org.bridgedb.sql.transative.TransitiveMapping 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.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.bridgedb.pairs.CodeMapper;
import org.bridgedb.pairs.IdSysCodePair;
import org.bridgedb.utils.BridgeDBException;
/**
*
* @author christian
*/
public class TransitiveMapping extends ClaimedMapping {
private static final String NEW_LINE = System.getProperty("line.separator");
private final Set sysCodesToCheck;
private boolean includesMappingToSelf = false;
public TransitiveMapping (ClaimedMapping previous, DirectMapping newMapping, String predicate,
String justification) throws BridgeDBException{
super(previous, newMapping, predicate, justification);
//Never expected but just in case
if (!previous.getTargetPair().equals(newMapping.getSourcePair())){
throw new BridgeDBException ("Unexpected broken mapping chain");
}
sysCodesToCheck = recordSysCodes(previous, newMapping);
}
private Set recordSysCodes(ClaimedMapping previous, DirectMapping newMapping) throws BridgeDBException {
//Check if new mapping is mapping to self.
//stem.out.println("recording System codes");
//ystem.out.println(previous);
//ystem.out.println(newMapping);
Set syscodes;
if (newMapping.getSourceSysCode().equals(newMapping.getTargetSysCode())){
if (previous.hasMappingToSelf()){
throw new BridgeDBException("Two mappings to self in same chain.");
} else {
//Ony code that matters is the last mapping which is added at the end.
syscodes = new HashSet();
includesMappingToSelf = true;
}
} else {
includesMappingToSelf = previous.hasMappingToSelf();
syscodes = new HashSet(previous.getSysCodesToCheck());
}
syscodes.add(newMapping.getTargetSysCode());
//ystem.out.println("==" + syscodes + "==");
return syscodes;
}
public boolean createsLoop(IdSysCodePair targetRef){
//ystem.out.println ("c " + this);
//ystem.out.println (targetRef);
//Check if incoming is a mapping to self (Same syscode)
if (getTargetSysCode().equals(targetRef.getSysCode())){
//Only allow one per transitive
//ystem.out.println("mapping to self");
return includesMappingToSelf;
}
//ystem.out.println ("!= " + getIdSysCodePairTarget().getSysCode());
//ystem.out.println(sysCodesToCheck);
//The target must be a new one
return sysCodesToCheck.contains(targetRef.getSysCode());
}
@Override
public boolean hasMappingToSelf() {
return includesMappingToSelf;
}
@Override
public Set getSysCodesToCheck() {
return sysCodesToCheck;
}
}
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