Examples with KeyValue org.vcell.util.document.KeyValue used on opensource projects

Example 11 with KeyValue

use of org.vcell.util.document.KeyValue 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 12 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class XmlReader method getGroupAccess.

/**
 * This method returns a GroupAccess object from an XML format.
 * Creation date: (5/23/2003 7:27:10 PM)
 * @return cbit.vcell.server.GroupAccess
 * @param xmlGroup org.jdom.Element
 */
private GroupAccess getGroupAccess(Element xmlGroup) {
    // guess the type of group
    String temp = xmlGroup.getAttributeValue(XMLTags.TypeAttrTag);
    java.math.BigDecimal type = new java.math.BigDecimal(temp);
    if (type.equals(GroupAccess.GROUPACCESS_ALL)) {
        // Type ALL
        return new GroupAccessAll();
    } else if (type.equals(GroupAccess.GROUPACCESS_NONE)) {
        // Type NONE
        return new GroupAccessNone();
    } else {
        // Type SOME
        // Read attributes
        // *groupid
        temp = xmlGroup.getAttributeValue(XMLTags.TypeAttrTag);
        java.math.BigDecimal groupid = new java.math.BigDecimal(temp);
        // *hash
        temp = xmlGroup.getAttributeValue(XMLTags.HashAttrTag);
        java.math.BigDecimal hashcode = new java.math.BigDecimal(temp);
        // *users
        List<Element> userlist = xmlGroup.getChildren(XMLTags.UserTag, vcNamespace);
        User[] userArray = new User[userlist.size()];
        boolean[] booleanArray = new boolean[userlist.size()];
        int counter = 0;
        for (Element userElement : userlist) {
            String userid = unMangle(userElement.getAttributeValue(XMLTags.NameAttrTag));
            KeyValue key = new KeyValue(userElement.getAttributeValue(XMLTags.KeyValueAttrTag));
            boolean hidden = Boolean.valueOf(userElement.getAttributeValue(XMLTags.HiddenTag)).booleanValue();
            userArray[counter] = new User(userid, key);
            booleanArray[counter] = hidden;
            counter++;
        }
        // create and return the GroupAccess
        return new GroupAccessSome(groupid, hashcode, userArray, booleanArray);
    }
}

Example 13 with KeyValue

use of org.vcell.util.document.KeyValue 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;
}

Example 14 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class XmlReader method getReactant.

/**
 * This method returns a Reactant object from a XML representation.
 * Creation date: (5/4/2001 2:22:56 PM)
 * @return cbit.vcell.model.Reactant
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
private Reactant getReactant(Element param, ReactionStep reaction, Model model) throws XmlParseException {
    // retrieve the key if there is one
    String keystring = param.getAttributeValue(XMLTags.KeyValueAttrTag);
    KeyValue key = null;
    if (keystring != null && keystring.length() > 0 && this.readKeysFlag) {
        key = new KeyValue(keystring);
    }
    String speccontref = unMangle(param.getAttributeValue(XMLTags.SpeciesContextRefAttrTag));
    SpeciesContext speccont = model.getSpeciesContext(speccontref);
    if (speccont == null) {
        throw new XmlParseException("The reference to the SpecieContext " + speccontref + " for a SimpleReaction could not be resolved!");
    }
    // Retrieve Stoichiometry
    int stoch = 1;
    org.jdom.Attribute tempArg = param.getAttribute(XMLTags.StoichiometryAttrTag);
    if (tempArg != null) {
        String tempValue = tempArg.getValue();
        if (tempValue.length() > 0)
            stoch = Integer.parseInt(tempValue);
    // param.getAttributeValue(XMLTags.StoichiometryAttrTag));
    }
    // return new Reactant(newkey, reaction, speccont, stoch);
    return new Reactant(key, reaction, speccont, stoch);
}

Example 15 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class XmlReader method getCatalyst.

/**
 * This method returns a Catalyst object from a XML representation.
 * Creation date: (5/4/2001 2:22:56 PM)
 * @return cbit.vcell.model.Product
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
private Catalyst getCatalyst(Element param, ReactionStep reaction, Model model) throws XmlParseException {
    // 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);
    }
    String speccontref = unMangle(param.getAttributeValue(XMLTags.SpeciesContextRefAttrTag));
    SpeciesContext speccont = model.getSpeciesContext(speccontref);
    if (speccont == null) {
        throw new XmlParseException("The reference to the SpecieContext " + speccontref + " for a Catalyst could not be resolved!");
    }
    return new Catalyst(key, reaction, speccont);
}