Package org.openbel.framework.common.protonetwork.model

Examples of org.openbel.framework.common.protonetwork.model.ProtoNetwork


        long t1 = currentTimeMillis();

        stageOutput(format("Processing orthology document '%s'", doc.getName()));
        p3.pruneOrthologyDocument(doc, pn);
        final ProtoNetwork opn = p3.compile(doc);

        long t2 = currentTimeMillis();

        final StringBuilder bldr = new StringBuilder();
        markTime(bldr, t1, t2);
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     */
    private int stage5Parameter(final ProtoNetwork network,
            Set<EquivalenceDataIndex> equivalences, final StringBuilder bldr) {
        bldr.append("Equivalencing parameters");
        stageOutput(bldr.toString());
        ProtoNetwork ret = network;
        int ct = 0;
        try {
            ct = p2.stage3EquivalenceParameters(ret, equivalences);
            stageOutput("(" + ct + " equivalences)");
        } catch (IOException ioex) {
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        ProtoNetworkDescriptor pnd = new BinaryProtoNetworkDescriptor(
                protoNetwork);

        BinaryProtoNetworkExternalizer bpne =
                new BinaryProtoNetworkExternalizer();
        ProtoNetwork gpn = null;
        try {
            gpn = bpne.readProtoNetwork(pnd);
        } catch (ProtoNetworkError e) {
            error("Unable to read merged network.");
            exit(ExitCode.NO_GLOBAL_PROTO_NETWORK);
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            try {
                Stage1Output s1o = phaseOne.stage1XBELValidation(xbelFile);
                phaseOne.stage2NamespaceCompilation(s1o.getDocument());
                phaseOne.stage3SymbolVerification(s1o.getDocument());
                phaseOne.stage4SemanticVerification(s1o.getDocument());
                ProtoNetwork pn = phaseOne.stage5Building(s1o.getDocument());
                phaseOne.stage6Expansion(s1o.getDocument(), pn, true);

                // assert proto network is valid.
                assertNotNull(pn);
            } catch (ResourceDownloadError e) {
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     * {@inheritDoc}
     */
    @Override
    public ProtoNetwork stage1Merger(
            Collection<ProtoNetworkDescriptor> protoNetworkDescriptors) {
        ProtoNetwork mergedNetwork = null;
        try {
            Iterator<ProtoNetworkDescriptor> it =
                    protoNetworkDescriptors.iterator();

            // Grab first proto network and iteratively merge the rest.
            ProtoNetworkDescriptor pnd = it.next();
            mergedNetwork = protoNetworkService.read(pnd);
            while (it.hasNext()) {
                ProtoNetwork nextPn = protoNetworkService.read(it.next());
                protoNetworkService.merge(mergedNetwork, nextPn);
            }
        } catch (ProtoNetworkError e) {
            e.printStackTrace();
            Throwable cause = e.getCause();
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