Examples of EquivalentParameter

org.openbel.framework.core.equivalence.EquivalentParameter
Immutable specialization of a common model {@link Parameter parameter}allowing for Java equivalence relations to function in tandem with framework parameter equivalencing.
If a bucket is provided during time of construction, the equivalence relation for these objects will be based solely on the bucket field. The effect of this is that for two equivalence parameter objects:
```
  x: (NAMESPACE1:VALUE1) y: (NAMESPACE2:VALUE2)  
```
If {@code x} and {@code y} have the same bucket, i.e., they both express thesame biological knowledge, the Java object representations are equal. Therefore {@code x.equals(y)} and {@code y.equals(x)}. Note that for parameters with no equivalences, these objects function identically to normal {@link Parameter} objects with the exception of their immutable nature.

Examples of org.openbel.framework.core.equivalence.EquivalentParameter

        final Namespace hgnc =
                new Namespace(
                        "HGNC",
                        "http://resource.belframework.org/belframework/1.0/namespace/hgnc-approved-symbols.belns");


        EquivalentParameter param1 = new EquivalentParameter(hgnc, "AKT1",
                SkinnyUUID.fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
        EquivalentTerm term1 = new EquivalentTerm(PROTEIN_ABUNDANCE,
                Arrays.asList((BELObject) param1));


        assertThat(term1.equals(term1), is(true));

View Full Code Here

Examples of org.openbel.framework.core.equivalence.EquivalentParameter

        final Namespace hgnc =
                new Namespace(
                        "HGNC",
                        "http://resource.belframework.org/belframework/1.0/namespace/hgnc-approved-symbols.belns");


        EquivalentParameter param1 = new EquivalentParameter(hgnc, "AKT1",
                SkinnyUUID.fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
        EquivalentTerm term1 = new EquivalentTerm(PROTEIN_ABUNDANCE,
                Arrays.asList((BELObject) param1));


        assertThat(term1.equals(new Object()), is(false));

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Examples of org.openbel.framework.core.equivalence.EquivalentParameter

    public void testExactMatchEquivalent() {
        final Namespace hgnc =
                new Namespace(
                        "HGNC",
                        "http://resource.belframework.org/belframework/1.0/namespace/hgnc-approved-symbols.belns");
        EquivalentParameter param1 = new EquivalentParameter(hgnc, "AKT1",
                SkinnyUUID.fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
        EquivalentTerm term1 = new EquivalentTerm(PROTEIN_ABUNDANCE,
                Arrays.asList((BELObject) param1));
        EquivalentParameter param2 = new EquivalentParameter(hgnc, "AKT1",
                SkinnyUUID.fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
        EquivalentTerm term2 = new EquivalentTerm(PROTEIN_ABUNDANCE,
                Arrays.asList((BELObject) param2));


        assertThat(term1.equals(term2), is(true));

View Full Code Here

Examples of org.openbel.framework.core.equivalence.EquivalentParameter

    public void testMismatchedFunctionUnequivalent() {
        final Namespace hgnc =
                new Namespace(
                        "HGNC",
                        "http://resource.belframework.org/belframework/1.0/namespace/hgnc-approved-symbols.belns");
        EquivalentParameter param1 = new EquivalentParameter(hgnc, "AKT1",
                SkinnyUUID.fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
        EquivalentTerm term1 = new EquivalentTerm(PROTEIN_ABUNDANCE,
                Arrays.asList((BELObject) param1));
        EquivalentParameter param2 = new EquivalentParameter(hgnc, "AKT1",
                SkinnyUUID.fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
        EquivalentTerm term2 = new EquivalentTerm(GENE_ABUNDANCE,
                Arrays.asList((BELObject) param2));


        assertThat(term1.equals(term2), is(false));

View Full Code Here

Examples of org.openbel.framework.core.equivalence.EquivalentParameter

                new Namespace(
                        "EGID",
                        "http://resource.belframework.org/belframework/1.0/namespace/entrez-gene-ids-hmr.belns");


        for (final FunctionEnum f : values()) {
            EquivalentParameter param1 =
                    new EquivalentParameter(
                            hgnc,
                            "AKT1",
                            SkinnyUUID
                                    .fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
            EquivalentParameter param2 =
                    new EquivalentParameter(
                            hgnc,
                            "AKT2",
                            SkinnyUUID
                                    .fromString("9be88c14-6311-4452-a911-9f02abcf6a1e"));
            EquivalentTerm term1 = new EquivalentTerm(f, Arrays.asList(
                    (BELObject) param1, (BELObject) param2));


            EquivalentParameter param4 =
                    new EquivalentParameter(
                            egid,
                            "207",
                            SkinnyUUID
                                    .fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
            EquivalentTerm term2 = new EquivalentTerm(f,

