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

        boolean skip = false;
        int i1 = 0, i2;
        while (i1 < length && length > 1) {
            i2 = i1 + 1;
            while (i2 < length) {
                Molecule m1 = moleculeArray.get(i1);
                Molecule m2 = moleculeArray.get(i2);
                Map<BlankNode, BlankNode> map = mapper.createMap(m1, m2);
                Molecule molecule = localMerger.merge(m1, m2, map);
                //map.clear();
                if (molecule != null) {
                    moleculeArray.remove(m1);
                    moleculeArray.remove(m2);
                    moleculeArray.add(molecule);

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    // TODO if a sub molecule is to be returned, the isTopLevel field isn't correctly set when creating the molecule.
    // TODO Maybe get the top-level molecule and return the subMolecule?
    private Molecule reconstructMolecule(Molecule parentMolecule, Long pid, Long mid) throws GraphException {
        Triple[] roots = iteratorAsTriples(readableIndex.findTriplesForMid(pid, mid));
        Map<BlankNode, Triple> rootTripleMap = getBNodeToRootMap(parentMolecule);
        Molecule molecule = new MoleculeImpl(moleculeComparator, roots);
        molecule = createSubMolecules(mid, molecule);
        if (null == parentMolecule) {
            return molecule;
        } else {
            Triple linkingTriple = findLinkingTriple(parentMolecule, roots, rootTripleMap, molecule);

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        ClosableIterator<Long> iterator = readableIndex.findMoleculeIDs(tripleAsLongs);
        try {
            while (iterator.hasNext()) {
                final Long mid = iterator.next();
                if (readableIndex.isSubmoleculeOfParentID(1L, mid)) {
                    Molecule m = handler.createMolecule(1L, mid);
                    if (m != null && moleculeComparator.compare(molecule, m) == 0) {
                        AddMoleculeToIndex amti = new AddMoleculeToIndex(writableIndex, localizer);
                        amti.handleTriple(rootTriple);
                        return molecule.add(rootTriple);
                    }

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        ClosableIterator<Long> iterator = readableIndex.findMoleculeIDs(tripleAsLongs);
        try {
            while (iterator.hasNext()) {
                Long aLong = iterator.next();
                if (readableIndex.isSubmoleculeOfParentID(1L, aLong)) {
                    Molecule m = handler.createMolecule(1L, aLong);
                    if (m != null && moleculeComparator.compare(molecule, m) == 0) {
                        return removeSubMolecules(molecule, rootTriple, tripleAsLongs, aLong);
                    }
                }
            }

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        try {
            ClosableIterator<Molecule> iterator = iterator();
            try {
                MoleculeHandler tmpHandler = new MoleculeToText(builder, localizer.getLocalizer());
                while (iterator.hasNext()) {
                    Molecule molecule = iterator.next();
                    traverser.traverse(molecule, tmpHandler);
                }
                return builder.toString();
            } finally {
                iterator.close();

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Related Classes of org.jrdf.graph.global.molecule.Molecule

org.jrdf.example.performance.DecomposerPerformance

org.jrdf.graph.global.molecule.mem.BlankNodeMapperImpl

org.jrdf.graph.global.molecule.mem.LocalMergeSubmoleculesImpl

org.jrdf.graph.global.molecule.mem.MergeSubmoleculesImpl

org.jrdf.graph.global.molecule.mem.MoleculeImpl

org.jrdf.graph.global.molecule.mem.NaiveGraphDecomposerImpl

org.jrdf.graph.global.MoleculeGraphHandlerImpl

org.jrdf.graph.global.MoleculeGraphImpl

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