/*
 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 fing.model.test;

import fing.model.FingRootGraphFactory;

import giny.model.RootGraph;

import java.io.IOException;
import java.io.InputStream;


/**
 *
 */
public final class RootGraphPerformanceTest {
	// No constructor.
	private RootGraphPerformanceTest() {
	}

	// Args:
	/**
	 *  DOCUMENT ME!
	 *
	 * @param args DOCUMENT ME!
	 *
	 * @throws ClassNotFoundException DOCUMENT ME!
	 * @throws InstantiationException DOCUMENT ME!
	 * @throws IllegalAccessException DOCUMENT ME!
	 * @throws IOException DOCUMENT ME!
	 */
	public static final void main(String[] args)
	    throws ClassNotFoundException, InstantiationException, IllegalAccessException, IOException {
		final RootGraph root = getRootGraph(args);
		final int[] nodes = createNodes(root, Integer.parseInt(args[0]));
		final int numDirectedEdges = Integer.parseInt(args[1]);
		final int numUndirectedEdges = Integer.parseInt(args[2]);
		final int[] sourceInxCreatedEdges = new int[numDirectedEdges + numUndirectedEdges];
		final int[] targetInxCreatedEdges = new int[numDirectedEdges + numUndirectedEdges];
		final boolean[] directednessCreatedEdges = new boolean[numDirectedEdges
		                                           + numUndirectedEdges];
		createEdges(root, numDirectedEdges, System.in, nodes, true, 0, sourceInxCreatedEdges,
		            targetInxCreatedEdges, directednessCreatedEdges);
		createEdges(root, numUndirectedEdges, System.in, nodes, false, numDirectedEdges,
		            sourceInxCreatedEdges, targetInxCreatedEdges, directednessCreatedEdges);

		long millisBegin = System.currentTimeMillis();
		testAdjacentEdges(root, nodes);

		long millisEnd = System.currentTimeMillis();
		System.out.println("adjacent edges test took " + (millisEnd - millisBegin)
		                   + " milliseconds");

		long millisBegin2 = System.currentTimeMillis();
		testConnectingEdges(root, nodes);

		long millisEnd2 = System.currentTimeMillis();
		System.out.println("connecting edges test took " + (millisEnd2 - millisBegin2)
		                   + " milliseconds");

		long millisBegin3 = System.currentTimeMillis();
		testNodeNeighbors(root, nodes);

		long millisEnd3 = System.currentTimeMillis();
		System.out.println("node neighbors test took " + (millisEnd3 - millisBegin3)
		                   + " milliseconds");

		long millisBegin4 = System.currentTimeMillis();
		testConnectingWeb(root, nodes);

		long millisEnd4 = System.currentTimeMillis();
		System.out.println("connecting web test took " + (millisEnd4 - millisBegin4)
		                   + " milliseconds");

		long millisBegin5 = System.currentTimeMillis();
		testAddRemove(root, nodes, sourceInxCreatedEdges, targetInxCreatedEdges,
		              directednessCreatedEdges);

		long millisEnd5 = System.currentTimeMillis();
		System.out.println("add/remove test took " + (millisEnd5 - millisBegin5) + " milliseconds");
	}

	private static final RootGraph getRootGraph(String[] mainArgs)
	    throws ClassNotFoundException, InstantiationException, IllegalAccessException {
		if ((mainArgs.length > 3) && mainArgs[3].equalsIgnoreCase("luna"))
			return (RootGraph) Class.forName("luna.LunaRootGraph").newInstance();
		else

			return FingRootGraphFactory.instantiateRootGraph();
	}

	private static final int[] createNodes(RootGraph root, int numNodes) {
		final int[] returnThis = new int[numNodes];

		for (int i = 0; i < returnThis.length; i++)
			returnThis[i] = root.createNode();

		return returnThis;
	}

	// sourceInxCreatedEdges, targetInxCreatedEdges, and directedCreatedEdges
	// are written to, not read from.
	private static final int[] createEdges(RootGraph root, int numEdges, InputStream in,
	                                       int[] nodes, boolean directed, int offsetCreatedEdges,
	                                       int[] sourceInxCreatedEdges,
	                                       int[] targetInxCreatedEdges,
	                                       boolean[] directedCreatedEdges)
	    throws IOException {
		final int[] returnThis = new int[numEdges];
		byte[] buff = new byte[8];
		int inx = 0;
		int off = 0;
		int read;

		while ((inx < numEdges) && ((read = in.read(buff, off, buff.length - off)) > 0)) {
			off += read;

			if (off < buff.length)
				continue;
			else
				off = 0;

			long randomLong = assembleLong(buff);
			int randomInt1 = (int) ((randomLong >> 32) & 0x00000000ffffffff);
			int randomInt2 = (int) (randomLong & 0x00000000ffffffff);
			int node1 = Math.abs(randomInt1) % nodes.length;
			int node2 = Math.abs(randomInt2) % nodes.length;
			sourceInxCreatedEdges[inx + offsetCreatedEdges] = node1;
			targetInxCreatedEdges[inx + offsetCreatedEdges] = node2;
			directedCreatedEdges[inx + offsetCreatedEdges] = directed && (node1 != node2);
			returnThis[inx++] = root.createEdge(nodes[node1], nodes[node2],
			                                    directed && (node1 != node2));
		}

