/*
 Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)

 The Cytoscape Consortium is:
 - Institute for Systems Biology
 - University of California San Diego
 - Memorial Sloan-Kettering Cancer Center
 - Institut Pasteur
 - Agilent Technologies

 This library 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 2.1 of the License, or
 any later version.

 This library 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.  The software and
 documentation provided hereunder is on an "as is" basis, and the
 Institute for Systems Biology and the Whitehead Institute
 have no obligations to provide maintenance, support,
 updates, enhancements or modifications.  In no event shall the
 Institute for Systems Biology and the Whitehead Institute
 be liable to any party for direct, indirect, special,
 incidental or consequential damages, including lost profits, arising
 out of the use of this software and its documentation, even if the
 Institute for Systems Biology and the Whitehead Institute
 have been advised of the possibility of such damage.  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 this library; if not, write to the Free Software Foundation,
 Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
*/
package cytoscape.data.synonyms;

import cytoscape.Cytoscape;

import cytoscape.data.CyAttributes;

import giny.model.Edge;
import giny.model.Node;

import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import java.util.TreeSet;


/**
 *
 * Simpler version of Thesaurus.<br>
 *
 * <p>
 * Purpose of this class is providing simple aliasing without biological
 * context. No species, commonname, nor canonical name are available. Just
 * maintains keys (IDs) and their aliases in CyAttributes.<br>
 * This will be used for importing attribute data.
 * </p>
 *
 * <p>
 * This class has no redundant data structure: everything will be stored in
 * CyAttributes, and uses immutable special attributes called Alias
 * </p>
 *
 * @since Cytoscape 2.4
 * @version 0.6
 *
 * @author kono
 *
 */
public class Aliases {
	/**
	 * Name of the attribute for aliases
	 */
	public static final String ALIAS = "cytoscape.alias.list";
	private final AliasType objectType;
	CyAttributes attributes;

	/**
	 * Constructor for the aliases object.<br>
	 *
	 * @param type
	 *            Type of alias: node, edge, or network.
	 */
	public Aliases(AliasType type) {
		this.objectType = type;

		switch (objectType) {
			case NODE:
				attributes = Cytoscape.getNodeAttributes();

				break;

			case EDGE:
				attributes = Cytoscape.getEdgeAttributes();

				break;

			case NETWORK:
				attributes = Cytoscape.getNetworkAttributes();

				break;

			default:
				// This should not happen
				attributes = null;
		}
	}

	/**
	 * Add new alias for an object.
	 *
	 * @param key
	 *            ID of the object.
	 * @param alias
	 *            New alias to be added.
	 */
	public void add(String key, String alias) {
		List<String> aliasList = attributes.getListAttribute(key, ALIAS);

		/*
		 * If there is no alias attributes, create new one.
		 */
		if (aliasList != null) {
			aliasList.add(alias);

			Set<String> aliasSet = new TreeSet<String>(aliasList);
			attributes.setListAttribute(key, ALIAS, new ArrayList<String>(aliasSet));
		} else {
			aliasList = new ArrayList<String>();
			aliasList.add(alias);
			attributes.setListAttribute(key, ALIAS, aliasList);
		}
	}

	/**
	 * Add list of aliases to the existing alias lists.<br>
	 *
	 * @param key
	 * @param aliaseList
	 */
	public void add(String key, List<String> aliasList) {
		List<String> curAliasList = attributes.getListAttribute(key, ALIAS);

		/*
		 * If there is no alias attributes, add the given list as the new one.
		 */
		if (curAliasList != null) {
			curAliasList.addAll(aliasList);
		}

		/*
		 * Remove duplicates
		 */
		Set<String> aliasSet = new TreeSet<String>(aliasList);
		attributes.setListAttribute(key, ALIAS, new ArrayList<String>(aliasSet));
	}

	/**
	 * Remove an alias.<br>
	 *
	 * @param key
	 *            ID of the object.
	 * @param alias
	 *            Alias to be removed.
	 */
	public void remove(String key, String alias) {
		List<String> curAliasList = attributes.getListAttribute(key, ALIAS);

		/*
		 * Need to remove the alias only when alias attributes exist.
		 */
		if (curAliasList != null) {
			curAliasList.remove(alias);
			attributes.setListAttribute(key, ALIAS, curAliasList);
		}
	}

	/**
	 *
	 * @param key
	 * @return
	 */
	public List<String> getAliases(String key) {
		return attributes.getListAttribute(key, ALIAS);
	}

	/**
	 *
	 * Returns true if the object with the alias wxists in the memory
	 * (rootGraph).
	 *
	 * This is an O(n) operation, which is expensive!
	 *
	 * @param key
	 * @param alias
	 * @return Key for this alias. If it does not exist, return null.
	 */
	public String getKey(String alias) {
		final Iterator it;
		String id = null;

		switch (objectType) {
			case NODE:
				it = Cytoscape.getRootGraph().nodesIterator();

				while (it.hasNext()) {
					id = ((Node) it.next()).getIdentifier();

					final List aliases = attributes.getListAttribute(id, ALIAS);

					if ((aliases != null) && aliases.contains(alias)) {
						return id;
					}
				}

				break;

			case EDGE:
				it = Cytoscape.getRootGraph().edgesIterator();

				while (it.hasNext()) {
					id = ((Edge) it.next()).getIdentifier();

					final List aliases = attributes.getListAttribute(id, ALIAS);

					if ((aliases != null) && aliases.contains(alias)) {
						return id;
					}
				}

				break;

			case NETWORK:
				it = Cytoscape.getNetworkSet().iterator();

				while (it.hasNext()) {
					id = ((Node) it.next()).getIdentifier();

					final List aliases = attributes.getListAttribute(id, ALIAS);

					if ((aliases != null) && aliases.contains(alias)) {
						return id;
					}
				}

				break;

			default:

			// This should not happen
		}

		return null;
	}

	/**
	 * Return set of all names for the key (including key itself.)
	 *
	 * @param key
	 * @return
	 */
	public Set<String> getIdSet(String key) {
		List<String> curAliases = attributes.getListAttribute(key, ALIAS);
		Set<String> allNames = new TreeSet<String>();

		if (curAliases != null) {
			allNames.addAll(curAliases);
		}

		allNames.add(key);

		return allNames;
	}
}