org.bridgedb.sql.transative.MappingsHandlers Maven / Gradle / Ivy
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// BridgeDb,
// An abstraction layer for identifier mapping services, both local and online.
//
// Copyright 2006-2009 BridgeDb developers
// Copyright 2012-2013 Christian Y. A. Brenninkmeijer
// Copyright 2012-2013 OpenPhacts
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
package org.bridgedb.sql.transative;
import java.util.ArrayDeque;
import java.util.HashSet;
import java.util.Set;
import org.bridgedb.pairs.IdSysCodePair;
import org.bridgedb.sql.justification.JustificationMaker;
import org.bridgedb.sql.predicate.PredicateMaker;
import org.bridgedb.uri.api.Mapping;
import org.bridgedb.utils.BridgeDBException;
/**
*
* @author christian
*/
public class MappingsHandlers {
private final IdSysCodePair sourceRef;
private final ArrayDeque toCheck = new ArrayDeque();
private final Set checkedPairs = new HashSet();
private final Set mappings = new HashSet();
private final PredicateMaker predicateMaker;
private final JustificationMaker justificationMaker;
public MappingsHandlers(IdSysCodePair sourceRef, PredicateMaker predicateMaker,
JustificationMaker justificationMaker){
this.sourceRef = sourceRef;
checkedPairs.add(sourceRef);
this.predicateMaker = predicateMaker;
this.justificationMaker = justificationMaker;
}
private void addMapping(ClaimedMapping mapping){
//ystem.out.println("+ " + mapping);
toCheck.push(mapping);
mappings.add(mapping);
checkedPairs.add(mapping.getTargetPair());
}
public final void addMappings(Set newMappings) {
for (DirectMapping mapping: newMappings){
if (checkedPairs.contains(mapping.getTargetPair())){
//ystem.out.println("Duplicate " + mapping.getIdSysCodePairTarget());
} else {
addMapping(mapping);
}
}
}
public final boolean moreToCheck() {
return !toCheck.isEmpty();
}
public final ClaimedMapping nextToCheck() {
return toCheck.pop();
}
public final void addMapping(ClaimedMapping previous, DirectMapping newMapping) throws BridgeDBException {
IdSysCodePair targetRef = newMapping.getTargetPair();
if (checkedPairs.contains(targetRef)){
//ystem.out.println("Duplicate " + targetRef);
return;
}
if (previous.createsLoop(targetRef)){
//ystem.out.println("Loop " + targetRef);
return;
}
String predicate = predicateMaker.possibleCombine(previous.getPredicate(), newMapping.getPredicate());
if (predicate == null){
//ystem.out.println("unable to combine " + previous.getPredicate() + " and " + newMapping.getPredicate());
return;
}
String justification = justificationMaker.possibleCombine(previous.getJustification(), newMapping.getJustification());
if (justification == null){
//ystem.out.println("unable to combine " + previous.getJustification() + " and " + newMapping.getJustification());
return;
}
TransitiveMapping transitiveMapping = new TransitiveMapping(previous, newMapping, predicate, justification);
//ystem.out.println("Adding " + transitiveMapping);
addMapping(transitiveMapping);
}
public final void addMappings(ClaimedMapping previous, Set newMappings) throws BridgeDBException {
for (DirectMapping newMapping: newMappings){
this.addMapping(previous, newMapping);
}
}
public final Set getMappings() {
return mappings;
}
}
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