/*
  File: CytoscapeFingRootGraph.java

  Copyright (c) 2006, 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.giny;

import cytoscape.*;

import cytoscape.util.intr.*;

import fing.model.*;

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

import java.util.Collection;
import java.util.Map;
import java.util.HashMap;


/**
 *
 */
public class CytoscapeFingRootGraph extends FingExtensibleRootGraph implements CytoscapeRootGraph {
	Map<String,Integer> node_name_index_map;
	Map<String,Integer> edge_name_index_map;

	/**
	 * Creates a new CytoscapeFingRootGraph object.
	 */
	public CytoscapeFingRootGraph() {
		super(new CyNodeDepot(), new CyEdgeDepot());

		node_name_index_map = new HashMap<String,Integer>();
		edge_name_index_map = new HashMap<String,Integer>();
	}

	/**
	 *  DOCUMENT ME!
	 *
	 * @param nodes DOCUMENT ME!
	 * @param edges DOCUMENT ME!
	 *
	 * @return  DOCUMENT ME!
	 */
	public CyNetwork createNetwork(Collection nodes, Collection edges) {
		Node[] node = (Node[]) nodes.toArray(new Node[] {  });
		Edge[] edge = (Edge[]) edges.toArray(new Edge[] {  });

		return createNetwork(node, edge);
	}

	/**
	 * Creates a new Network
	 */
	public CyNetwork createNetwork(Node[] nodes, Edge[] edges) {
		final Node[] nodeArr = ((nodes != null) ? nodes : new Node[0]);
		final Edge[] edgeArr = ((edges != null) ? edges : new Edge[0]);
		final RootGraph root = this;

		try {
			return new FingCyNetwork(this,
			                         new IntIterator() {
					private int index = 0;

					public boolean hasNext() {
						return index < nodeArr.length;
					}

					public int nextInt() {
						if ((nodeArr[index] == null) || (nodeArr[index].getRootGraph() != root))
							throw new IllegalArgumentException();

						return nodeArr[index++].getRootGraphIndex();
					}
				},
			                         new IntIterator() {
					private int index = 0;

					public boolean hasNext() {
						return index < edgeArr.length;
					}

					public int nextInt() {
						if ((edgeArr[index] == null) || (edgeArr[index].getRootGraph() != root))
							throw new IllegalArgumentException();

						return edgeArr[index++].getRootGraphIndex();
					}
				});
		} catch (IllegalArgumentException exc) {
			return null;
		}
	}

	/**
	 * Uses Code copied from ColtRootGraph to create a new Network.
	 */
	public CyNetwork createNetwork(int[] nodeInx, int[] edgeInx) {
		if (nodeInx == null)
			nodeInx = new int[0];

		if (edgeInx == null)
			edgeInx = new int[0];

		try {
			return new FingCyNetwork(this, new ArrayIntIterator(nodeInx, 0, nodeInx.length),
			                         new ArrayIntIterator(edgeInx, 0, edgeInx.length));
		} catch (IllegalArgumentException exc) {
			return null;
		}
	}

	/**
	 *  DOCUMENT ME!
	 *
	 * @param identifier DOCUMENT ME!
	 *
	 * @return  DOCUMENT ME!
	 */
	public CyNode getNode(String identifier) {
		Integer nodeId = node_name_index_map.get(identifier);
		if ( nodeId != null )
			return (CyNode) getNode(nodeId.intValue());
		else
			return null;
	}

	/**
	 *  DOCUMENT ME!
	 *
	 * @param identifier DOCUMENT ME!
	 *
	 * @return  DOCUMENT ME!
	 */
	public CyEdge getEdge(String identifier) {
		Integer edgeId = edge_name_index_map.get(identifier);
		if ( edgeId != null )
			return (CyEdge) getEdge(edgeId.intValue());
		else
			return null;
	}

	/**
	 *  DOCUMENT ME!
	 *
	 * @param identifier DOCUMENT ME!
	 * @param index DOCUMENT ME!
	 */
	public void setNodeIdentifier(String identifier, int index) {
		if (index == 0) {
			node_name_index_map.remove(identifier);
		} else {
			node_name_index_map.put(identifier, index);
		}
	}

	/**
	 *  DOCUMENT ME!
	 *
	 * @param identifier DOCUMENT ME!
	 * @param index DOCUMENT ME!
	 */
	public void setEdgeIdentifier(String identifier, int index) {
		if (index == 0) {
			edge_name_index_map.remove(identifier);
		} else {
			edge_name_index_map.put(identifier, index);
		}
	}
}