/**
* 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.common.protonetwork.model;
import java.io.IOException;
import java.io.ObjectInput;
import java.io.ObjectOutput;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.openbel.framework.common.InvalidArgument;
import org.openbel.framework.common.external.ExternalType;
import org.openbel.framework.common.external.ReadCache;
import org.openbel.framework.common.external.WriteCache;
/**
* StatementAnnotationMapTable holds the index mapping from statement id to
* annotation definition / value index pairs.
*
* @author Anthony Bargnesi {@code <abargnesi@selventa.com>}
* @version 1.3 Derives from {@link ExternalType}
*/
public class StatementAnnotationMapTable extends ExternalType {
private static final long serialVersionUID = -6486699009265767018L;
/**
* Defines a map from statement index value to a set of annotation pairs.
* Note: This collection is backed by {@link LinkedHashMap} which is not
* thread-safe.
*/
private Map<Integer, Set<AnnotationPair>> statementAnnotationPairsIndex =
new LinkedHashMap<Integer, Set<AnnotationPair>>();
/**
* Adds a mapping of {@code statementIndex} to
* {@code annotationValueDefinitionPairs} in the
* {@code statementAnnotationIndex} map. A {@code statementIndex} will not
* be indexed if the {@code annotationValueDefinitionPairs} collection is
* empty.
*
* @param statementIndex {@link Integer}, the statement index as the key,
* must not be null
* @param annotationPairs {@link List} of {@code Integer[]}, the annotation
* value / definition index, which cannot be null, and if empty the
* {@code statementIndex} will not be indexed
* @throws InvalidArgument Thrown if {@code statementIndex} or
* {@code annotationValueDefinitionPairs} is null
*/
public void addStatementAnnotation(Integer statementIndex,
Set<AnnotationPair> annotationPairs) {
if (statementIndex == null) {
throw new InvalidArgument("statementIndex is null");
}
if (annotationPairs == null) {
throw new InvalidArgument("annotationValueDefinitionPairs is null.");
}
if (annotationPairs.isEmpty()) {
return;
}
Set<AnnotationPair> annotationValueDefinitions =
statementAnnotationPairsIndex
.get(statementIndex);
if (annotationValueDefinitions == null) {
statementAnnotationPairsIndex.put(statementIndex,
annotationPairs);
} else {
annotationValueDefinitions.addAll(annotationPairs);
}
}
/**
* Returns the statement annotation map table's statement index to
* annotation pairs map. This map is mutable to allow reindexing during
* phase II proto network merging.
*
* @return {@link Map}, which cannot be null
*/
public Map<Integer, Set<AnnotationPair>> getStatementAnnotationPairsIndex() {
return statementAnnotationPairsIndex;
}
/**
* {@inheritDoc}
*/
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime
* result
+ ((statementAnnotationPairsIndex == null) ? 0
: statementAnnotationPairsIndex.hashCode());
return result;
}
/**
* {@inheritDoc}
*/
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
StatementAnnotationMapTable other = (StatementAnnotationMapTable) obj;
if (statementAnnotationPairsIndex == null) {
if (other.statementAnnotationPairsIndex != null)
return false;
} else if (!statementAnnotationPairsIndex
.equals(other.statementAnnotationPairsIndex))
return false;
return true;
}
/**
* {@inheritDoc}
*/
@Override
protected void _from(ObjectInput in) throws IOException,
ClassNotFoundException {
final int size = in.readInt();
for (int i = 0; i < size; i++) {
final int statementIndex = in.readInt();
final int annotationPairsSize = in.readInt();
Set<AnnotationPair> annotationPairs =
new HashSet<AnnotationPair>(annotationPairsSize);
for (int j = 0; j < annotationPairsSize; ++j) {
AnnotationPair pair = new AnnotationPair();
pair.readExternal(in);
annotationPairs.add(pair);
}
addStatementAnnotation(statementIndex, annotationPairs);
}
}
/**
* {@inheritDoc}
*/
@Override
protected void _to(ObjectOutput out) throws IOException {
final int size = statementAnnotationPairsIndex.size();
out.writeInt(size);
for (Map.Entry<Integer, Set<AnnotationPair>> entry : statementAnnotationPairsIndex
.entrySet()) {
out.writeInt(entry.getKey().intValue());
final Set<AnnotationPair> annotationPairs = entry.getValue();
final int annotationPairsSize = annotationPairs.size();
out.writeInt(annotationPairsSize);
for (AnnotationPair pair : annotationPairs) {
pair.writeExternal(out);
}
}
}
/**
* {@inheritDoc}
*/
@Override
protected void _from(ObjectInput in, ReadCache cache)
throws IOException,
ClassNotFoundException {
throw new UnsupportedOperationException();
}
/**
* {@inheritDoc}
*/
@Override
protected void _to(ObjectOutput out, WriteCache cache)
throws IOException {
throw new UnsupportedOperationException();
}
/**
* AnnotationPair represents an integer pair of annotation definition id and
* an annotation value id. An {@code Integer[]} array would not work since a
* {@link Set} cannot perform equality between them.
