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.
  *
  */
  
  package com.actelion.research.chem.shredder;
  
  import com.actelion.research.chem.StereoMolecule;
  import com.actelion.research.util.datamodel.IDCodeCoord;
  
  /**
   * Fragment
   * Jan 18, 2013 MvK Start implementation
   */
  public class Fragment extends IDCodeCoord {
  	
      public static final String TAG_FREQUENCY_ONE_PER_MOLECULE = "FrequencyOnePerMolecule";
      
      public static final String TAG_FREQUENCY = "FrequencySumAll";
      
      public static final String TAG_RELATIVE_FREQUNCY = "Relative frequencySumAll";
      
      public static final String TAG_SIZE = "Size fragment"; 
  
      // This frequency term is only incremented ones per molecule.
  	private int frequencyOnePerMol;
  	
  	// This frequency term counts all fragments. One molecule can have several identical fragments. 
  	private int frequencySumAll;
  	
  	private int size;
  	
  	private StereoMolecule mol;
  	
  
  	public Fragment(String idcode) {
  		super(idcode);
  	}
  
  	
  	/**
  	 * @param idcode
  	 * @param coordinates
  	 */
  	public Fragment(String idcode, String coordinates) {
  		super(idcode, coordinates);
  	}
  
  
  
  	/**
  	 * @return the frequencyOnePermol
  	 */
  	public int getFrequencyOnePerMol() {
  		return frequencyOnePerMol;
  	}
  
  
  	/**
  	 * @param frequencyOnePerMol the frequencyOnePermol to set
  	 */
  	public void setFrequencyOnePerMol(int frequencyOnePerMol) {
  		this.frequencyOnePerMol = frequencyOnePerMol;
  	}
  
  
  	/**
  	 * @return the frequency
  	 */
  	public int getFrequencySumAll() {
  		return frequencySumAll;
  	}
  
  
  	/**
  	 * @param frequency the frequency to set
  	 */
  	public void setFrequencySumAll(int frequency) {
  		this.frequencySumAll = frequency;
  	}
  
  	public void incrementFrequencySumAll() {
  		this.frequencySumAll++;
  	}
  	
  	public void incrementFrequencyOnePerMol() {
  		this.frequencyOnePerMol++;
  	}
  	
  
  	/**
  	 * @return the size
  	 */
  	public int getSize() {
  		return size;
  	}
  
  
  	/**
  	 * @param size the size to set
  	 */
  	public void setSize(int size) {
  		this.size = size;
  	}
  	
  	public boolean equals(Object o) {
  		
  		boolean equals = true;
  		
  		if(!(o instanceof Fragment)){
  			return false;
  		}
  		
  		Fragment f = (Fragment) o;
  		
  		if(!idcode.equals(f.idcode)){
  			equals = false;
  		}
  				
  		return equals;
  	}
  	
  	/**
  	 * @return the mol
  	 */
  	public StereoMolecule getMol() {
  		return mol;
  	}
  
  
  	/**
  	 * @param mol the mol to set
  	 */
  	public void setMol(StereoMolecule mol) {
  		this.mol = mol;
  	}
  
  
  
  }
  