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

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

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     * @param networks
     */
    private void processDirectories(final File[] networks) {
        phaseOutput(format("=== %s ===", getApplicationName()));

        ProtoNetwork network = stage1(networks);
        Set<EquivalenceDataIndex> eqs = stage2();

        if (!eqs.isEmpty()) {
            network = stage3(network, eqs);
        }
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            final String netPath = asPath(root, PROTO_NETWORK_FILENAME);
            final File networkBin = new File(netPath);
            nds.add(new BinaryProtoNetworkDescriptor(networkBin));
        }

        ProtoNetwork ret = p2.stage1Merger(nds);

        new File(artifactPath.getAbsolutePath() + "/merged").mkdirs();

        p2.stage4WriteEquivalentProtoNetwork(ret,
                artifactPath.getAbsolutePath() + "/merged");
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     */
    private int stage3Parameter(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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    private void reconstituteNetwork(final File file) {

        BinaryProtoNetworkDescriptor inputProtoNetworkDesc =
                new BinaryProtoNetworkDescriptor(file);
        ProtoNetworkExternalizer pne = new BinaryProtoNetworkExternalizer();
        ProtoNetwork global = null;

        try {
            global = pne.readProtoNetwork(inputProtoNetworkDesc);
        } catch (ProtoNetworkError e) {
            error(e.getUserFacingMessage());
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     *
     * @param pn Proto-network input by user
     */
    private void processNetwork(final ProtoNetwork pn) {
        // Inject protein families
        ProtoNetwork pfamMerged = stage1(pn);
        // Inject named complexes
        ProtoNetwork ncMerged = stage2(pfamMerged);
        // Inject gene scaffolding
        ProtoNetwork geneMerged = stage3(ncMerged);
        // Inject homology knowledge
        ProtoNetwork orthoMerged = stage4(geneMerged);
        // Equivalence the network
        ProtoNetwork equived = stage5(orthoMerged);
        stage6(equived);
    }
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        }
        stageOutput(bldr.toString());

        stageOutput("Compiling pruned protein families");
        t1 = currentTimeMillis();
        ProtoNetwork pfpn = p3.compile(pfDoc);
        t2 = currentTimeMillis();

        bldr.setLength(0);
        markTime(bldr, t1, t2);
        stageOutput(bldr.toString());
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        bldr.append(" statements remain after pruning");
        stageOutput(bldr.toString());

        stageOutput("Compiling named complexes proto-network");
        t1 = currentTimeMillis();
        ProtoNetwork ncpn = p3.compile(ncDoc);
        t2 = currentTimeMillis();

        bldr.setLength(0);
        markTime(bldr, t1, t2);
        stageOutput(bldr.toString());
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        bldr.append(" statements remain after pruning");
        stageOutput(bldr.toString());

        stageOutput("Compiling gene scaffolding proto-network");
        t1 = currentTimeMillis();
        ProtoNetwork gpn = p3.compile(gsDoc);
        t2 = currentTimeMillis();

        bldr.setLength(0);
        markTime(bldr, t1, t2);
        stageOutput(bldr.toString());
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        }

        final Iterator<ResourceLocation> it = resources.iterator();

        final ResourceLocation first = it.next();
        final ProtoNetwork orthoMerge = pruneResource(pn, first);

        while (it.hasNext()) {
            final ResourceLocation resource = it.next();
            final ProtoNetwork opn = pruneResource(pn, resource);

            try {
                p3.merge(orthoMerge, opn);
            } catch (ProtoNetworkError e) {
                e.printStackTrace();
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                .getProteinFamilyResource();

        final Document pfdoc = readResource(pfResource);
        p3.pruneFamilies(false, pfdoc, orthoPn);
        p3.inferFamilies(pfdoc, orthoPn);
        final ProtoNetwork pfpn = p3.compile(pfdoc);
        p3.merge(orthoPn, pfpn);

        final ResourceLocation ncResource = resourceIndex
                .getNamedComplexesResource();
        final Document ncdoc = readResource(ncResource);
        p3.pruneComplexes(false, ncdoc, orthoPn);
        final ProtoNetwork ncpn = p3.compile(ncdoc);
        p3.merge(orthoPn, ncpn);

        final ResourceLocation gsResource = resourceIndex
                .getGeneScaffoldingResource();
        final Document gsdoc = readResource(gsResource);
        p3.pruneGene(gsdoc, orthoPn);
        final ProtoNetwork gspn = p3.compile(gsdoc);
        p3.merge(orthoPn, gspn);
    }
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Related Classes of org.openbel.framework.common.protonetwork.model.ProtoNetwork

  • org.openbel.framework.common.protonetwork.model.NamespaceTable.TableNamespace
  • org.openbel.framework.common.protonetwork.model.ParameterTable.TableParameter
  • org.openbel.framework.compiler.PhaseTwoImpl
  • org.openbel.framework.core.compiler.PhaseOneIntegrationTest
  • org.openbel.framework.core.equivalence.BucketEquivalencerTest
  • org.openbel.framework.core.protonetwork.BinaryProtoNetworkExternalizer
  • org.openbel.framework.core.protonetwork.BinaryProtoNetworkIOTest
  • org.openbel.framework.core.protonetwork.ProtoNetworkBuilderTest
  • org.openbel.framework.core.protonetwork.ProtoNetworkMerge_CommutativeTest
  • org.openbel.framework.tools.PhaseFourApplication
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