Package org.openbel.framework.common.enums

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

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                    : e.getSourceNode());

            // handle ACTS_IN edge independently since we care about similar
            // activity functions
            if (e.getRelationshipType() == ACTS_IN) {
                final FunctionEnum actfun = opnode.getFunctionType();

                // lookup first seen node for activity function
                KamNode node = acts.get(actfun);

                // if not yet seen mark opposite node and edge as species collapse
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        return new Statement(subject, comment, ag, object, rel);
    }

    static void writeTerm(ObjectOutput out, Term term) throws IOException {
        // 1: function enum, never null
        FunctionEnum fx = term.getFunctionEnum();
        out.writeObject(fx);
        // 2: function arguments, may be null
        List<BELObject> fxargs = term.getFunctionArguments();
        if (fxargs == null) {
            out.writeByte(0);
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    }

    static Term readTerm(ObjectInput in) throws IOException,
            ClassNotFoundException {
        // 1: function enum
        FunctionEnum fx = (FunctionEnum) in.readObject();
        // 2: functions arguments
        List<BELObject> fxargs = null;
        byte obyte = in.readByte();
        if (obyte == 1) {
            int size = in.readInt();
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    /**
     * {@inheritDoc}
     */
    @Override
    public boolean match(Term term) {
        FunctionEnum fx = term.getFunctionEnum();
        if (!fx.isTranslocating()) {
            // Translocating functions only
            return false;
        }

        List<BELObject> args = term.getFunctionArguments();
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    /**
     * {@inheritDoc}
     */
    @Override
    public boolean match(Term term) {
        FunctionEnum fx = term.getFunctionEnum();
        if (fx != COMPLEX_ABUNDANCE) {
            // Complex abundance functions only
            return false;
        }

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    /**
     * {@inheritDoc}
     */
    @Override
    public boolean match(Term term) {
        FunctionEnum fx = term.getFunctionEnum();
        if (!getActivities().contains(fx)) {
            // Activity functions only
            return false;
        }

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    public boolean match(Term term) {

        // XXX the checks here essentially reproduce the
        // semantics of the reaction function

        FunctionEnum fx = term.getFunctionEnum();
        if (fx != REACTION) {
            // Reaction functions only
            return false;
        }
        List<BELObject> args = term.getFunctionArguments();
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    /**
     * {@inheritDoc}
     */
    @Override
    public boolean match(Term term) {
        FunctionEnum fx = term.getFunctionEnum();
        if (fx != DEGRADATION) {
            // Degradation functions only
            return false;
        }
        List<BELObject> args = term.getFunctionArguments();
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    /**
     * {@inheritDoc}
     */
    @Override
    public boolean match(Term term) {
        FunctionEnum fx = term.getFunctionEnum();
        if (fx != COMPOSITE_ABUNDANCE) {
            // Composite abundance functions only
            return false;
        }
        List<BELObject> args = term.getFunctionArguments();
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    }

    @Test(expected = SemanticWarning.class)
    public void testNoArgumentFailure() throws SemanticWarning {
        err.println("testNoArgumentFailure");
        FunctionEnum funcEnum = FunctionEnum.COMPLEX_ABUNDANCE;
        List<BELObject> args = new ArrayList<BELObject>();
        Term t = new Term(funcEnum, args);

        subject.checkParameterizedTerm(t);
        fail("expected semantic failure");
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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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