List of writeProtoNetwork() Examples

Examples of writeProtoNetwork()

org.openbel.framework.core.protonetwork.BinaryProtoNetworkExternalizer.writeProtoNetwork()
Writes a binary-based proto network and produces a descriptor including the binary file. @param protoNetwork {@link ProtoNetwork}, the proto network, which cannot be null @param protoNetworkRootPath {@link String}, the root path where proto network files should be created @return {@link ProtoNetworkDescriptor}, the proto network descriptor @throws ProtoNetworkError , if there was an error writing the {@link ProtoNetwork}
org.openbel.framework.core.protonetwork.ProtoNetworkExternalizer.writeProtoNetwork()
Writes a proto network and produces a descriptor. @param protoNetwork {@link ProtoNetwork}, the proto network, which cannot be null @param protoNetworkRootPath {@link String}, the root path where proto network files should be created @return {@link ProtoNetworkDescriptor}, the proto network descriptor @throws ProtoNetworkError , if there was an error writing the {@link ProtoNetwork}
org.openbel.framework.core.protonetwork.TextProtoNetworkExternalizer.writeProtoNetwork()
Writes a text table-based proto network and produces a descriptor including all of the table files. @param pn {@link ProtoNetwork}, the proto network, which cannot be null @param protoNetworkRootPath {@link String}, the root path where proto network files should be created @return {@link ProtoNetworkDescriptor}, the proto network descriptor @throws ProtoNetworkError Thrown if there was an error writing the {@link ProtoNetwork} @throws InvalidArgument Thrown if {@code protoNetwork} is null

Examples of org.openbel.framework.core.protonetwork.BinaryProtoNetworkExternalizer.writeProtoNetwork()

                new BinaryProtoNetworkExternalizer();


        try {
            // test write
            protoNetworkDescriptor =
                    protoNetworkExternalizer.writeProtoNetwork(protoNetwork,
                            System.getProperty("user.dir"));


            // test read
            ProtoNetwork serializedProtoNetwork =
                    protoNetworkExternalizer

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Examples of org.openbel.framework.core.protonetwork.BinaryProtoNetworkExternalizer.writeProtoNetwork()

            // Change the input proto-network descriptor to merged network
            ProtoNetworkExternalizer pne = new BinaryProtoNetworkExternalizer();
            final String artpath = artifactPath.getAbsolutePath();
            final String s1path = asPath(artpath, STAGE1_OUTPUT);
            createDirectoryArtifact(artifactPath, STAGE1_OUTPUT);
            pne.writeProtoNetwork(pn, s1path);


            // if debug, then save the text-based merged network
            if (withDebug()) {
                TextProtoNetworkExternalizer textExternalizer =
                        new TextProtoNetworkExternalizer();

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Examples of org.openbel.framework.core.protonetwork.BinaryProtoNetworkExternalizer.writeProtoNetwork()

            // Change the input proto-network descriptor to merged network
            ProtoNetworkExternalizer pne = new BinaryProtoNetworkExternalizer();
            final String artpath = artifactPath.getAbsolutePath();
            final String s2path = asPath(artpath, STAGE2_OUTPUT);
            createDirectoryArtifact(artifactPath, STAGE2_OUTPUT);
            pne.writeProtoNetwork(pn, s2path);


            // if debug, then save the text-based merged network
            if (withDebug()) {
                TextProtoNetworkExternalizer textExternalizer =
                        new TextProtoNetworkExternalizer();

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Examples of org.openbel.framework.core.protonetwork.BinaryProtoNetworkExternalizer.writeProtoNetwork()

            // Change the input proto-network descriptor to merged network
            ProtoNetworkExternalizer pne = new BinaryProtoNetworkExternalizer();
            final String artpath = artifactPath.getAbsolutePath();
            final String s3path = asPath(artpath, STAGE3_OUTPUT);
            createDirectoryArtifact(artifactPath, STAGE3_OUTPUT);
            pne.writeProtoNetwork(pn, s3path);


