Package org.openbel.framework.common.enums

Examples of org.openbel.framework.common.enums.FunctionEnum

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                        .createEvidence(
                                "the elevation of intracellular cAMP concentration that results from increased glucagon production also plays a role in the down-regulation process"));

        statementGroup.setAnnotationGroup(annotationGroup);

        FunctionEnum p = FunctionEnum.PROTEIN_ABUNDANCE;
        List<BELObject> args = new ArrayList<BELObject>();

        args.add(CommonModelFactory.getInstance().createParameter(hgncNs,
                "NFKB"));
        Term t = new Term(p, args);

        FunctionEnum r = FunctionEnum.RNA_ABUNDANCE;
        args = new ArrayList<BELObject>();
        args.add(CommonModelFactory.getInstance()
                .createParameter(hgncNs, "FAS"));
        Term t2 = new Term(r, args);
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                                        + "on lipogenic gene expression in the liver, indirectly, by increasing glucose flux through glucokinase, "
                                        + "and/or directly, by activation of lipogenic gene expression"));

        statementGroup.setAnnotationGroup(annotationGroup);

        FunctionEnum fp = FunctionEnum.PROTEIN_ABUNDANCE;
        List<BELObject> args = new ArrayList<BELObject>();
        args.add(CommonModelFactory.getInstance().createParameter(hgncNs,
                "TXNIP"));
        Term t = new Term(fp, args);

        FunctionEnum ft = FunctionEnum.TRANSCRIPTIONAL_ACTIVITY;
        args = new ArrayList<BELObject>();
        args.add(CommonModelFactory.getInstance().createParameter(hgncNs,
                "IL3RA"));
        Term t2 = new Term(ft, args);

        FunctionEnum fr = FunctionEnum.RIBOSYLATION_ACTIVITY;
        args = new ArrayList<BELObject>();
        args.add(t2);
        Term t3 = new Term(fr, args);

        args = new ArrayList<BELObject>();
        args.add(CommonModelFactory.getInstance().createParameter(hgncNs,
                "ESR1"));
        Term t4 = new Term(fp, args);

        args = new ArrayList<BELObject>();
        args.add(CommonModelFactory.getInstance().createParameter(hgncNs,
                "BRCA1"));
        Term t5 = new Term(fp, args);

        args = new ArrayList<BELObject>();
        args.add(t4);
        Term t6 = new Term(ft, args);

        FunctionEnum fg = FunctionEnum.GENE_ABUNDANCE;
        args = new ArrayList<BELObject>();
        args.add(CommonModelFactory.getInstance().createParameter(hgncNs,
                "TXNIP"));
        Term t7 = new Term(fg, args);
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    public Term convert(final XBELTerm source) {
        if (source == null) return null;

        // Set term function
        Function f = source.getFunction();
        FunctionEnum funcEnum = fromString(f.value());

        // Destination type
        Term dest = new Term(funcEnum);

        // Schema defines either a list of arg values or terms
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    public XBELTerm convert(Term source) {
        if (source == null) return null;

        XBELTerm xt = new XBELTerm();

        FunctionEnum functionEnum = source.getFunctionEnum();
        Function func = Function.fromValue(functionEnum.getDisplayValue());
        xt.setFunction(func);

        List<BELObject> functionArgs = source.getFunctionArguments();
        List<JAXBElement> prmtrms = xt.getParameterOrTerm();
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     *
     * @param s String
     * @return boolean
     */
    private boolean validFunction(final String s) {
        FunctionEnum fe = getFunctionEnum(s);
        if (fe != null) return true;
        return false;
    }
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        out.println();

        out.println("Function definitions:");
        // Print the function and function signatures.
        for (int i = 1; i <= values.length; i++) {
            FunctionEnum fe = values[i - 1];
            out.println("\t" + i + ": " + fe);
            out.println("\t\treturns: " + fe.getReturnType());
            out.println("\t\tsignatures:");
            for (final Signature sig : fe.getFunction().getSignatures()) {
                out.println("\t\t\t" + sig);
            }
            out.println();
        }
    }
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     *
     * @param t {@link Term}
     * @param b {@link StringBuilder}
     */
    private static void replaceParameters(Term t, StringBuilder b) {
        FunctionEnum f = t.getFunctionEnum();
        String fx = f.getShortestForm();
        b.append(fx).append("(");
        if (hasItems(t.getFunctionArguments())) {
            for (BELObject bo : t.getFunctionArguments()) {
                if (Term.class.isAssignableFrom(bo.getClass())) {
                    Term inner = (Term) bo;
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            // rule out invalid or non-orthologous statements
            if (validOrthologousStatement(orthoStmt)) {
                // break down subject
                final Term sub = orthoStmt.getSubject();
                final FunctionEnum subf = sub.getFunctionEnum();
                final List<Parameter> subp = sub.getParameters();
                final Parameter subjectParam = subp.get(0);

                // break down object
                final Term obj = orthoStmt.getObject().getTerm();
                final FunctionEnum objf = obj.getFunctionEnum();
                final List<Parameter> objp = obj.getParameters();
                final Parameter objectParam = objp.get(0);

                // lookup exact match of subject term
                if (pnterms.contains(sub)) {
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Related Classes of org.openbel.framework.common.enums.FunctionEnum

  • org.openbel.framework.api.DefaultOrthologize
  • org.openbel.framework.api.internal.Iter
  • org.openbel.framework.api.internal.KAMStoreDaoImpl
  • org.openbel.framework.common.lang.Signature
  • org.openbel.framework.common.model.Term
  • org.openbel.framework.common.protonetwork.model.StatementTable
  • org.openbel.framework.common.xbel.converters.TermConverter
  • org.openbel.framework.compiler.PhaseThreeImpl
  • org.openbel.framework.core.compiler.expansion.ComplexAbundanceExpansionRule
  • org.openbel.framework.core.compiler.expansion.CompositeAbundanceExpansionRule
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