/** * Copyright (C) 2012-2013 Selventa, Inc. * * This file is part of the OpenBEL Framework. * * This program is free software; you can redistribute it and/or modify it * under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * The OpenBEL Framework is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY * or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public * License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with the OpenBEL Framework. If not, see <http://www.gnu.org/licenses/>. * * Additional Terms under LGPL v3: * * This license does not authorize you and you are prohibited from using the * name, trademarks, service marks, logos or similar indicia of Selventa, Inc., * or, in the discretion of other licensors or authors of the program, the * name, trademarks, service marks, logos or similar indicia of such authors or * licensors, in any marketing or advertising materials relating to your * distribution of the program or any covered product. This restriction does * not waive or limit your obligation to keep intact all copyright notices set * forth in the program as delivered to you. * * If you distribute the program in whole or in part, or any modified version * of the program, and you assume contractual liability to the recipient with * respect to the program or modified version, then you will indemnify the * authors and licensors of the program for any liabilities that these * contractual assumptions directly impose on those licensors and authors. */ package org.openbel.framework.core.compiler.expansion; import static org.openbel.framework.common.BELUtilities.noItems; import static org.openbel.framework.common.enums.FunctionEnum.getActivities; import static org.openbel.framework.common.enums.RelationshipType.ACTS_IN; import java.util.ArrayList; import java.util.List; import org.openbel.framework.common.enums.FunctionEnum; import org.openbel.framework.common.model.BELObject; import org.openbel.framework.common.model.Statement; import org.openbel.framework.common.model.Term; import org.openbel.framework.common.model.Statement.Object; /** * Molecular activities connect to its abundance term with ACTS_IN relationship. */ class MolecularActivityExpansionRule extends ExpansionRule<Term> { /** * {@inheritDoc} */ @Override public String getName() { return "Molecular Activity expansion rule"; } /** * {@inheritDoc} */ @Override public boolean match(Term term) { FunctionEnum fx = term.getFunctionEnum(); if (!getActivities().contains(fx)) { // Activity functions only return false; } List<BELObject> args = term.getFunctionArguments(); if (noItems(args)) { // Must have at least one function argument return false; } BELObject x = args.get(0); if (!(x instanceof Term)) { // First argument must be a term return false; } return true; } /** * {@inheritDoc} */ @Override public List<Statement> expand(Term activity) { List<Statement> statements = new ArrayList<Statement>(); 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); return statements; } }