Examples with DeltaG org.vcell.pathway.DeltaG used on opensource projects

Example 1 with DeltaG

use of org.vcell.pathway.DeltaG in project vcell by virtualcell.

the class PathwayReaderBiopax3 method addObjectDeltaG.

private DeltaG addObjectDeltaG(Element element) {
    DeltaG deltaG = new DeltaG();
    addAttributes(deltaG, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentDeltaG(deltaG, element, childElement)) {
                showUnexpected(childElement);
            }
        }
    }
    pathwayModel.add(deltaG);
    return deltaG;
}

Example 2 with DeltaG

use of org.vcell.pathway.DeltaG in project vcell by virtualcell.

the class PathwayProducerBiopax3 method addContentBiochemicalReaction.

// deltaG 		DeltaG 		multiple
// kEQ 		KPrime 		multiple
// eCNumber 	String 		multiple
// deltaS 		Float 		multiple
// deltaH 		Float 		multiple
private Element addContentBiochemicalReaction(BioPaxObject bpObject, Element element) {
    element = addContentConversion(bpObject, element);
    BiochemicalReaction ob = (BiochemicalReaction) bpObject;
    Element tmpElement = null;
    if (ob.getDeltaG() != null && ob.getDeltaG().size() > 0) {
        List<DeltaG> list = ob.getDeltaG();
        for (DeltaG item : list) {
            tmpElement = new Element("deltaG", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getkEQ() != null && ob.getkEQ().size() > 0) {
        List<KPrime> list = ob.getkEQ();
        for (KPrime item : list) {
            tmpElement = new Element("kEQ", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getECNumber() != null && ob.getECNumber().size() > 0) {
        List<String> list = ob.getECNumber();
        for (String item : list) {
            tmpElement = new Element("eCNumber", bp);
            tmpElement.setAttribute("datatype", schemaString, rdf);
            tmpElement.setText(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getDeltaS() != null && ob.getDeltaS().size() > 0) {
        List<Double> list = ob.getDeltaS();
        for (Double item : list) {
            tmpElement = new Element("deltaS", bp);
            tmpElement.setAttribute("datatype", schemaDouble, rdf);
            tmpElement.setText(item.toString());
            element.addContent(tmpElement);
        }
    }
    if (ob.getDeltaH() != null && ob.getDeltaH().size() > 0) {
        List<Double> list = ob.getDeltaH();
        for (Double item : list) {
            tmpElement = new Element("deltaH", bp);
            tmpElement.setAttribute("datatype", schemaDouble, rdf);
            tmpElement.setText(item.toString());
            element.addContent(tmpElement);
        }
    }
    return element;
}

Example 3 with DeltaG

use of org.vcell.pathway.DeltaG in project vcell by virtualcell.

the class PathwayProducerBiopax3 method addContentDeltaG.

private Element addContentDeltaG(BioPaxObject bpObject, Element element) {
    element = addContentUtilityClass(bpObject, element);
    DeltaG ob = (DeltaG) bpObject;
    Element tmpElement = null;
    return element;
}

Example 4 with DeltaG

use of org.vcell.pathway.DeltaG in project vcell by virtualcell.

the class PathwayProducerBiopax3 method addContentTransportWithBiochemicalReaction.

// deltaG 		DeltaG 		multiple
// kEQ 		KPrime 		multiple
// eCNumber 	String 		multiple
// deltaS 		Float 		multiple
// deltaH 		Float 		multiple
private Element addContentTransportWithBiochemicalReaction(BioPaxObject bpObject, Element element) {
    // element = addContentTransport(bpObject, element);
    element = addContentBiochemicalReaction(bpObject, element);
    TransportWithBiochemicalReaction ob = (TransportWithBiochemicalReaction) bpObject;
    Element tmpElement = null;
    if (ob.getDeltaG() != null && ob.getDeltaG().size() > 0) {
        List<DeltaG> list = ob.getDeltaG();
        for (DeltaG item : list) {
            tmpElement = new Element("deltaG", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getkEQ() != null && ob.getkEQ().size() > 0) {
        List<KPrime> list = ob.getkEQ();
        for (KPrime item : list) {
            tmpElement = new Element("kEQ", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getECNumber() != null && ob.getECNumber().size() > 0) {
        List<String> list = ob.getECNumber();
        for (String item : list) {
            tmpElement = new Element("eCNumber", bp);
            tmpElement.setAttribute("datatype", schemaString, rdf);
            tmpElement.setText(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getDeltaS() != null && ob.getDeltaS().size() > 0) {
        List<Double> list = ob.getDeltaS();
        for (Double item : list) {
            tmpElement = new Element("deltaS", bp);
            tmpElement.setAttribute("datatype", schemaDouble, rdf);
            tmpElement.setText(item.toString());
            element.addContent(tmpElement);
        }
    }
    if (ob.getDeltaH() != null && ob.getDeltaH().size() > 0) {
        List<Double> list = ob.getDeltaH();
        for (Double item : list) {
            tmpElement = new Element("deltaH", bp);
            tmpElement.setAttribute("datatype", schemaDouble, rdf);
            tmpElement.setText(item.toString());
            element.addContent(tmpElement);
        }
    }
    return element;
}

Example 5 with DeltaG

use of org.vcell.pathway.DeltaG in project vcell by virtualcell.

the class PathwayReader method addObjectDeltaG.

private DeltaG addObjectDeltaG(Element element) {
    DeltaG deltaG = new DeltaG();
    addAttributes(deltaG, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentDeltaG(deltaG, element, childElement)) {
                showUnexpected(childElement, deltaG);
            }
        }
    }
    pathwayModel.add(deltaG);
    return deltaG;
}