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/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
*    list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
*    this list of conditions and the following disclaimer in the documentation
*    and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
*    names of its contributors may be used to endorse or promote products
*    derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*/

package com.actelion.research.chem;

import com.actelion.research.chem.reaction.Reaction;
import com.actelion.research.chem.reaction.ReactionArrow;

import java.awt.*;
import java.awt.geom.Rectangle2D;



public class ExtendedDepictor {
	public static final int TYPE_MOLECULES = 0;
	public static final int TYPE_REACTION = 1;
	public static final int TYPE_MARKUSH = 2;

    private StereoMolecule[]		mMolecule,mCatalyst;
    private Reaction				mReaction;
    private AbstractDepictor[]		mDepictor,mCatalystDepictor;
    private DrawingObjectList		mDrawingObjectList;
    private int						mDisplayMode,mReactantCount,mMarkushCoreCount,mChemistryType;
    private boolean					mUseGraphics2D,mReactionLayoutNeeded;
    private DepictorTransformation	mTransformation;
    private Color                   mFragmentNoColor;

    public ExtendedDepictor(StereoMolecule mol, DrawingObjectList drawingObjectList, boolean useGraphics2D) {
        if (mol != null) {
            mMolecule = new StereoMolecule[1];
            mMolecule[0] = mol;
            }
		mChemistryType = TYPE_MOLECULES;
        mDrawingObjectList = drawingObjectList;
        mUseGraphics2D = useGraphics2D;
        initialize();
        }

    public ExtendedDepictor(StereoMolecule[] mol, DrawingObjectList drawingObjectList, boolean useGraphics2D) {
        mMolecule = mol;
		mChemistryType = TYPE_MOLECULES;
        mDrawingObjectList = drawingObjectList;
        mUseGraphics2D = useGraphics2D;
        initialize();
        }

    /**
     * Use this constructor for markush structures. The first fragments in the list
     * are the Markush core structures (typically only one), decorated with R1,R2,R3,...
     * The remaining fragments need to contain one atom with atomicNo=0 each, that
     * indicates the attachment point. They also may contain Rn atoms.
     * Any of the fragments may contain query features.
     * @param mol
     * @param markushCoreCount
     * @param drawingObjectList
     * @param useGraphics2D
     */
    public ExtendedDepictor(StereoMolecule[] mol, int markushCoreCount, DrawingObjectList drawingObjectList, boolean useGraphics2D) {
        mMolecule = mol;
		mChemistryType = TYPE_MARKUSH;
        mDrawingObjectList = drawingObjectList;
        mUseGraphics2D = useGraphics2D;
        mMarkushCoreCount = markushCoreCount;
        initialize();
        }

    public ExtendedDepictor(Reaction reaction, DrawingObjectList drawingObjectList, boolean layoutReaction, boolean useGraphics2D) {
		mReaction = reaction;
        if (reaction != null) {
            mMolecule = new StereoMolecule[reaction.getMolecules()];
            for (int i=0; i= mReactantOrCoreCount) {
                        Rectangle2D.Float r = mDepictor[i].getBoundingRect();
                        if (r != null) {
                            g.drawRect((int)r.x-8, (int)r.y-8, (int)r.width+16, (int)r.height+16);
                            g.drawRect((int)r.x-7, (int)r.y-7, (int)r.width+14, (int)r.height+14);
                            }
                        } */
                    }
                }
            }
        }

    public void paintStructures(Object g) {
        if (mDepictor != null) {
            for (int i=0; i