/**
* 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 static org.openbel.framework.common.BELUtilities.entries;
import static org.openbel.framework.common.BELUtilities.index;
import java.io.IOException;
import java.io.ObjectInput;
import java.io.ObjectOutput;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.LinkedHashSet;
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;
import org.openbel.framework.common.model.Namespace;
/**
* NamespaceTable holds the namespaces seen from documents. This class manages
* the {@code namespaces} through the {@link #addNamespace(TableNamespace, int)}
* operation.
*
* @author Anthony Bargnesi {@code <abargnesi@selventa.com>}
* @version 1.3 Derives from {@link ExternalType}
*/
public class NamespaceTable extends ExternalType {
private static final long serialVersionUID = -6486699009265767005L;
/**
* Defines a unique collection to hold namespace values. Note: This
* collection is backed by {@link LinkedHashSet} which is not thread-safe.
*/
private Set<TableNamespace> namespaces =
new LinkedHashSet<TableNamespace>();
/**
* Defines a map from {@link TableNamespace} to an index representing
* insertion order in {@code namespaces}. Note: This collection is backed by
* {@link HashMap} which is not thread-safe.
*/
private Map<TableNamespace, Integer> namespaceIndex =
new HashMap<TableNamespace, Integer>();
/**
* Defines a map from index to {@link TableNamespace}. Note: This collection
* is backed by {@code HashMap} which is not threadsafe.
*/
private Map<Integer, TableNamespace> indexNamespace =
new HashMap<Integer, NamespaceTable.TableNamespace>();
/**
* Defines a map from document index to a {@link List} of namespace index.
* Note: This collection is backed by {@code LinkedHashMap} which is not
* threadsafe.
*/
private Map<Integer, List<Integer>> documentNamespaces =
new LinkedHashMap<Integer, List<Integer>>();
/**
* Adds a namespace to the {@code namespaces} set. The insertion index is
* captured by {@code namespaceIndex}. The association of document to
* namespaces is also captured using the {@code documentNamespaces} map.
*
* @param namespace {@link TableNamespace}, the namespace to add, which
* cannot be null
* @param did {@code int}, the document id that this {@code namespace} is
* contained in
* @return {@code int}, the index of the added namespace ({@code > 0})
* @throws InvalidArgument Thrown if {@code namespace} is null
*/
public int addNamespace(TableNamespace namespace, int did) {
if (namespaces == null) {
throw new InvalidArgument("namespace is null");
}
if (namespaces.add(namespace)) {
int nextIndex = namespaces.size() - 1;
namespaceIndex.put(namespace, nextIndex);
indexNamespace.put(nextIndex, namespace);
}
Integer nsindex = namespaceIndex.get(namespace);
List<Integer> nsi = documentNamespaces.get(did);
if (nsi == null) {
nsi = new ArrayList<Integer>();
documentNamespaces.put(did, nsi);
}
nsi.add(nsindex);
return nsindex;
}
/**
* Returns the table namespace by index.
*
* @param nid Table namespace index
* @return TableNamespace
*/
public TableNamespace getTableNamespace(int nid) {
return indexNamespace.get(nid);
}
/**
* Returns the namespace table's {@code namespaces} set. This set is
* unmodifiable to preserve the state of the namespace table.
*
* @return {@link Set}, which cannot be null or modified
*/
public Set<TableNamespace> getNamespaces() {
return Collections.unmodifiableSet(namespaces);
}
/**
* Returns the map of {@link TableNamespace} to index. This map is
* unmodifiable to preserve the state of the namespace table.
*
* @return {@link Map}, which cannot be null or modified
*/
public Map<TableNamespace, Integer> getNamespaceIndex() {
return Collections.unmodifiableMap(namespaceIndex);
}
/**
* Returns the map of index to {@link TableNamespace}. This map is
* unmodifiable to preserve the state of the namespace table.
*
* @return {@link Map}, which cannot be null or modified
*/
public Map<Integer, TableNamespace> getIndexNamespace() {
return Collections.unmodifiableMap(indexNamespace);
}
/**
* Returns the map of document index to {@link List} of {@link Integer}
* namespace indexes. This map is unmodifiable to preserve the state of the
* namespace table.
