/**
* 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.PRODUCTS;
import static org.openbel.framework.common.enums.FunctionEnum.REACTANTS;
import static org.openbel.framework.common.enums.FunctionEnum.REACTION;
import static org.openbel.framework.common.enums.RelationshipType.HAS_PRODUCT;
import static org.openbel.framework.common.enums.RelationshipType.REACTANT_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;
/**
* All reactants connect to the reaction with REACTANT_IN relationship. A
* reaction connects to its products with HAS_PRODUCT relationship.
*/
class ReactionExpansionRule extends ExpansionRule<Term> {
/**
* {@inheritDoc}
*/
@Override
public String getName() {
return "Reaction expansion rule";
}
/**
* {@inheritDoc}
*/
@Override
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();
if (noItems(args) || args.size() != 2) {
// Two function arguments only
return false;
}
BELObject x = args.get(0);
if (!(x instanceof Term)) {
// First argument must be a term
return false;
}
BELObject y = args.get(1);
if (!(y instanceof Term)) {
// Second argument must be a term
return false;
}
Term xtrm = (Term) x;
if (xtrm.getFunctionEnum() != REACTANTS) {
// First argument must be a reactants function
return false;
}
Term ytrm = (Term) y;
if (ytrm.getFunctionEnum() != PRODUCTS) {
// Second argument must be a products function
return false;
}
List<BELObject> xtrmArgs = xtrm.getFunctionArguments();
if (noItems(xtrmArgs)) {
// At least one argument to the reactants function is necessary
return false;
}
List<BELObject> ytrmArgs = ytrm.getFunctionArguments();
if (noItems(ytrmArgs)) {
// At least one argument to the products function is necessary
return false;
}
for (final BELObject o : xtrmArgs) {
// All arguments must be terms
if (!(o instanceof Term)) {
return false;
}
}
for (final BELObject o : ytrmArgs) {
// All arguments must be terms
if (!(o instanceof Term)) {
return false;
}
}
return true;
}
/**
* {@inheritDoc}
*/
@Override
public List<Statement> expand(Term reaction) {
List<Statement> statements = new ArrayList<Statement>();
BELObject firstArgument = reaction.getFunctionArguments().get(0);
BELObject secondArgument = reaction.getFunctionArguments().get(1);
// first argument of a reaction is the reactants
Term reactants = (Term) firstArgument;
// second argument of a reaction is the products
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);
}
return statements;
}
}