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 java.io.BufferedReader;
  import java.io.File;
  import java.io.FileReader;
  import java.io.IOException;
  import java.io.PrintWriter;
  import java.util.HashMap;
  import java.util.List;
  import java.util.Map;
  
  public class MMPairs {
  	private File temp = File.createTempFile("matchedmolecularpairs", ".tmp");
  	private PrintWriter mmpWriter = new PrintWriter(temp);
  	private int numberOfLines = 0;
  	
  	MMPairs() throws IOException {
  		mmpWriter.println("value1FragmentIndex\tvalue1Atoms\tvalue2FragmentIndex\tvalue2Atoms\tcutType\tnumberOfExamples\texamples");
  	}
  	
  	/**
  	 * Writes the Matched Molecular Pairs into a temporary file
  	 * @param mMPs Matched Molecular Pairs to be written
  	 * @throws IOException
  	 */
  	public void writeMMPEnumeration(HashMap<String, List<String[]>> mMPs) throws IOException {
  		if (mMPs != null && mMPs.size() > 0) { 
  			for (Map.Entry<String, List<String[]>> entry: mMPs.entrySet()) {
  				String examples = "";
  				for (String[] example: entry.getValue()) {
  					if (examples == "") {
  						examples = example[0] + "," + example[1];
  					}
  					else {
  						examples += "|" + example[0] + "," + example[1];
  					}
  				}
  				mmpWriter.println(entry.getKey() + "\t" + Integer.toString(entry.getValue().size()) + "\t" + examples);
  				numberOfLines++;
  			}
  		}
  	}
  	
  	/**
  	 * Get the number of Matched Molecular Pairs
  	 * @return
  	 */
  	public int getMMPsCount() {
  		return numberOfLines;
  	}
  	
  	/**
  	 * Writes the Matched Molecular Pairs block
  	 * @param printWriter
  	 */
  	public void writeMMPs(PrintWriter printWriter) throws IOException  {
  		mmpWriter.close();
  		printWriter.println("<matchedMolecularPairs>");
  		printWriter.println("<column properties>");
  		printWriter.println("<columnName=\"value1FragmentIndex\">");
  		printWriter.println("<columnName=\"value1Atoms\">");
  		printWriter.println("<columnName=\"value2FragmentIndex\">");
  		printWriter.println("<columnName=\"value2Atoms\">");
  		printWriter.println("<columnName=\"cutType\">");
  		printWriter.println("<columnName=\"numberOfExamples\">");
  		printWriter.println("<columnName=\"examples\">");
  		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("</matchedMolecularPairs>");
  	}
  }
  