Examples with ONDEXConcept net.sourceforge.ondex.core.ONDEXConcept used on opensource projects

Example 1 with ONDEXConcept

use of net.sourceforge.ondex.core.ONDEXConcept in project knetbuilder by Rothamsted.

the class GraphElementManipulation method changeAttributeValue.

public static void changeAttributeValue(ONDEXEntity e, AttributeName n, Object value) {
    if (e instanceof ONDEXConcept) {
        ONDEXConcept c = (ONDEXConcept) e;
        boolean doIndex = c.getAttribute(n).isDoIndex();
        c.deleteAttribute(n);
        c.createAttribute(n, value, doIndex);
    }
    if (e instanceof ONDEXRelation) {
        ONDEXRelation r = (ONDEXRelation) e;
        boolean doIndex = r.getAttribute(n).isDoIndex();
        r.deleteAttribute(n);
        r.createAttribute(n, value, doIndex);
    } else {
        throw new IllegalArgumentException("This method only works with Ondex concepts and relations.");
    }
}

Example 2 with ONDEXConcept

use of net.sourceforge.ondex.core.ONDEXConcept in project knetbuilder by Rothamsted.

the class GraphElementManipulation method copyConcept.

/**
 * Creates a copy of a concept and provides an opportunity to select a new
 * concept class and new DataSource.
 *
 * @param graph
 *            - graph
 * @param c
 *            - original concept that will be copied
 * @param newCC
 *            - new concept class that the copy will have
 * @param newDataSource
 *            - new DataSource that the copy will have
 * @return concept that was created
 */
public static ONDEXConcept copyConcept(ONDEXGraph graph, ONDEXConcept c, ConceptClass newCC, DataSource newDataSource) {
    EvidenceType der = ControledVocabularyHelper.createEvidence(graph, "Derived_copy");
    ONDEXConcept nc = graph.getFactory().createConcept(c.getPID(), newDataSource, newCC, der);
    copyConceptData(graph, c, nc);
    nc.removeEvidenceType(der);
    return nc;
}

Example 3 with ONDEXConcept

use of net.sourceforge.ondex.core.ONDEXConcept in project knetbuilder by Rothamsted.

the class GraphElementManipulation method oneToManyCollapse.

/**
 * Creates a one-to-many collapsed concept by creating collapsed concept of
 * a source to all targets. Source concept is NOT deleted by this method.
 *
 * @param graph
 * @param source
 * @param targets
 */
public static final Set<ONDEXConcept> oneToManyCollapse(ONDEXGraph graph, ONDEXConcept source, Collection<ONDEXConcept> targets) {
    boolean createNewTarget = false;
    Set<ONDEXConcept> result = new HashSet<ONDEXConcept>();
    System.err.println("Targets number:" + targets.size());
    for (ONDEXConcept target : targets) {
        System.err.println(target.getOfType());
        ConceptClass newClass = target.getOfType();
        Set<ConceptClass> set = new HashSet<ConceptClass>();
        set.add(newClass);
        set.add(source.getOfType());
        if (set.size() > 1) {
            createNewTarget = true;
            newClass = getCompoundConceptClass(graph, set);
        }
        DataSource newDataSource = target.getElementOf();
        Set<DataSource> allDataSources = new HashSet<DataSource>();
        allDataSources.add(newDataSource);
        allDataSources.add(source.getElementOf());
        if (allDataSources.size() > 1) {
            createNewTarget = true;
            newDataSource = getCompoundDataSource(graph, allDataSources);
        }
        ONDEXConcept realTarget = target;
        if (createNewTarget) {
            realTarget = copyConcept(graph, target, newClass, newDataSource);
            copyRelations(graph, target, realTarget);
            graph.deleteConcept(target.getId());
        }
        copyConceptData(graph, source, realTarget);
        copyRelations(graph, source, realTarget);
        result.add(realTarget);
    }
    return result;
}

Example 4 with ONDEXConcept

use of net.sourceforge.ondex.core.ONDEXConcept in project knetbuilder by Rothamsted.

the class GraphElementManipulation method conceptToCluster.

/**
 * Swaps hub concept for a cluster where every concept is connected to every
 * other concept by relation of specified type set. Use only with
 * non-directional relation types
 *
 * @param c
 *            - hub concept
 * @param clusterRel
 *            - relation type set to use in the cluster
 * @param graph
 *            - graph
 * @param rtss
 *            - relation type set() that define the cluster
 * @throws AccessDeniedException
 * @throws NullValueException
 */
public static void conceptToCluster(ONDEXConcept c, RelationType clusterRel, ONDEXGraph graph, RelationType... rtss) throws NullValueException, AccessDeniedException {
    Set<RelationType> ts = new HashSet<RelationType>(Arrays.asList(rtss));
    List<ONDEXConcept> cluster = new ArrayList<ONDEXConcept>();
    for (ONDEXRelation r : graph.getRelationsOfConcept(c)) {
        if (ts.contains(r.getOfType())) {
            if (c.equals(r.getFromConcept()) && c.equals(r.getToConcept()))
                continue;
            if (c.equals(r.getFromConcept()))
                cluster.add(r.getToConcept());
            else if (c.equals(r.getToConcept()))
                cluster.add(r.getFromConcept());
        }
    }
    Collection<EvidenceType> evidence = new ArrayList<EvidenceType>();
    for (EvidenceType et : c.getEvidence()) evidence.add(et);
    for (int i = 0; i < cluster.size(); i++) {
        for (int j = i + 1; j < cluster.size(); j++) {
            graph.createRelation(cluster.get(i), cluster.get(j), clusterRel, evidence);
        }
    }
    graph.deleteConcept(c.getId());
}

Example 5 with ONDEXConcept

use of net.sourceforge.ondex.core.ONDEXConcept in project knetbuilder by Rothamsted.

the class GraphElementManipulation method conceptToAttribute.

/**
 * Makes concept into an attribute with the value of concept name on all of
 * the concepts connected to it via relations of specified type set. Use
 * only with non-directional relation types.
 *
 * @param c
 *            - defining concept
 * @param attName
 *            - name to use for the attribute
 * @param graph
 *            - graph
 * @param rtss
 *            - valid set of relation type sets
 * @throws EmptyStringException
 * @throws NullValueException
 */
public static void conceptToAttribute(ONDEXConcept c, String attName, ONDEXGraph graph, RelationType... rtss) throws NullValueException, EmptyStringException {
    ONDEXGraphMetaData data = graph.getMetaData();
    AttributeName an = data.getAttributeName(attName);
    if (an == null)
        an = data.getFactory().createAttributeName(attName, String.class);
    Set<RelationType> ts = new HashSet<RelationType>(Arrays.asList(rtss));
    List<ONDEXConcept> cluster = new ArrayList<ONDEXConcept>();
    for (ONDEXRelation r : graph.getRelationsOfConcept(c)) {
        if (ts.contains(r.getOfType())) {
            if (c.equals(r.getFromConcept()) && c.equals(r.getToConcept()))
                continue;
            if (c.equals(r.getFromConcept()))
                cluster.add(r.getToConcept());
            else if (c.equals(r.getToConcept()))
                cluster.add(r.getFromConcept());
        }
    }
    String value = c.getConceptName().getName();
    for (ONDEXConcept d : cluster) {
        d.createAttribute(an, value, false);
    }
    graph.deleteConcept(c.getId());
}