            // if debug, then save the text-based merged network
            if (withDebug()) {
                TextProtoNetworkExternalizer textExternalizer =
                        new TextProtoNetworkExternalizer();

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Examples of org.openbel.framework.core.protonetwork.ProtoNetworkExternalizer.writeProtoNetwork()

                new BinaryProtoNetworkExternalizer();


        try {
            // test write
            protoNetworkDescriptor =
                    protoNetworkExternalizer.writeProtoNetwork(protoNetwork,
                            System.getProperty("user.dir"));


            // test read
            ProtoNetwork serializedProtoNetwork =
                    protoNetworkExternalizer

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Examples of org.openbel.framework.core.protonetwork.ProtoNetworkExternalizer.writeProtoNetwork()

        ProtoNetworkExternalizer protoNetworkExternalizer =
                new TextProtoNetworkExternalizer();


        try {
            protoNetworkDescriptor =
                    (TextProtoNetworkDescriptor) protoNetworkExternalizer
                            .writeProtoNetwork(protoNetwork,
                                    System.getProperty("user.dir"));


            for (final File symt : protoNetworkDescriptor.getSymbolTables()) {
                FileUtils.readFileToString(symt);

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Examples of org.openbel.framework.core.protonetwork.ProtoNetworkExternalizer.writeProtoNetwork()

            // Change the input proto-network descriptor to merged network
            ProtoNetworkExternalizer pne = new BinaryProtoNetworkExternalizer();
            final String artpath = artifactPath.getAbsolutePath();
            final String s1path = asPath(artpath, STAGE1_OUTPUT);
            createDirectoryArtifact(artifactPath, STAGE1_OUTPUT);
            pne.writeProtoNetwork(pn, s1path);


            // if debug, then save the text-based merged network
            if (withDebug()) {
                TextProtoNetworkExternalizer textExternalizer =
                        new TextProtoNetworkExternalizer();

View Full Code Here

Examples of org.openbel.framework.core.protonetwork.ProtoNetworkExternalizer.writeProtoNetwork()

            // Change the input proto-network descriptor to merged network
            ProtoNetworkExternalizer pne = new BinaryProtoNetworkExternalizer();
            final String artpath = artifactPath.getAbsolutePath();
            final String s2path = asPath(artpath, STAGE2_OUTPUT);
            createDirectoryArtifact(artifactPath, STAGE2_OUTPUT);
            pne.writeProtoNetwork(pn, s2path);


            // if debug, then save the text-based merged network
            if (withDebug()) {
                TextProtoNetworkExternalizer textExternalizer =
                        new TextProtoNetworkExternalizer();

View Full Code Here

Examples of org.openbel.framework.core.protonetwork.ProtoNetworkExternalizer.writeProtoNetwork()

            // Change the input proto-network descriptor to merged network
            ProtoNetworkExternalizer pne = new BinaryProtoNetworkExternalizer();
            final String artpath = artifactPath.getAbsolutePath();
            final String s3path = asPath(artpath, STAGE3_OUTPUT);
            createDirectoryArtifact(artifactPath, STAGE3_OUTPUT);
            pne.writeProtoNetwork(pn, s3path);


            // if debug, then save the text-based merged network
            if (withDebug()) {
                TextProtoNetworkExternalizer textExternalizer =
                        new TextProtoNetworkExternalizer();

View Full Code Here

Examples of org.openbel.framework.core.protonetwork.TextProtoNetworkExternalizer.writeProtoNetwork()

        ProtoNetworkExternalizer protoNetworkExternalizer =
                new TextProtoNetworkExternalizer();


        try {
            protoNetworkDescriptor =
                    (TextProtoNetworkDescriptor) protoNetworkExternalizer
                            .writeProtoNetwork(protoNetwork,
                                    System.getProperty("user.dir"));


            for (final File symt : protoNetworkDescriptor.getSymbolTables()) {
                FileUtils.readFileToString(symt);

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