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

Example 1 with SequenceInterval

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

the class PathwayReaderBiopax3 method addObjectSequenceLocation.

private SequenceLocation addObjectSequenceLocation(Element element) {
    if (element.getChildren().size() == 0) {
        // if there are no children it must be a resource inside another object
        SequenceLocationProxy proxy = new SequenceLocationProxy();
        addAttributes(proxy, element);
        pathwayModel.add(proxy);
        return proxy;
    }
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (childElement.getName().equals("SequenceInterval")) {
                SequenceInterval thingie = addObjectSequenceInterval(childElement);
                pathwayModel.add(thingie);
                return thingie;
            }
        } else if (child instanceof Element) {
            Element childElement = (Element) child;
            if (childElement.getName().equals("SequenceSite")) {
                SequenceSite thingie = addObjectSequenceSite(childElement);
                pathwayModel.add(thingie);
                return thingie;
            }
        }
    }
    SequenceLocation sequenceLocation = new SequenceLocation();
    addAttributes(sequenceLocation, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentSequenceLocation(sequenceLocation, element, childElement)) {
                showUnexpected(childElement);
            }
        }
    }
    pathwayModel.add(sequenceLocation);
    return sequenceLocation;
}

Example 2 with SequenceInterval

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

the class PathwayReaderBiopax3 method addObjectSequenceInterval.

private SequenceInterval addObjectSequenceInterval(Element element) {
    SequenceInterval sequenceInterval = new SequenceInterval();
    addAttributes(sequenceInterval, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentSequenceInterval(sequenceInterval, element, childElement)) {
                showUnexpected(childElement);
            }
        }
    }
    pathwayModel.add(sequenceInterval);
    return sequenceInterval;
}

Example 3 with SequenceInterval

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

the class PathwayProducerBiopax3 method addContentSequenceInterval.

// sequenceIntervalBegin 	SequenceSite 	single
// sequenceIntervalEnd 	SequenceSite 	single
private Element addContentSequenceInterval(BioPaxObject bpObject, Element element) {
    element = addContentSequenceLocation(bpObject, element);
    SequenceInterval ob = (SequenceInterval) bpObject;
    Element tmpElement = null;
    if (ob.getSequenceIntervalBegin() != null) {
        tmpElement = new Element("sequenceIntervalBegin", bp);
        addIDToProperty(tmpElement, ob.getSequenceIntervalBegin());
        mustPrintObject(ob.getSequenceIntervalBegin());
        element.addContent(tmpElement);
    }
    if (ob.getSequenceIntervalEnd() != null) {
        tmpElement = new Element("sequenceIntervalEnd", bp);
        addIDToProperty(tmpElement, ob.getSequenceIntervalEnd());
        mustPrintObject(ob.getSequenceIntervalEnd());
        element.addContent(tmpElement);
    }
    return element;
}

Example 4 with SequenceInterval

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

the class PathwayReader method addObjectSequenceInterval.

private SequenceInterval addObjectSequenceInterval(Element element) {
    SequenceInterval sequenceInterval = new SequenceInterval();
    addAttributes(sequenceInterval, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentSequenceInterval(sequenceInterval, element, childElement)) {
                showUnexpected(childElement, sequenceInterval);
            }
        }
    }
    pathwayModel.add(sequenceInterval);
    return sequenceInterval;
}