Examples of Molecule

org.jrdf.graph.global.molecule.Molecule
A molecule is a container of a subgraph of RDF triples. It contains a collection of triples that share some common chain of blank nodes. Molecules consist of a set of root triples. These share a blank node - typically the subject but it can be the object as well. For example, _1 p o, s p2 _1 is a simple molecule. The highest in this set of root triples (as defined by some ordering) is the head triple. The typical ordering is most grounded (fewest blank nodes), followed by URIs, Literals and then alphabetical ordering. The chain of blank nodes creates a molecule that contains submolecules. If a triple in the root has a blank node as its object it is a linking triple. This is how the chains to submolecules are created. From one molecule to the next the object and subject nodes are swapped. For example, the linking triple _1 p _2 will link to a triple in a submolecule _2 p o. @author Andrew Newman @version $Id: Molecule.java 2894 2009-01-27 21:25:13Z newmana $
org.openscience.cdk.Molecule
org.wymiwyg.rdf.molecules.Molecule
A set of triples that cannot be decomposed without reducing its meaning. A Molecule is not necessarly a Graph, as the identity may be determined by the id of b-nodes, this is in a model-referencing decomposition @author reto

Examples of org.jrdf.graph.global.molecule.Molecule

        SortedSet<Molecule> moleculeSet = subMolecules.get(triple);
        if (moleculeSet == null) {
            moleculeSet = new TreeSet<Molecule>(moleculeComparator);
        }
        if (isDoubleLinkedTriple(newTriple)) {
            Molecule newMolecule = new MoleculeImpl(moleculeComparator, newTriple);
            moleculeSet.add(newMolecule);
            ((MoleculeImpl) newMolecule).isTopLevel = false;
            subMolecules.put(triple, moleculeSet);
        } else {
            if (moleculeSet.isEmpty()) {
                Molecule newMolecule = new MoleculeImpl(moleculeComparator, newTriple);
                ((MoleculeImpl) newMolecule).isTopLevel = false;
                moleculeSet.add(newMolecule);
                subMolecules.put(triple, moleculeSet);
            } else {
                moleculeSet.last().add(newTriple);

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Examples of org.jrdf.graph.global.molecule.Molecule

            if (!triplesChecked.contains(currentTriple)) {
                Triple newStartingPoint = new FindEntryNodeImpl().find(graph, currentTriple);
                if (tripleComparator.compare(newStartingPoint, currentTriple) < 0) {
                    currentTriple = newStartingPoint;
                }
                Molecule molecule = moleculeFactory.createMolecule();
                molecule = molecule.add(currentTriple);
                triplesChecked.add(currentTriple);
                molecule = convertTripleToMolecule(molecule);
                molecules.add(molecule);
            }
        }

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Examples of org.jrdf.graph.global.molecule.Molecule

        triples.iterator().close();
        return molecule;
    }


    private Molecule addLinkedTriple(Molecule molecule, Triple triple) throws GraphException {
        Molecule subMolecule = moleculeFactory.createMolecule();
        subMolecule.add(triple);
        triplesChecked.add(triple);
        // Put submolecule inside molecule's head triple
        if (isDoubleLinkedTriple(molecule.getHeadTriple()) &&
            molecule.getHeadTriple().getObject().equals(triple.getSubject())) {
            getSubMolecule(subMolecule, triple);
            return molecule.add(molecule.getHeadTriple(), subMolecule);
            // Put molecule inside submolecule
        } else if (triple.getObject().equals(molecule.getHeadTriple().getSubject())) {
            getSubMolecule(subMolecule, triple);
            return subMolecule.add(triple, molecule);
            // Put submolecule inside molecule
        } else {
            getSubMolecule(subMolecule, triple);
            if (isDoubleLinkedTriple(triple)) {
                Set<Molecule> subMolecules = subMolecule.getSubMolecules(triple);
                for (Molecule newMole : subMolecules) {
                    molecule.add(triple, newMole);
                }
            }
            subMolecule.remove(triple);
            getNewRootTriples(molecule, triple);
            return molecule.add(triple, subMolecule);
        }
    }