*
* @return {@link Map}, which cannot be null or modified
*/
public Map<Integer, List<Integer>> getDocumentNamespaces() {
return Collections.unmodifiableMap(documentNamespaces);
}
/**
* {@inheritDoc}
*/
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result
+ ((indexNamespace == null) ? 0 : indexNamespace.hashCode());
result = prime * result
+ ((namespaceIndex == null) ? 0 : namespaceIndex.hashCode());
result = prime * result
+ ((namespaces == null) ? 0 : namespaces.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;
NamespaceTable other = (NamespaceTable) obj;
if (indexNamespace == null) {
if (other.indexNamespace != null)
return false;
} else if (!indexNamespace.equals(other.indexNamespace))
return false;
if (namespaceIndex == null) {
if (other.namespaceIndex != null)
return false;
} else if (!namespaceIndex.equals(other.namespaceIndex))
return false;
if (namespaces == null) {
if (other.namespaces != null)
return false;
} else if (!namespaces.equals(other.namespaces))
return false;
return true;
}
/**
* {@inheritDoc}
*/
@Override
protected void _from(ObjectInput in) throws IOException,
ClassNotFoundException {
// 1: read number of table namespaces
final int size = in.readInt();
for (int i = 0; i < size; i++) {
final TableNamespace ns = new TableNamespace();
// 1: read table namespace
ns.readExternal(in);
// 2: read number of documents
final int documentsSize = in.readInt();
for (int j = 0; j < documentsSize; j++) {
// 1: read document index
addNamespace(ns, in.readInt());
}
}
}
/**
* {@inheritDoc}
*/
@Override
protected void _to(ObjectOutput out) throws IOException {
TableNamespace[] tblnss = index(TableNamespace.class, indexNamespace);
// 1: write number of table namespaces
out.writeInt(tblnss.length);
for (int i = 0; i < tblnss.length; i++) {
final TableNamespace ns = tblnss[i];
// 1: write table namespace
ns.writeExternal(out);
Set<Integer> documents = new HashSet<Integer>();
for (Map.Entry<Integer, List<Integer>> entry : entries(documentNamespaces)) {
if (entry.getValue().contains(i)) {
documents.add(entry.getKey());
}
}
// 2: write number of documents
out.writeInt(documents.size());
for (Integer document : documents) {
// 1: write document index
out.writeInt(document.intValue());
}
}
}
/**
* {@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();
}
/**
* Table namespace encapsulates a document namespace. The table namespace
* holds the {@code prefix} and {@code resourceLocation} URL, but the prefix
* can be null if the namespace was the default on the document.
*
* @author Anthony Bargnesi {@code <abargnesi@selventa.com>}
* @version 1.3 Derives from {@link ExternalType}
*/
public static class TableNamespace extends ExternalType {
private static final long serialVersionUID = -6486699009265767004L;
/**
* Defines the prefix used to represent the table namespace. The prefix
* can be null for a document's default namespace.
*/
private/* final */String prefix;
/**
* Defines the resource location URL where the namespace file is
* located.
*/
private/* final */String resourceLocation;
/**
* Defines the hash for {@link TableNamespace this table namespace}.
*/
private/* final */int hash;
/**
* Creates a table namespace from the {@code resourceLocation} URL and
* sets a null {@code prefix}.
*
* @param resourceLocation {@link String}, the resource location URL,
* which cannot be null
* @throws InvalidArgument Thrown if the {@code resourceLocation} is
* null
*/
public TableNamespace(String resourceLocation) {
if (resourceLocation == null) {
throw new InvalidArgument("resourceLocation is null");
}
this.prefix = null;
this.resourceLocation = resourceLocation;
this.hash = computeHash();
}
/**
* Creates a table namespace from the bel
* {@link org.openbel.framework.common.model.Namespace}.
*
* @param belNamespace
* {@link org.openbel.framework.common.model.Namespace}, the bel
* namespace, which cannot be null
* @throws InvalidArgument Thrown if {@code belNamespace} is null
*/
public TableNamespace(Namespace belNamespace) {
if (belNamespace == null) {
throw new InvalidArgument("belNamespace is null");
}
this.prefix = belNamespace.getPrefix();
this.resourceLocation = belNamespace.getResourceLocation();
this.hash = computeHash();
}
/**
* Creates a table namespace. This public, no-argument constructor is
* required when implementing Externalizable but it is not meant to be
* used for anything else.
*/
public TableNamespace() {
}
/**
* Returns the table namespace prefix.
*
* @return {@link String}, the table namespace prefix, which can be null
*/
public String getPrefix() {
return prefix;
}
/**
* Returns the table namespace resource location.
*
* @return {@link String}, the namespace resource location, which cannot
* be null
*/
public String getResourceLocation() {
return resourceLocation;
}
/**
* Compute the hashCode of {@link TableNamespace this table namespace}.
*
* @return the hashCode
*/
private int computeHash() {
final int prime = 31;
int result = 1;
result = prime * result
+ ((prefix == null) ? 0 : prefix.hashCode());
result = prime
* result
+ ((resourceLocation == null) ? 0 : resourceLocation
.hashCode());
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;
TableNamespace other = (TableNamespace) obj;
if (prefix == null) {
if (other.prefix != null)
return false;
} else if (!prefix.equals(other.prefix))
return false;
if (resourceLocation == null) {
if (other.resourceLocation != null)
return false;
} else if (!resourceLocation.equals(other.resourceLocation))
return false;
return true;
}
/**
* {@inheritDoc}
*/
@Override
protected void _from(ObjectInput in) throws IOException,
ClassNotFoundException {
prefix = readString(in);
resourceLocation = readString(in);
hash = computeHash();
}
/**
* {@inheritDoc}
*/
@Override
protected void _to(ObjectOutput out) throws IOException {
out.writeObject(prefix);
out.writeObject(resourceLocation);
}
/**
* {@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();
}
}
}