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

Example 1 with BiochemicalPathwayStep

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

the class PathwayReaderBiopax3 method addObjectBiochemicalPathwayStep.

private BiochemicalPathwayStep addObjectBiochemicalPathwayStep(Element element) {
    BiochemicalPathwayStep biochemicalPathwayStep = new BiochemicalPathwayStep();
    addAttributes(biochemicalPathwayStep, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentBiochemicalPathwayStep(biochemicalPathwayStep, element, childElement)) {
                showUnexpected(childElement);
            }
        }
    }
    pathwayModel.add(biochemicalPathwayStep);
    return biochemicalPathwayStep;
}

Example 2 with BiochemicalPathwayStep

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

the class PathwayProducerBiopax3 method addContentBiochemicalPathwayStep.

// stepConversion 	Conversion 	single
// stepDirection 	String 		single
private Element addContentBiochemicalPathwayStep(BioPaxObject bpObject, Element element) {
    element = addContentPathwayStep(bpObject, element);
    BiochemicalPathwayStep ob = (BiochemicalPathwayStep) bpObject;
    Element tmpElement = null;
    if (ob.getStepConversion() != null) {
        tmpElement = new Element("stepConversion", bp);
        addIDToProperty(tmpElement, ob.getStepConversion());
        mustPrintObject(ob.getStepConversion());
        element.addContent(tmpElement);
    }
    if (ob.getStepDirection() != null && ob.getStepDirection().length() > 0) {
        tmpElement = new Element("stepDirection", bp);
        tmpElement.setAttribute("datatype", schemaString, rdf);
        tmpElement.setText(ob.getStepDirection());
        element.addContent(tmpElement);
    }
    return element;
}

Example 3 with BiochemicalPathwayStep

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

the class PathwayReader method addObjectBiochemicalPathwayStep.

private BiochemicalPathwayStep addObjectBiochemicalPathwayStep(Element element) {
    BiochemicalPathwayStep biochemicalPathwayStep = new BiochemicalPathwayStep();
    addAttributes(biochemicalPathwayStep, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentBiochemicalPathwayStep(biochemicalPathwayStep, element, childElement)) {
                showUnexpected(childElement, biochemicalPathwayStep);
            }
        }
    }
    pathwayModel.add(biochemicalPathwayStep);
    return biochemicalPathwayStep;
}