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Examples of org.jrdf.graph.global.molecule.Molecule

    public Molecule merge(Molecule molecule1, Molecule molecule2) {
        if (subsumption.subsumes(molecule1, molecule2)) {
            SortedSet<Triple> newRootTriples = new TreeSet<Triple>(comparator);
            addRootTriples(molecule1, newRootTriples);
            addRootTriples(molecule2, newRootTriples);
            Molecule newMolecule = moleculeFactory.createMolecule(newRootTriples);
            Iterator<Triple> subMoleculeIter = newMolecule.getRootTriples();
            while (subMoleculeIter.hasNext()) {
                Triple currentTriple = subMoleculeIter.next();
                newMolecule.specialAdd(merge(currentTriple, molecule1, molecule2));
            }
            return newMolecule;
        } else {
            throw new IllegalArgumentException("Cannot merge molecules with different head triples.");
        }

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Examples of org.jrdf.graph.global.molecule.Molecule

            throw new IllegalArgumentException("Cannot merge molecules with different head triples.");
        }
    }


    public Molecule merge(Triple triple, Molecule molecule1, Molecule molecule2) {
        Molecule newMolecule = moleculeFactory.createMolecule();
        Iterator<Molecule> curr1Iterator = molecule1.getSubMolecules(triple).iterator();
        Iterator<Molecule> curr2Iterator = molecule2.getSubMolecules(triple).iterator();
        iterateAndMergeMolecules(newMolecule, triple, curr1Iterator, curr2Iterator);
        return newMolecule;
    }

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Examples of org.jrdf.graph.global.molecule.Molecule


    private void iterateAndMergeMolecules(Molecule newMolecule, Triple currentTriple,
        Iterator<Molecule> curr1Iterator, Iterator<Molecule> curr2Iterator) {
        boolean endIterator1 = curr1Iterator.hasNext();
        boolean endIterator2 = curr2Iterator.hasNext();
        Molecule currentMolecule1 = getNextFromIterator(curr1Iterator);
        Molecule currentMolecule2 = getNextFromIterator(curr2Iterator);
        while (endIterator1 || endIterator2) {
            int result = moleculeComparator.compare(currentMolecule1, currentMolecule2);
            if (result == 1) {
                endIterator1 = curr1Iterator.hasNext();
                currentMolecule1 = addMolecule(newMolecule, currentTriple, currentMolecule1, curr1Iterator);

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Examples of org.jrdf.graph.global.molecule.Molecule

        }
    }


    private Molecule addMolecule(Molecule newMolecule, Triple currentTriple, Molecule currentMolecule,
        Iterator<Molecule> moleculeIterator) {
        Molecule tmpMolecule = currentMolecule;
        newMolecule.add(currentTriple, tmpMolecule);
        tmpMolecule = getNextFromIterator(moleculeIterator);
        return tmpMolecule;
    }

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Examples of org.jrdf.graph.global.molecule.Molecule

        tmpMolecule = getNextFromIterator(moleculeIterator);
        return tmpMolecule;
    }


    private Molecule getNextFromIterator(Iterator<Molecule> moleculeIterator) {
        Molecule tmpMolecule;
        if (moleculeIterator.hasNext()) {
            tmpMolecule = moleculeIterator.next();
        } else {
            tmpMolecule = NULL_MOLECULE;
        }

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Examples of org.jrdf.graph.global.molecule.Molecule

            findCorrespondingTriple(m1Roots, m2RootTriple, map);
            Set<Molecule> sm1s = m1.getSubMolecules(m2RootTriple);
            Set<Molecule> sm2s = m2.getSubMolecules(m2RootTriple);
            if (!sm1s.isEmpty() && !sm2s.isEmpty()) {
                if (sm1s.size() == 1 && sm2s.size() == 1) {
                    Molecule sm1 = sm1s.iterator().next();
                    Molecule sm2 = sm2s.iterator().next();
                    Map<BlankNode, BlankNode> curMap = startPopulateMap(sm1, sm2);
                    if (curMap.isEmpty()) {
                        return curMap;
                    } else {
                        for (Map.Entry<BlankNode, BlankNode> entry : curMap.entrySet()) {

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Examples of org.jrdf.graph.global.molecule.Molecule

            return null;
        }
    }


    private Molecule convertMolecule(Molecule molecule) {
        final Molecule newMolecule = convertRootTriples(molecule);
        final Iterator<Triple> triples = molecule.getRootTriples();
        while (triples.hasNext()) {
            final Triple triple = triples.next();
            final Set<Molecule> moleculeSet = molecule.getSubMolecules(triple);
            for (final Molecule subMolecule : moleculeSet) {
                final Molecule convertedSubMolecule = convertMolecule(subMolecule);
                newMolecule.add(convertTriple(triple), convertedSubMolecule);
            }
        }
        return newMolecule;
    }

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