/**
* 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.PROTEIN_ABUNDANCE;
import static org.openbel.framework.common.enums.FunctionEnum.isMutation;
import static org.openbel.framework.common.enums.FunctionEnum.isProteinDecorator;
import static org.openbel.framework.common.enums.RelationshipType.HAS_MODIFICATION;
import static org.openbel.framework.common.enums.RelationshipType.HAS_VARIANT;
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.Parameter;
import org.openbel.framework.common.model.Statement;
import org.openbel.framework.common.model.Term;
import org.openbel.framework.common.model.Statement.Object;
/**
* Protein term connects to its protein Modifications with a HAS_MODIFICATION
* relationship. Protein term connects to its mutation with a HAS_VARIANT
* relationship.
*/
class ModificationExpansionRule extends ExpansionRule<Term> {
/**
* {@inheritDoc}
*/
@Override
public String getName() {
return "ProteinModification expansion rule";
}
/**
* {@inheritDoc}
*/
@Override
public boolean match(Term term) {
FunctionEnum fx = term.getFunctionEnum();
if (fx != PROTEIN_ABUNDANCE) {
// Protein abundance 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 Parameter)) {
// First argument must be a parameter
return false;
}
BELObject y = args.get(1);
if (!(y instanceof Term)) {
// Second argument must be a term
return false;
}
Term ytrm = (Term) y;
if (!isProteinDecorator(ytrm.getFunctionEnum())) {
// Protein decorator functions only
return false;
}
return true;
}
/**
* {@inheritDoc}
*/
@Override
public List<Statement> expand(Term term) {
List<Statement> statements = new ArrayList<Statement>();
// first argument of a protein mod term is the protein parameter
BELObject proteinArgument = term.getFunctionArguments().get(0);
Parameter pp = (Parameter) proteinArgument;
// second argument of a protein mod term is the modification
BELObject modArgument = term.getFunctionArguments().get(1);
Term mt = (Term) modArgument;
FunctionEnum fx = mt.getFunctionEnum();
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);
} else {
// modified protein
// protein term connects to its modification with HAS_MODIFICATION
// relationship
stmt = new Statement(proteinTrm, null, null, obj, HAS_MODIFICATION);
}
attachExpansionRuleCitation(stmt);
statements.add(stmt);
return statements;
}
}