View Full Code Here

Examples of org.openbel.framework.core.equivalence.EquivalentParameter

                new Namespace(
                        "HGNC",
                        "http://resource.belframework.org/belframework/1.0/namespace/hgnc-approved-symbols.belns");


        // different parameter uuids, not equivalent
        EquivalentParameter param1 = new EquivalentParameter(hgnc, "AKT1",
                SkinnyUUID.fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
        EquivalentTerm term1 = new EquivalentTerm(PROTEIN_ABUNDANCE,
                Arrays.asList((BELObject) param1));
        EquivalentParameter param2 = new EquivalentParameter(hgnc, "AKT1",
                SkinnyUUID.fromString("27e0ab06-6644-42fc-b1f7-0b98bf4e6858"));
        EquivalentTerm term2 = new EquivalentTerm(PROTEIN_ABUNDANCE,
                Arrays.asList((BELObject) param2));


        assertThat(term1.equals(term2), is(false));

View Full Code Here

Examples of org.openbel.framework.core.equivalence.EquivalentParameter

        final Namespace hgnc =
                new Namespace(
                        "HGNC",
                        "http://resource.belframework.org/belframework/1.0/namespace/hgnc-approved-symbols.belns");


        EquivalentParameter param1 = new EquivalentParameter(hgnc, "AKT1",
                SkinnyUUID.fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
        EquivalentTerm term1 = new EquivalentTerm(PROTEIN_ABUNDANCE,
                Arrays.asList((BELObject) param1));
        EquivalentParameter param2 = new EquivalentParameter(hgnc, "AKT2",
                SkinnyUUID.fromString("9be88c14-6311-4452-a911-9f02abcf6a1e"));
        EquivalentTerm term2 = new EquivalentTerm(PROTEIN_ABUNDANCE,
                Arrays.asList((BELObject) param2));


        assertThat(term1.equals(term2), is(false));

View Full Code Here

Examples of org.openbel.framework.core.equivalence.EquivalentParameter

        final Namespace egid =
                new Namespace(
                        "EGID",
                        "http://resource.belframework.org/belframework/1.0/namespace/entrez-gene-ids-hmr.belns");


        EquivalentParameter param1 = new EquivalentParameter(hgnc, "AKT1",
                SkinnyUUID.fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
        EquivalentTerm term1 = new EquivalentTerm(PROTEIN_ABUNDANCE,
                Arrays.asList((BELObject) param1));
        EquivalentParameter param2 = new EquivalentParameter(egid, "207",
                SkinnyUUID.fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
        EquivalentTerm term2 = new EquivalentTerm(PROTEIN_ABUNDANCE,
                Arrays.asList((BELObject) param2));


        assertThat(term1.equals(term2), is(true));

View Full Code Here

Examples of org.openbel.framework.core.equivalence.EquivalentParameter

        final Namespace egid =
                new Namespace(
                        "EGID",
                        "http://resource.belframework.org/belframework/1.0/namespace/entrez-gene-ids-hmr.belns");


        EquivalentParameter param1 = new EquivalentParameter(hgnc, "AKT1",
                SkinnyUUID.fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
        EquivalentTerm term1 = new EquivalentTerm(PROTEIN_ABUNDANCE,
                Arrays.asList((BELObject) param1));
        EquivalentParameter param2 = new EquivalentParameter(egid, "257",
                SkinnyUUID.fromString("aae305e5-bb6d-4e75-ac0b-85a76e1e8e09"));
        EquivalentTerm term2 = new EquivalentTerm(PROTEIN_ABUNDANCE,
                Arrays.asList((BELObject) param2));


        assertThat(term1.equals(term2), is(false));

View Full Code Here

Examples of org.openbel.framework.core.equivalence.EquivalentParameter

                        "EGID",
                        "http://resource.belframework.org/belframework/1.0/namespace/entrez-gene-ids-hmr.belns");


        for (final FunctionEnum f : values()) {
            if (f.isSequential()) {
                EquivalentParameter param1 =
                        new EquivalentParameter(
                                hgnc,
                                "AKT1",
                                SkinnyUUID
                                        .fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
                EquivalentParameter param2 =
                        new EquivalentParameter(
                                hgnc,
                                "AKT2",
                                SkinnyUUID
                                        .fromString("9be88c14-6311-4452-a911-9f02abcf6a1e"));
                EquivalentTerm term1 = new EquivalentTerm(f, Arrays.asList(
                        (BELObject) param1, (BELObject) param2));


                EquivalentParameter param3 =
                        new EquivalentParameter(
                                egid,
                                "207",
                                SkinnyUUID
                                        .fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
                EquivalentParameter param4 =
                        new EquivalentParameter(
                                egid,
                                "208",
                                SkinnyUUID
                                        .fromString("9be88c14-6311-4452-a911-9f02abcf6a1e"));
                EquivalentTerm term2 = new EquivalentTerm(f, Arrays.asList(

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