Examples with Feature cbit.vcell.model.Feature used on opensource projects

Example 56 with Feature

use of cbit.vcell.model.Feature in project vcell by virtualcell.

the class XmlReader method getFeature.

/**
 * This method returns a Feature object (Structure) from a XML representation.
 * Creation date: (3/15/2001 6:12:36 PM)
 * @return cbit.vcell.model.Structure
 * @param param org.jdom.Element
 */
private Structure getFeature(Element param) throws XmlParseException {
    Feature newfeature = null;
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    // 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);
    }
    // ---Create the new feature---
    try {
        newfeature = new Feature(key, name);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("An error occurred while creating the feature " + param.getAttributeValue(XMLTags.NameAttrTag), e);
    }
    return newfeature;
}

Example 57 with Feature

use of cbit.vcell.model.Feature in project vcell by virtualcell.

the class XmlReader method getFeatureMapping.

/**
 * This method retuns a FeatureMapping object from a XML representation.
 * Creation date: (5/7/2001 4:12:03 PM)
 * @return cbit.vcell.mapping.FeatureMapping
 * @param param org.jdom.Element
 */
private FeatureMapping getFeatureMapping(Element param, SimulationContext simulationContext) throws XmlParseException {
    // Retrieve attributes
    String featurename = unMangle(param.getAttributeValue(XMLTags.FeatureAttrTag));
    String geometryClassName = param.getAttributeValue(XMLTags.SubVolumeAttrTag);
    if (geometryClassName != null) {
        geometryClassName = unMangle(geometryClassName);
    } else {
        geometryClassName = param.getAttributeValue(XMLTags.GeometryClassAttrTag);
        if (geometryClassName != null) {
            geometryClassName = unMangle(geometryClassName);
        }
    }
    Feature featureref = (Feature) simulationContext.getModel().getStructure(featurename);
    if (featureref == null) {
        throw new XmlParseException("The Feature " + featurename + " could not be resolved!");
    }
    // *** Create new Feature Mapping ****
    FeatureMapping feamap = new FeatureMapping(featureref, simulationContext, simulationContext.getModel().getUnitSystem());
    // Set Size
    if (param.getAttributeValue(XMLTags.SizeTag) != null) {
        String size = unMangle(param.getAttributeValue(XMLTags.SizeTag));
        try {
            feamap.getSizeParameter().setExpression(unMangleExpression(size));
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("An expressionException was fired when setting the size Expression " + size + " to a featureMapping!", e);
        }
    } else {
        try {
            feamap.getSizeParameter().setExpression(null);
        } catch (Exception e) {
            e.printStackTrace();
            throw new RuntimeException("unexpected exception while setting structure size: " + e.getMessage());
        }
    }
    // Set Volume/unit_area if it exists
    if (param.getAttributeValue(XMLTags.VolumePerUnitAreaTag) != null) {
        String volPerUnitArea = unMangle(param.getAttributeValue(XMLTags.VolumePerUnitAreaTag));
        try {
            feamap.getVolumePerUnitAreaParameter().setExpression(unMangleExpression(volPerUnitArea));
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("An expressionException was fired when setting the VolumePerUnitArea Expression " + volPerUnitArea + " to a featureMapping!", e);
        }
    }
    // Set Volume/unitVol if it exists
    if (param.getAttributeValue(XMLTags.VolumePerUnitVolumeTag) != null) {
        String volPerUnitVol = unMangle(param.getAttributeValue(XMLTags.VolumePerUnitVolumeTag));
        try {
            feamap.getVolumePerUnitVolumeParameter().setExpression(unMangleExpression(volPerUnitVol));
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("An expressionException was fired when setting the size Expression " + volPerUnitVol + " to a featureMapping!", e);
        }
    }
    if (geometryClassName != null) {
        GeometryClass[] geometryClasses = simulationContext.getGeometry().getGeometryClasses();
        for (int i = 0; i < geometryClasses.length; i++) {
            if (geometryClasses[i].getName().equals(geometryClassName)) {
                try {
                    feamap.setGeometryClass(geometryClasses[i]);
                } catch (PropertyVetoException e) {
                    e.printStackTrace(System.out);
                    throw new XmlParseException("A propertyVetoException was fired when trying to set the subvolume or surface " + geometryClassName + " to a MembraneMapping!", e);
                }
            }
        }
    }
    // Set Boundary conditions
    Element tempElement = param.getChild(XMLTags.BoundariesTypesTag, vcNamespace);
    // Xm
    String temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueXm);
    BoundaryConditionType bct = new BoundaryConditionType(temp);
    feamap.setBoundaryConditionTypeXm(bct);
    // Xp
    temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueXp);
    bct = new BoundaryConditionType(temp);
    feamap.setBoundaryConditionTypeXp(bct);
    // Ym
    temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueYm);
    bct = new BoundaryConditionType(temp);
    feamap.setBoundaryConditionTypeYm(bct);
    // Yp
    temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueYp);
    bct = new BoundaryConditionType(temp);
    feamap.setBoundaryConditionTypeYp(bct);
    // Zm
    temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueZm);
    bct = new BoundaryConditionType(temp);
    feamap.setBoundaryConditionTypeZm(bct);
    // Zp
    temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueZp);
    bct = new BoundaryConditionType(temp);
    feamap.setBoundaryConditionTypeZp(bct);
    return feamap;
}

Example 58 with Feature

use of cbit.vcell.model.Feature in project vcell by virtualcell.

the class Xmlproducer method getXML.

