Reactant to this SimpleReaction
            fluxreaction.addReactionParticipant(getReactant(temp, fluxreaction, model));
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("Error adding a reactant to the reaction " + name + " : " + e.getMessage());
    }
    // Add Products, if any
    try {
        Iterator<Element> iterator = param.getChildren(XMLTags.ProductTag, vcNamespace).iterator();
        while (iterator.hasNext()) {
            Element temp = iterator.next();
            // Add Product to this simplereaction
            fluxreaction.addReactionParticipant(getProduct(temp, fluxreaction, model));
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("Error adding a product to the reaction " + name + " : " + e.getMessage());
    }
    // Add Catalyst(Modifiers) (if there are)
    Iterator<Element> iterator = param.getChildren(XMLTags.CatalystTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element temp = iterator.next();
        fluxreaction.addReactionParticipant(getCatalyst(temp, fluxreaction, model));
    }
    // Add Kinetics
    fluxreaction.setKinetics(getKinetics(param.getChild(XMLTags.KineticsTag, vcNamespace), fluxreaction, model));
    // set the valence (for legacy support for "chargeCarrierValence" stored with reaction).
    String valenceString = null;
    try {
        valenceString = unMangle(param.getAttributeValue(XMLTags.FluxCarrierValenceAttrTag));
        if (valenceString != null && valenceString.length() > 0) {
            KineticsParameter chargeValenceParameter = fluxreaction.getKinetics().getChargeValenceParameter();
            if (chargeValenceParameter != null) {
                chargeValenceParameter.setExpression(new Expression(Integer.parseInt(unMangle(valenceString))));
            }
        }
    } catch (NumberFormatException e) {
        e.printStackTrace();
        throw new XmlParseException("A NumberFormatException was fired when setting the (integer) valence '" + valenceString + "' (integer) to the flux reaction " + name, e);
    }
    return fluxreaction;
}