content: /*
   * 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.
   *
   * @author Thomas Sander
   */
  
  package com.actelion.research.chem.coords;
  
  /**
   * Created by thomas on 9/23/16.
   */
  public class FragmentAssociation {
  	private InventorFragment[] mFragment;
  	private double[] mX,mY;
  	private int[] mCount;
  
  	public FragmentAssociation(InventorFragment f1, InventorFragment f2, int atomIndex1, int atomIndex2) {
  		mFragment = new InventorFragment[2];
  		mFragment[0] = f1;
  		mFragment[1] = f2;
  		mX = new double[2];
  		mY = new double[2];
  		mX[0] = mFragment[0].getAtomX(atomIndex1);
  		mY[0] = mFragment[0].getAtomY(atomIndex1);
  		mX[1] = mFragment[1].getAtomX(atomIndex2);
  		mY[1] = mFragment[1].getAtomY(atomIndex2);
  		mCount = new int[2];
  		mCount[0] = 1;
  		mCount[1] = 1;
  		}
  
  	/**
  	 * Uses center of gravity of the fragments as anchor points
  	 * @param f1
  	 * @param f2
  	 */
  	public FragmentAssociation(InventorFragment f1, InventorFragment f2) {
  		mFragment = new InventorFragment[2];
  		mFragment[0] = f1;
  		mFragment[1] = f2;
  		mX = new double[2];
  		mY = new double[2];
  		mCount = new int[2];
  		for (int i=0; i<2; i++) {
  			for (int j=0; j<mFragment[i].size(); j++) {
  				mX[i] += mFragment[i].getAtomX(j);
  				mY[i] += mFragment[i].getAtomY(j);
  				}
  			mCount[i] = mFragment[i].size();
  			}
  		}
  
  	public void add(int atomIndex1, int atomIndex2) {
  		mX[0] += mFragment[0].getAtomX(atomIndex1);
  		mY[0] += mFragment[0].getAtomY(atomIndex1);
  		mX[1] += mFragment[1].getAtomX(atomIndex2);
  		mY[1] += mFragment[1].getAtomY(atomIndex2);
  		mCount[0]++;
  		mCount[1]++;
  		}
  
  	public InventorFragment getFragment(int i) {
  		return mFragment[i];
  		}
  
  	public int getPriority() {
  		return mFragment[0].size() * mFragment[1].size();
  		}
  
  	public void arrange(double minDistance, boolean keepFirstFragment) {
  		double[] angle = new double[2];
  		for (int i=0; i<2; i++) {
  			mX[i] /= mCount[i];
  			mY[i] /= mCount[i];
  			angle[i] = mFragment[i].calculatePreferredAttachmentAngle(mX[i], mY[i], mFragment[1-i].size(), minDistance);
  			}
  
  		mFragment[0].rotate(mX[0], mY[0], Math.PI/2.0 - angle[0]);
  		mFragment[1].rotate(mX[1], mY[1], Math.PI*3.0/2.0 - angle[1]);
  
  		double yMin = Double.MAX_VALUE;
  		double yMax = -Double.MAX_VALUE;
  		double dy = mY[0] - mY[1];
  		for (int i=0; i<mFragment[1].mAtomY.length; i++) {
  			mFragment[1].mAtomY[i] += dy;
  			if (yMin > mFragment[1].mAtomY[i])
  				yMin = mFragment[1].mAtomY[i];
  			if (yMax < mFragment[1].mAtomY[i])
  				yMax = mFragment[1].mAtomY[i];
  			}
  
  		double range = yMax - yMin + 2*minDistance;
  		int binCount = (int)Math.ceil(range);
  		yMin += (range - binCount) / 2 - minDistance;
  		double[] leftX = new double[binCount];
  		for (int i=0; i<binCount; i++)
  			leftX[i] = mX[1] + minDistance;
  		for (int i=0; i<mFragment[1].mAtomY.length; i++) {
  			double relY = mFragment[1].mAtomY[i] - yMin;
  			int low = (int)(relY - minDistance);
  			int high = Math.min((int)(relY + minDistance), binCount-1);
  			for (int j=low; j<=high; j++) {
  				if (leftX[j] > mFragment[1].mAtomX[i])
  					leftX[j] = mFragment[1].mAtomX[i];
  				}
  			}
  
  		for (int i=0; i<binCount; i++)
  			leftX[i] -= minDistance;
  
  		double dx = mX[0] - mX[1];
  		for (int i=0; i<mFragment[0].mAtomX.length; i++) {
  			int index = (int)(mFragment[0].mAtomY[i] - yMin);
  			if (index >= 0 && index < leftX.length
  			 && dx < mFragment[0].mAtomX[i] - leftX[index])
  				dx = mFragment[0].mAtomX[i] - leftX[index];
  			}
  
  		for (int i=0; i<mFragment[1].mAtomX.length; i++)
  			mFragment[1].mAtomX[i] += dx;
  
  		if (keepFirstFragment) {
  			mFragment[0].rotate(mX[0], mY[0], angle[0] - Math.PI / 2.0);
  			mFragment[1].rotate(mX[0], mY[0], angle[0] - Math.PI / 2.0);
  			}
  		}
  	}
  