/**
 * Outputs a XML version of a Model object
 * Creation date: (2/15/2001 11:39:27 AM)
 * @return Element
 * @param param cbit.vcell.model.Model
 */
private Element getXML(Model param) throws XmlParseException /*, cbit.vcell.parser.ExpressionException */
{
    Element modelnode = new Element(XMLTags.ModelTag);
    String versionName = (param.getName() != null) ? mangle(param.getName()) : "unnamed_model";
    // get Attributes
    modelnode.setAttribute(XMLTags.NameAttrTag, versionName);
    // modelnode.setAttribute(XMLTags.AnnotationAttrTag, this.mangle(param.getDescription()));
    if (param.getDescription() != null && param.getDescription().length() > 0) {
        Element annotationElem = new Element(XMLTags.AnnotationTag);
        annotationElem.setText(mangle(param.getDescription()));
        modelnode.addContent(annotationElem);
    }
    // get global parameters
    ModelParameter[] modelGlobals = param.getModelParameters();
    if (modelGlobals != null && modelGlobals.length > 0) {
        modelnode.addContent(getXML(modelGlobals));
    }
    // Get Species
    Species[] array = param.getSpecies();
    for (int i = 0; i < array.length; i++) {
        modelnode.addContent(getXML(array[i]));
    }
    // Get Structures(Features and Membranes). Add them in an ordered fashion, but it does not matter who comes first.
    try {
        ArrayList<Element> list = new ArrayList<Element>();
        Structure[] structarray = param.getStructures();
        for (int i = 0; i < structarray.length; i++) {
            Element structure = getXML(structarray[i], param);
            if (structarray[i] instanceof Feature)
                modelnode.addContent(structure);
            else
                list.add(structure);
        }
        for (int i = 0; i < list.size(); i++) {
            modelnode.addContent((Element) list.get(i));
        }
    } catch (XmlParseException e) {
        e.printStackTrace();
        throw new XmlParseException("An error occurred while procesing a Structure for the model " + versionName, e);
    }
    // Process SpeciesContexts
    SpeciesContext[] specarray = param.getSpeciesContexts();
    for (int i = 0; i < specarray.length; i++) {
        modelnode.addContent(getXML(specarray[i]));
    }
    // Get reaction Steps(Simple Reactions and Fluxtep)
    ReactionStep[] reactarray = param.getReactionSteps();
    for (int i = 0; i < reactarray.length; i++) {
        modelnode.addContent(getXML(reactarray[i]));
    }
    // add the rbmModelContainer elements
    RbmModelContainer rbmModelContainer = param.getRbmModelContainer();
    if (rbmModelContainer != null && !rbmModelContainer.isEmpty()) {
        Element rbmModelContainerElement = getXML(rbmModelContainer);
        {
            // for testing purposes only
            Document doc = new Document();
            Element clone = (Element) rbmModelContainerElement.clone();
            doc.setRootElement(clone);
            String xmlString = XmlUtil.xmlToString(doc, false);
            System.out.println(xmlString);
        }
        modelnode.addContent(rbmModelContainerElement);
    }
    // // Add rate rules
    // if (param.getRateRuleVariables()!=null && param.getRateRuleVariables().length>0){
    // modelnode.addContent( getXML(param.getRateRuleVariables()) );
    // }
    // Get Diagrams
    Diagram[] diagarray = param.getDiagrams();
    for (int i = 0; i < diagarray.length; i++) {
        modelnode.addContent(getXML(diagarray[i]));
    }
    // Add Metadata information
    if (param.getVersion() != null) {
        modelnode.addContent(getXML(param.getVersion(), param));
    }
    // add model UnitSystem
    ModelUnitSystem unitSystem = param.getUnitSystem();
    if (unitSystem != null) {
        modelnode.addContent(getXML(unitSystem));
    }
    return modelnode;
}

Example 59 with Feature

use of cbit.vcell.model.Feature in project vcell by virtualcell.

the class XmlReader method getElectrode.

/**
 * This method returns an Electrode object from a XML representation.
 * Creation date: (6/6/2002 4:22:55 PM)
 * @return cbit.vcell.mapping.Electrode
 */
private Electrode getElectrode(org.jdom.Element elem, SimulationContext currentSimulationContext) {
    // retrieve feature
    String featureName = unMangle(elem.getAttributeValue(XMLTags.FeatureAttrTag));
    Feature feature = (Feature) currentSimulationContext.getModel().getStructure(featureName);
    // retrieve position
    Coordinate position = getCoordinate(elem.getChild(XMLTags.CoordinateTag, vcNamespace));
    Electrode newElect = new Electrode(feature, position);
    return newElect;
}

Example 60 with Feature

use of cbit.vcell.model.Feature in project vcell by virtualcell.

the class StructurePropertiesPanel method getExplanationText.

private String getExplanationText() {
    if (structure instanceof Membrane) {
        Membrane membrane = (Membrane) structure;
        String voltageName = membrane.getMembraneVoltage().getName();
        Feature posFeature = fieldModel.getElectricalTopology().getPositiveFeature(membrane);
        Feature negFeature = fieldModel.getElectricalTopology().getNegativeFeature(membrane);
        String posCompName = (posFeature != null) ? posFeature.getName() : "inside (+) compartment";
        String negCompName = (negFeature != null) ? negFeature.getName() : "outside (-) compartment";
        return "<html><b>membrane voltage</i>:</b> <font color=\"blue\">\"" + voltageName + "\"</font> = voltage(<font color=\"blue\">" + posCompName + "</font>) - voltage(<font color=\"blue\">" + negCompName + "</font>)</i><br/>" + "<b>inward currents:</b> from compartment <font color=\"blue\">\"" + negCompName + "\"</font> into compartment <font color=\"blue\">\"" + posCompName + "\"</font>" + "<font color=\"red\"><i><br/>Note: VCell reactions and fluxes specify inward currents (- to +) rather than conventional currents (+ to -).</i></font>" + "</html>";
    } else {
        return "";
    }
}