package com.hfg.chem;


import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.HashMap;
import java.util.Map;
import java.util.regex.Pattern;

import com.hfg.exception.ProgrammingException;
import com.hfg.util.StringUtil;
import com.hfg.util.io.CSV;
import com.hfg.util.io.StreamUtil;

//------------------------------------------------------------------------------
/**
 Isotope. Data from NIST.
 <div>
 @author J. Alex Taylor, hairyfatguy.com
 </div>
 */
//------------------------------------------------------------------------------
// com.hfg XML/HTML Coding Library
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
//
// J. Alex Taylor, President, Founder, CEO, COO, CFO, OOPS hairyfatguy.com
// jataylor@hairyfatguy.com
//------------------------------------------------------------------------------

public class Isotope extends Element
{
   //##########################################################################
   // PRIVATE FIELDS
   //##########################################################################

   private Element mElement;
   private int     mMassNum; // The number of protons plus the number of neutrons
   private Double  mIsotopicComposition;

   // This declaration has to come before the public constants below.
   private static Map<Element, Map<Integer, Isotope>> sValueMap = new HashMap<>();

   static
   {
      init();
   }

   //##########################################################################
   // CONSTRUCTORS
   //##########################################################################

   //--------------------------------------------------------------------------
   private Isotope(String inName, Element inElement, int inMassNum,
                   double inMonoMass, double inIsotopicComposition)
   {
      this(inName, inElement, inMassNum, inMonoMass);
      setIsotopicComposition(inIsotopicComposition);
   }

   //--------------------------------------------------------------------------
   private Isotope(String inName, Element inElement, int inMassNum,
                   double inMonoMass)
   {
      super(inName, inMassNum + inElement.getSymbol(), inElement.getAtomicNum(), inMonoMass, inMonoMass);
      mElement = inElement;
      mMassNum = inMassNum;

      Map<Integer, Isotope> isotopeMap = sValueMap.get(inElement);
      if (null == isotopeMap)
      {
         isotopeMap = new HashMap<>(5);
         sValueMap.put(inElement, isotopeMap);
      }

      isotopeMap.put(inMassNum, this);
   }

   //##########################################################################
   // PUBLIC METHODS
   //##########################################################################

   //--------------------------------------------------------------------------
   public static Map<Integer, Isotope> valuesForElement(Element inElement)
   {
      return sValueMap.get(inElement);
   }

   //--------------------------------------------------------------------------
   public static Isotope valueOf(Element inElement, int inMassNum)
   {
      return sValueMap.get(inElement).get(inMassNum);
   }

   //--------------------------------------------------------------------------
   public Element getElement()
   {
      return mElement;
   }

   //--------------------------------------------------------------------------
   /**
    Returns the mass number (the number of protons plus neutrons) of the isotope.
    @return the mass number (the number of protons plus neutrons) of the isotope
    */
   public int getMassNumber()
   {
      return mMassNum;
   }

   //--------------------------------------------------------------------------
   @Override
   public String getSymbol()
   {
      return getMassNumber() + getElement().getSymbol();
   }

   //--------------------------------------------------------------------------
   /**
    Specifies the isotopic composition (mole fraction) for the isotope.
    * @return this Isotope object to enable method chaining
    */
   private Isotope setIsotopicComposition(double inValue)
   {
      mIsotopicComposition = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   /**
    Specifies the isotopic composition (mole fraction) for the isotope.
    * @return the isotopic composition (mole fraction) for the isotope
    */
   public Double getIsotopicComposition()
   {
      return mIsotopicComposition;
   }

   //##########################################################################
   // PRIVATE METHODS
   //##########################################################################

   //--------------------------------------------------------------------------
   private static void init()
   {
      Pattern noDataLinePattern = Pattern.compile("[\\s\u00A0,]+");

      String rsrc = "rsrc/isotope_data.csv";
      InputStream stream = Isotope.class.getResourceAsStream(rsrc);
      if (null == stream)
      {
         throw new ProgrammingException("The rsrc " + rsrc + " couldn't be found!?");
      }

      BufferedReader reader = null;
      try
      {
         reader = new BufferedReader(new InputStreamReader(stream));
         String line;
         int lineNum = 0;
         Element currentElement = null;
         while ((line = reader.readLine()) != null)
         {
            lineNum++;

            if (!StringUtil.isSet(line) // Skip blank lines
                  || 1 == lineNum // Skip the header line
                || line.startsWith("#") // Skip comment lines
                || noDataLinePattern.matcher(line).matches()) // Skip lines with all empty fields
            {
               continue;
            }

            String[] fields = CSV.parseLine(line);
            if (StringUtil.isSet(fields[0]))
            {
               currentElement = Element.valueOf(Integer.parseInt(fields[0].trim()));
            }

            String monoMassString = StringUtil.removeWhitespace(fields[3]);
            int uncertaintyIndex = monoMassString.indexOf("(");
            if (uncertaintyIndex > 0)
            {
               monoMassString = monoMassString.substring(0, uncertaintyIndex);
            }

            String isotopicCompostionString = StringUtil.removeWhitespace(fields[4]);
            if (StringUtil.isSet(isotopicCompostionString))
            {
               uncertaintyIndex = isotopicCompostionString.indexOf("(");
               if (uncertaintyIndex > 0)
               {
                  isotopicCompostionString = isotopicCompostionString.substring(0, uncertaintyIndex);
               }

               new Isotope(currentElement.getName() + " " + fields[2], currentElement, Integer.parseInt(fields[2]), Double.parseDouble(monoMassString), Double.parseDouble(isotopicCompostionString));
            }
            else
            {
               new Isotope(currentElement.getName() + " " + fields[2], currentElement, Integer.parseInt(fields[2]), Double.parseDouble(monoMassString));
            }
         }
      }
      catch (IOException e)
      {
         throw new RuntimeException("Problem initializing isotope data!", e);
      }
      finally
      {
         StreamUtil.close(reader);
      }
   }
}