*
* @author Anthony Bargnesi {@code <abargnesi@selventa.com>}
* @version 1.3 Derives from {@link ExternalType}
*/
public static class AnnotationPair extends ExternalType {
private static final long serialVersionUID = -6486699009265767019L;
/**
* Defines the annotation definition id.
*/
private/* final */int annotationDefinitionId;
/**
* Defines the annotation value id.
*/
private/* final */int annotationValueId;
/**
* Defines the hash for {@link AnnotationPair this annotation pair}.
*/
private/* final */int hash;
/**
* Creates an annotation pair from a {@code annotationDefinitionId} and
* an {@code annotationValueId}.
*
* @param annotationDefinitionId {@code int}, the annotation definition
* id
* @param annotationValueId {@code int}, the annotation value id
*/
public AnnotationPair(int annotationDefinitionId, int annotationValueId) {
this.annotationDefinitionId = annotationDefinitionId;
this.annotationValueId = annotationValueId;
this.hash = computeHash();
}
/**
* Creates an annotation pair. This public, no-argument constructor is
* required when implementing Externalizable but it is not meant to be
* used for anything else.
*/
public AnnotationPair() {
}
/**
* Returns the annotation definition id.
*
* @return {@code int}, the annotation definition id
*/
public int getAnnotationDefinitionId() {
return annotationDefinitionId;
}
/**
* Returns the annotation value id.
*
* @return {@code int}, the annotation value id
*/
public int getAnnotationValueId() {
return annotationValueId;
}
/**
* Computes the hash for {@link AnnotationPair this annotation pair}.
*
* @return the computed hash
*/
private int computeHash() {
final int prime = 31;
int result = 1;
result = prime * result + annotationDefinitionId;
result = prime * result + annotationValueId;
return result;
}
/**
* {@inheritDoc}
*/
@Override
public int hashCode() {
return hash;
}
/**
* {@inheritDoc}
*/
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
AnnotationPair other = (AnnotationPair) obj;
if (annotationDefinitionId != other.annotationDefinitionId)
return false;
if (annotationValueId != other.annotationValueId)
return false;
return true;
}
/**
* {@inheritDoc}
*/
@Override
protected void _from(ObjectInput in) throws IOException,
ClassNotFoundException {
annotationDefinitionId = in.readInt();
annotationValueId = in.readInt();
hash = computeHash();
}
/**
* {@inheritDoc}
*/
@Override
protected void _to(ObjectOutput out) throws IOException {
out.writeInt(annotationDefinitionId);
out.writeInt(annotationValueId);
}
/**
* {@inheritDoc}
*/
@Override
protected void _from(ObjectInput in, ReadCache cache)
throws IOException,
ClassNotFoundException {
throw new UnsupportedOperationException();
}
/**
* {@inheritDoc}
*/
@Override
protected void _to(ObjectOutput out, WriteCache cache)
throws IOException {
throw new UnsupportedOperationException();
}
}
}