content: /*
   * Copyright (c) 2017
   * 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 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 Gregori Gerebtzoff
   */
  
  package com.actelion.research.chem.mmp;
  
  import com.actelion.research.chem.mmp.MMPFragmenter.MoleculeIndexID;
  
  import java.io.*;
  import java.util.List;
  
  
  public class MMPFragments {
  	private File temp = File.createTempFile("fragments", ".tmp");
  	private PrintWriter fragmentsWriter = new PrintWriter(temp);
  	private int numberOfLines = 0;
  	
  	public MMPFragments() throws IOException {
  		fragmentsWriter.println("key1FragmentIndex\tkey2FragmentIndex\tvalueFragmentIndex\tcutType\tmoleculeIndex");
  	}
  	
  	/**
  	 * Adds all molecule fragmentation variations
  	 * @param moleculeIndex Index of the molecule
  	 * @param moleculeIndexesID All fragmentation variations
  	 */
  	public void addFragments(int moleculeIndex, List<MoleculeIndexID> moleculeIndexesID) {
  		for (MoleculeIndexID moleculeIndexID: moleculeIndexesID) {
  			addFragments(moleculeIndex, moleculeIndexID);
  		}
  	}
  	
  	/**
  	 * Adds a new molecule fragment
  	 * @param moleculeIndex Index of the molecule
  	 * @param moleculeIndexID One fragmentation variation of the molecule
  	 */
  	public void addFragments(int moleculeIndex, MoleculeIndexID moleculeIndexID) {
  		int[] keysSize = moleculeIndexID.getKeysIDAtoms();
  		int[] keysIndex = moleculeIndexID.getKeysIndex();
  		if (keysSize.length == 1) { // single cut
  			fragmentsWriter.println(Integer.toString(keysIndex[0]) + "\t\t" + Integer.toString(moleculeIndexID.getValueIndex()) + "\t1\t" + Integer.toString(moleculeIndex));
  		}
  		else { // double cut
  			fragmentsWriter.println(Integer.toString(keysIndex[0]) + "\t" + Integer.toString(keysIndex[1]) + "\t" +  Integer.toString(moleculeIndexID.getValueIndex()) + "\t2\t" + Integer.toString(moleculeIndex));
  		}
  		numberOfLines++;
  	}
  	
  	/**
  	 * Writes the Molecules Fragments block
  	 * @param printWriter
  	 */
  	public void writeFragments(PrintWriter printWriter) throws IOException  {
  		fragmentsWriter.close();
  		printWriter.println("<mmpFragments>");
  		printWriter.println("<column properties>");
  		printWriter.println("<columnName=\"key1FragmentIndex\">");
  		printWriter.println("<columnName=\"key2FragmentIndex\">");
  		printWriter.println("<columnName=\"valueFragmentIndex\">");
  		printWriter.println("<columnName=\"cutType\">");
  		printWriter.println("<columnName=\"moleculeIndex\">");
  		printWriter.println("</column properties>");
  		BufferedReader br = new BufferedReader(new FileReader(temp));
  		String strLine;
  		while ((strLine = br.readLine()) != null)   {
  			printWriter.println(strLine);
  		}
  		br.close();
  		temp.delete();
  		printWriter.println("</mmpFragments>");
  	}
  	
  	/**
  	 * Get the number of fragments
  	 * @return
  	 */
  	public int getFragmentsCount() {
  		return numberOfLines;
  	}	
  }
  