Package org.openbel.framework.common.model.Statement

Examples of org.openbel.framework.common.model.Statement.Object

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        Term proteinTrm = new Term(PROTEIN_ABUNDANCE);
        proteinTrm.addFunctionArgument(pp);

        Statement stmt = null;
        final Object obj = new Object(term);
        if (isMutation(fx)) {
            // mutation
            // protein term connects to its mutation with HAS_VARIANT
            // relationship
            stmt = new Statement(proteinTrm, null, null, obj, HAS_VARIANT);
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     */
    @Override
    public void checkRelationship(final Statement statement)
            throws SemanticWarning {
        RelationshipType r = statement.getRelationshipType();
        Object o = statement.getObject();

        if (o != null) {

            // Relationship must be present.
            if (r == null) {
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     */
    @Override
    public void checkListUsage(final Statement statement,
            final Document document)
            throws SemanticWarning {
        Object object = statement.getObject();

        if (object != null && !statement.hasNestedStatement() &&
                object.getTerm().getFunctionEnum() == FunctionEnum.LIST &&
                !statement.getRelationshipType().isListable()) {

            if (document != null) {
                pruneStatement(statement, document);
            }
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        Term sub = s.getSubject();
        Term obj = s.getObject().getTerm();
        final RelationshipType rel = s.getRelationshipType();

        final Statement stmt = new Statement(obj);
        stmt.setObject(new Object(sub));
        stmt.setRelationshipType(rel);

        return asList(new Statement[] { stmt });
    }
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                                               // translocation term is the
                                               // abundance
        // tranlocation connects the abundance term with TRANSLOCATES
        // relationship
        Statement statement =
                new Statement(translocation, null, null, new Object(abundance),
                        TRANSLOCATES);
        attachExpansionRuleCitation(statement);
        statements.add(statement);

        return statements;
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        List<Statement> statements = new ArrayList<Statement>();

        // Complex connects to its components with HAS_COMPONENT relationship
        for (BELObject o : term.getFunctionArguments()) {
            Term t = (Term) o;
            Object obj = new Object(t);
            Statement s = new Statement(term, null, null, obj, HAS_COMPONENT);
            attachExpansionRuleCitation(s);
            statements.add(s);
        }
        return statements;
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        BELObject firstArgument = activity.getFunctionArguments().get(0);
        Term abundance = (Term) firstArgument; // only argument of a moleculary
                                               // activity term is the abundance
        // Molecular activities connect to its abundance term with ACTS_IN
        // relationship
        final Object obj = new Object(activity);
        Statement statement =
                new Statement(abundance, null, null, obj, ACTS_IN);
        attachExpansionRuleCitation(statement);
        statements.add(statement);
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        Term products = (Term) secondArgument;

        // all reactants connect to reaction with REACTANT_IN relationship
        for (BELObject reactant : reactants.getFunctionArguments()) {
            Term sub = (Term) reactant;
            Object obj = new Object(reaction);
            Statement stmt = new Statement(sub, null, null, obj, REACTANT_IN);
            attachExpansionRuleCitation(stmt);
            statements.add(stmt);
        }

        // a reaction connects to its products with HAS_PRODUCT relationship
        for (BELObject product : products.getFunctionArguments()) {
            Term sub = (Term) product;
            Object obj = new Object(sub);
            Statement stmt =
                    new Statement(reaction, null, null, obj, HAS_PRODUCT);
            attachExpansionRuleCitation(stmt);
            statements.add(stmt);
        }
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        Term protein = (Term) firstArgument; // only argument of a protein
                                             // degradation term is the protein

        // Protein degradation term connects to its protein with
        // DIRECTLY_DECREASES relationship
        final Object obj = new Object(protein);
        Statement statement =
                new Statement(degradation, null, null, obj, DIRECTLY_DECREASES);
        attachExpansionRuleCitation(statement);
        statements.add(statement);
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        // compositeAbundance connects to its abundance terms with INCLUDES
        // relationship
        for (BELObject o : term.getFunctionArguments()) {
            Term t = (Term) o; // component of the composite term
            final Object obj = new Object(t);
            Statement s = new Statement(term, null, null, obj, INCLUDES);
            attachExpansionRuleCitation(s);
            statements.add(s);
        }
        return statements;
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Related Classes of org.openbel.framework.common.model.Statement.Object

  • org.openbel.framework.common.xbel.converters.StatementConverter
  • org.openbel.framework.compiler.PhaseThreeImpl
  • org.openbel.framework.core.compiler.expansion.ComplexAbundanceExpansionRule
  • org.openbel.framework.core.compiler.expansion.CompositeAbundanceExpansionRule
  • org.openbel.framework.core.compiler.expansion.DegradationExpansionRule
  • org.openbel.framework.core.compiler.expansion.ModificationExpansionRule
  • org.openbel.framework.core.compiler.expansion.MolecularActivityExpansionRule
  • org.openbel.framework.core.compiler.expansion.ReactionExpansionRule
  • org.openbel.framework.core.compiler.expansion.ReciprocalExpansionRule
  • org.openbel.framework.core.compiler.expansion.TranslocationExpansionRule
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