		if (inx < numEdges)
			throw new IOException("premature end of input");

		return returnThis;
	}

	private static final long assembleLong(byte[] eightConsecutiveBytes) {
		long firstByte = (((long) eightConsecutiveBytes[0]) & 0x00000000000000ff) << 56;
		long secondByte = (((long) eightConsecutiveBytes[1]) & 0x00000000000000ff) << 48;
		long thirdByte = (((long) eightConsecutiveBytes[2]) & 0x00000000000000ff) << 40;
		long fourthByte = (((long) eightConsecutiveBytes[3]) & 0x00000000000000ff) << 32;
		long fifthByte = (((long) eightConsecutiveBytes[4]) & 0x00000000000000ff) << 24;
		long sixthByte = (((long) eightConsecutiveBytes[5]) & 0x00000000000000ff) << 16;
		long seventhByte = (((long) eightConsecutiveBytes[6]) & 0x00000000000000ff) << 8;
		long eighthByte = (((long) eightConsecutiveBytes[7]) & 0x00000000000000ff);

		return firstByte | secondByte | thirdByte | fourthByte | fifthByte | sixthByte
		       | seventhByte | eighthByte;
	}

	// This test actually fail with luna when calling several combinations:
	/**
	 *  DOCUMENT ME!
	 *
	 * @param root DOCUMENT ME!
	 * @param nodes DOCUMENT ME!
	 */
	public static final void testAdjacentEdges(RootGraph root, int[] nodes) {
		for (int i = 0; i < 4; i++) {
			boolean undirected;
			boolean incoming;
			boolean outgoing;

			if (i == 0) {
				undirected = true;
				incoming = true;
				outgoing = true;
			} else if (i == 1) {
				undirected = true;
				incoming = false;
				outgoing = true;
			} else if (i == 2) {
				undirected = false;
				incoming = false;
				outgoing = true;
			} else {
				undirected = false;
				incoming = false;
				outgoing = false;
			}

			for (int j = 0; j < nodes.length; j++) {
				root.getAdjacentEdgeIndicesArray(nodes[j], undirected, incoming, outgoing);
			}
		}
	}

	/**
	 *  DOCUMENT ME!
	 *
	 * @param root DOCUMENT ME!
	 * @param nodes DOCUMENT ME!
	 */
	public static final void testConnectingEdges(RootGraph root, int[] nodes) {
		for (int i = 0; i < 4; i++) {
			boolean undirected;
			boolean bothDirections;

			if (i == 0) {
				undirected = true;
				bothDirections = true;
			} else if (i == 1) {
				undirected = true;
				bothDirections = false;
			} else if (i == 2) {
				undirected = false;
				bothDirections = true;
			} else {
				undirected = false;
				bothDirections = false;
			}

			for (int j = 1; j < nodes.length; j++) {
				root.getEdgeIndicesArray(nodes[j - 1], nodes[j], undirected, bothDirections);
			}
		}
	}

	/**
	 *  DOCUMENT ME!
	 *
	 * @param root DOCUMENT ME!
	 * @param nodes DOCUMENT ME!
	 */
	public static final void testNodeNeighbors(RootGraph root, int[] nodes) {
		for (int j = 1; j < nodes.length; j++) {
			root.neighborsList(root.getNode(nodes[j]));
		}
	}

	/**
	 *  DOCUMENT ME!
	 *
	 * @param root DOCUMENT ME!
	 * @param nodes DOCUMENT ME!
	 */
	public static final void testConnectingWeb(RootGraph root, int[] nodes) {
		final int[] nodesWeb = new int[nodes.length / 2];
		System.arraycopy(nodes, 0, nodesWeb, 0, nodesWeb.length);

		int numIters = Math.min(100, nodesWeb.length);

		for (int i = 0; i < numIters; i++) {
			root.getConnectingEdgeIndicesArray(nodesWeb);
			nodesWeb[i] = nodes[nodesWeb.length + i];
		}
	}

	/**
	 *  DOCUMENT ME!
	 *
	 * @param root DOCUMENT ME!
	 * @param nodes DOCUMENT ME!
	 * @param edgeSources DOCUMENT ME!
	 * @param edgeTargets DOCUMENT ME!
	 * @param edgeDirectedness DOCUMENT ME!
	 */
	public static final void testAddRemove(RootGraph root, int[] nodes, int[] edgeSources,
	                                       int[] edgeTargets, boolean[] edgeDirectedness) {
		for (int i = 0; i < 10; i++) {
			for (int j = 0; j < nodes.length; j++)
				root.removeNode(nodes[j]);

			if ((root.getNodeCount() != 0) || (root.getEdgeCount() != 0))
				throw new IllegalStateException("node/edge count not 0");

			for (int j = 0; j < nodes.length; j++)
				nodes[j] = root.createNode();

			for (int j = 0; j < edgeSources.length; j++)
				root.createEdge(nodes[edgeSources[j]], nodes[edgeTargets[i]], edgeDirectedness[j]);

			if ((root.getNodeCount() != nodes.length)
			    || (root.getEdgeCount() != edgeSources.length))
				throw new IllegalStateException("node/edge count not what expected");
		}
	}
}