org.bridgedb.uri.api.Mapping Maven / Gradle / Ivy
// 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.uri.api;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.bridgedb.Xref;
import org.bridgedb.pairs.CodeMapper;
import org.bridgedb.pairs.IdSysCodePair;
import org.bridgedb.utils.BridgeDBException;
/**
* Contains the information held for a particular mapping.
*
* See getMethods for what is returned.
*
* @author Christian
*/
public class Mapping implements Comparable{
//Both ASSERTED and TRANSITIVE mappings have these
private final String justification;
private final String lens;
private final String predicate;
//Only ASSERTED mappings have these
private final String mappingResource;
private final String mappingSource;
private final String id;
//Only TRANSITIVE mappings have these
private final List viaMappings;
//All three types can have these
//These are set later if required
protected Xref source = null;
protected Xref target = null;
protected Set sourceUri = new HashSet();
protected Set targetUri = new HashSet();
/**
*
* @param predicate
* @param justification
* @param mappingSetId
* @param mappingResource
* @param mappingSource
* @param lens
*/
public Mapping(String predicate, String justification, int mappingSetId, String mappingResource, String mappingSource, String lens){
this.predicate = predicate;
this.justification = justification;
this.id = "" + mappingSetId;
this.lens = lens;
this.mappingResource = mappingResource;
this.mappingSource = mappingSource;
viaMappings = new ArrayList();
}
public Mapping(Mapping previous, Mapping newMapping, String predicate, String justification){
this.predicate = predicate;
this.justification = justification;
this.lens = previous.lens;
this.id = previous.id + "_" + newMapping.id;
this.mappingResource = null;
this.mappingSource = null;
viaMappings = new ArrayList();
if (previous.isTransitive()){
this.viaMappings.addAll(previous.getViaMappings());
} else {
this.viaMappings.add(previous);
}
if (newMapping.isTransitive()){
this.viaMappings.addAll(newMapping.viaMappings);
} else {
this.viaMappings.add(newMapping);
}
}
public Mapping(){
this.predicate = null;
this.justification = null;
this.id = "self";
this.lens = null;
this.mappingResource = null;
this.mappingSource = null;
viaMappings = new ArrayList();
}
//From Bean
public Mapping(Xref source, Xref target, Set sourceUri, Set targetUri,
String justification, String predicate, String lens, String mappingResource, String mappingSource,
String mappingSetId, List vias){
this.source = source;
this.target = target;
this.sourceUri = sourceUri;
this.targetUri = targetUri;
this.predicate = predicate;
this.justification = justification;
this.id = mappingSetId;
this.lens = lens;
this.mappingResource = mappingResource;
this.mappingSource = mappingSource;
this.viaMappings = vias;
}
public Mapping (String uri, Set targetUris){
this.sourceUri.add(uri);
this.targetUri.addAll(targetUris);
this.predicate = null;
this.justification = null;
this.id = "self";
this.lens = null;
this.mappingResource = null;
this.mappingSource = null;
viaMappings = new ArrayList();
}
public Mapping (String uri, IdSysCodePair pair){
this.sourceUri.add(uri);
this.targetUri.add(uri);
this.predicate = null;
this.justification = null;
this.id = null;
this.lens = null;
this.mappingResource = null;
this.mappingSource = null;
viaMappings = new ArrayList();
}
/**
* @return the sourceUris
*/
public final Set getSourceUri() {
return sourceUri;
}
public final void addSourceUri(String sourceUri){
getSourceUri().add(sourceUri);
}
public final void addSourceUris(Collection sourceUris){
getSourceUri().addAll(sourceUris);
}
/**
* @return the target Uris
*/
public final Set getTargetUri() {
return targetUri;
}
public final void addTargetUri(String targetUri){
getTargetUri().add(targetUri);
}
public final void addTargetUris(Collection extraTargetUris){
getTargetUri().addAll(extraTargetUris);
}
public final String getMappingSetId(){
return id;
}
/**
* @return the predicate
*/
public final String getPredicate() {
return predicate;
}
/**
* @return the source
*/
public final Xref getSource() {
return source;
}
/**
* @return the target
*/
public final Xref getTarget() {
return target;
}
/**
* @param sourceUris the sourceUris to set
*/
public final void setSourceUri(Set sourceUris) {
this.sourceUri = sourceUris;
}
/**
* @param targetUris the targetUris to set
*/
public final void setTargetUri(Set targetUris) {
this.targetUri = targetUris;
}
public final String getLens() {
return lens;
}
/**
* @return the justification
*/
public final String getJustification() {
return justification;
}
/**
* @param source the source to set
*/
public final void setSource(Xref source) {
this.source = source;
}
/**
* @param target the target to set
*/
public final void setTarget(Xref target) {
this.target = target;
}
/**
* @return the mappingResource
*/
public String getMappingResource() {
return mappingResource;
}
/**
* @return the mappingSource
*/
public final String getMappingSource() {
return mappingSource;
}
/**
* @return the viaMappings
*/
public List getViaMappings() {
return viaMappings;
}
public final boolean isMappingToSelf() {
return predicate == null;
}
public final boolean isTransitive() {
return !viaMappings.isEmpty();
}
@Override
public int compareTo(Mapping o) {
return 0;
}
}