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

Example 1 with Evidence

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

the class PathwayReader method addObjectEvidence.

private Evidence addObjectEvidence(Element element) {
    if (element.getName().equals("EVIDENCE")) {
        Element evidenceChild = element.getChild("evidence", bp);
        if (evidenceChild != null) {
            element = evidenceChild;
        }
    }
    Evidence evidence = new Evidence();
    addAttributes(evidence, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentEvidence(evidence, element, childElement)) {
                showUnexpected(childElement, evidence);
            }
        }
    }
    pathwayModel.add(evidence);
    return evidence;
}

Example 2 with Evidence

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

the class PathwayProducerBiopax3 method addContentPathwayStep.

// stepProcess 	Interaction 	multiple
// stepProcess 	Pathway 		multiple
// nextStep 		PathwayStep 	multiple
// evidence 		Evidence 		multiple
private Element addContentPathwayStep(BioPaxObject bpObject, Element element) {
    element = addContentUtilityClass(bpObject, element);
    PathwayStep ob = (PathwayStep) bpObject;
    Element tmpElement = null;
    if (ob.getStepProcessInteraction() != null && ob.getStepProcessInteraction().size() > 0) {
        List<Interaction> list = ob.getStepProcessInteraction();
        for (Interaction item : list) {
            tmpElement = new Element("stepProcess", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getStepProcessPathway() != null && ob.getStepProcessPathway().size() > 0) {
        List<Pathway> list = ob.getStepProcessPathway();
        for (Pathway item : list) {
            tmpElement = new Element("stepProcess", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getNextStep() != null && ob.getNextStep().size() > 0) {
        List<PathwayStep> list = ob.getNextStep();
        for (PathwayStep item : list) {
            tmpElement = new Element("nextStep", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getEvidence() != null && ob.getEvidence().size() > 0) {
        List<Evidence> list = ob.getEvidence();
        for (Evidence item : list) {
            tmpElement = new Element("evidence", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    return element;
}

Example 3 with Evidence

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

the class PathwayProducerBiopax3 method addContentEntity.

// dataSource		Provenance	multiple
// availability	String		multiple
// name			String		multiple
// xref			Xref		multiple
// evidence		Evidence	multiple
private Element addContentEntity(BioPaxObject bpObject, Element element) {
    element = addContentBioPaxObject(bpObject, element);
    Entity ob = (Entity) bpObject;
    Element tmpElement = null;
    if (ob.getDataSource() != null && ob.getDataSource().size() > 0) {
        ArrayList<Provenance> list = ob.getDataSource();
        for (Provenance item : list) {
            tmpElement = new Element("dataSource", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getAvailability() != null && ob.getAvailability().size() > 0) {
        ArrayList<String> list = ob.getAvailability();
        for (String item : list) {
            tmpElement = new Element("availability", bp);
            tmpElement.setAttribute("datatype", schemaString, rdf);
            tmpElement.setText(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getName() != null && ob.getName().size() > 0) {
        ArrayList<String> list = ob.getName();
        for (String item : list) {
            tmpElement = new Element("name", bp);
            tmpElement.setAttribute("datatype", schemaString, rdf);
            tmpElement.setText(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getxRef() != null && ob.getxRef().size() > 0) {
        ArrayList<Xref> list = ob.getxRef();
        for (Xref item : list) {
            String elementName = "xref";
            tmpElement = new Element(elementName, bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getEvidence() != null && ob.getEvidence().size() > 0) {
        ArrayList<Evidence> list = ob.getEvidence();
        for (Evidence item : list) {
            tmpElement = new Element("evidence", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getSBSubEntity() != null && ob.getSBSubEntity().size() > 0) {
        ArrayList<SBEntity> list = ob.getSBSubEntity();
        for (SBEntity item : list) {
            tmpElement = new Element("sbSubEntity", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    return element;
}

Example 4 with Evidence

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

the class PathwayProducerBiopax3 method addContentEntityReference.

// memberEntityReference	EntityReference					multiple
// entityReferenceType		EntityReferenceTypeVocabulary	single
// entityFeature			EntityFeature					multiple
// name					String							multiple
// xref					Xref							multiple
// evidence				Evidence						multiple
private Element addContentEntityReference(BioPaxObject bpObject, Element element) {
    element = addContentUtilityClass(bpObject, element);
    EntityReference ob = (EntityReference) bpObject;
    Element tmpElement = null;
    if (ob.getMemberEntityReference() != null && ob.getMemberEntityReference().size() > 0) {
        List<EntityReference> list = ob.getMemberEntityReference();
        for (EntityReference item : list) {
            tmpElement = new Element("memberEntityReference", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getEntityReferenceType() != null) {
        tmpElement = new Element("entityReferenceType", bp);
        addIDToProperty(tmpElement, ob.getEntityReferenceType());
        mustPrintObject(ob.getEntityReferenceType());
        element.addContent(tmpElement);
    }
    if (ob.getEntityFeature() != null && ob.getEntityFeature().size() > 0) {
        List<EntityFeature> list = ob.getEntityFeature();
        for (EntityFeature item : list) {
            tmpElement = new Element("entityFeature", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getName() != null && ob.getName().size() > 0) {
        List<String> list = ob.getName();
        for (String item : list) {
            tmpElement = new Element("name", bp);
            tmpElement.setAttribute("datatype", schemaString, rdf);
            tmpElement.setText(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getxRef() != null && ob.getxRef().size() > 0) {
        List<Xref> list = ob.getxRef();
        for (Xref item : list) {
            tmpElement = new Element("xref", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getEvidence() != null && ob.getEvidence().size() > 0) {
        List<Evidence> list = ob.getEvidence();
        for (Evidence item : list) {
            tmpElement = new Element("evidence", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    return element;
}

Example 5 with Evidence

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

the class PathwayProducerBiopax3 method addContentEntityFeature.

// featureLocation 		SequenceLocation 			multiple
// featureLocationType 	SequenceRegionVocabulary 	multiple
// memberFeature 			EntityFeature 				multiple
// evidence 				Evidence 					multiple
private Element addContentEntityFeature(BioPaxObject bpObject, Element element) {
    element = addContentUtilityClass(bpObject, element);
    EntityFeature ob = (EntityFeature) bpObject;
    Element tmpElement = null;
    if (ob.getFeatureLocation() != null && ob.getFeatureLocation().size() > 0) {
        List<SequenceLocation> list = ob.getFeatureLocation();
        for (SequenceLocation item : list) {
            tmpElement = new Element("featureLocation", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getFeatureLocationType() != null && ob.getFeatureLocationType().size() > 0) {
        List<SequenceRegionVocabulary> list = ob.getFeatureLocationType();
        for (SequenceRegionVocabulary item : list) {
            tmpElement = new Element("featureLocationType", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getMemberFeature() != null && ob.getMemberFeature().size() > 0) {
        List<EntityFeature> list = ob.getMemberFeature();
        for (EntityFeature item : list) {
            tmpElement = new Element("memberFeature", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getEvidence() != null && ob.getEvidence().size() > 0) {
        List<Evidence> list = ob.getEvidence();
        for (Evidence item : list) {
            tmpElement = new Element("evidence", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    return element;
}